From d65d8aadcec45113946e8c5e22541bdc9a34dbbc Mon Sep 17 00:00:00 2001 From: Sateesh Peri Date: Sun, 29 Oct 2023 10:35:40 -0400 Subject: [PATCH 01/30] post-release dev bump version and snapshots --- assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- tests/pipeline/bismark/main.nf.test.snap | 10 +++++----- tests/pipeline/bismark_hisat/main.nf.test.snap | 4 ++-- tests/pipeline/bwameth/main.nf.test.snap | 4 ++-- 5 files changed, 12 insertions(+), 12 deletions(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 1f6b6f02..408c5646 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/methylseq + This report has been generated by the nf-core/methylseq analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-methylseq-methods-description": order: -1000 diff --git a/nextflow.config b/nextflow.config index 141d7e5b..591852e5 100644 --- a/nextflow.config +++ b/nextflow.config @@ -299,7 +299,7 @@ manifest { description = """Methylation (Bisulfite-Sequencing) Best Practice analysis pipeline, part of the nf-core community.""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '2.5.0' + version = '2.6.0dev' doi = '10.5281/zenodo.1343417' } diff --git a/tests/pipeline/bismark/main.nf.test.snap b/tests/pipeline/bismark/main.nf.test.snap index 86e57c54..68a6e38b 100644 --- a/tests/pipeline/bismark/main.nf.test.snap +++ b/tests/pipeline/bismark/main.nf.test.snap @@ -1,13 +1,13 @@ { "single_end_software_versions": { "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.5.0}}" + "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0dev}}" ], "timestamp": "2023-08-28T08:46:48+0000" }, "single_end_nomeseq_software_versions": { "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.5.0}}" + "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0dev}}" ], "timestamp": "2023-08-28T08:46:48+0000" }, @@ -49,19 +49,19 @@ }, "single_end_rrbs_software_versions": { "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.5.0dev}}" + "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.6.0dev}}" ], "timestamp": "2023-08-28T08:46:48+0000" }, "single_end__nomeseq_software_versions": { "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.5.0dev}}" + "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0dev}}" ], "timestamp": "2023-08-28T08:46:48+0000" }, "clip_r1_software_versions": { "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.5.0dev}}" + "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0dev}}" ], "timestamp": "2023-08-28T08:46:48+0000" }, diff --git a/tests/pipeline/bismark_hisat/main.nf.test.snap b/tests/pipeline/bismark_hisat/main.nf.test.snap index 5b1816cd..8c8c482c 100644 --- a/tests/pipeline/bismark_hisat/main.nf.test.snap +++ b/tests/pipeline/bismark_hisat/main.nf.test.snap @@ -1,13 +1,13 @@ { "single_end_software_versions": { "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.5.0}}" + "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0dev}}" ], "timestamp": "2023-08-28T10:04:42+0000" }, "single_end_rrbs_software_versions": { "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.5.0}}" + "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.6.0dev}}" ], "timestamp": "2023-08-28T10:04:42+0000" }, diff --git a/tests/pipeline/bwameth/main.nf.test.snap b/tests/pipeline/bwameth/main.nf.test.snap index 50a79bf2..fb74d28f 100644 --- a/tests/pipeline/bwameth/main.nf.test.snap +++ b/tests/pipeline/bwameth/main.nf.test.snap @@ -1,13 +1,13 @@ { "single_end_software_versions": { "content": [ - "{BWAMETH_ALIGN={bwameth=0.2.2}, BWAMETH_INDEX={bwameth=0.2.2}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.5.0}}" + "{BWAMETH_ALIGN={bwameth=0.2.2}, BWAMETH_INDEX={bwameth=0.2.2}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0dev}}" ], "timestamp": "2023-08-28T00:28:04+0000" }, "single_end_rrbs_software_versions": { "content": [ - "{BWAMETH_ALIGN={bwameth=0.2.2}, BWAMETH_INDEX={bwameth=0.2.2}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.5.0}}" + "{BWAMETH_ALIGN={bwameth=0.2.2}, BWAMETH_INDEX={bwameth=0.2.2}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.6.0dev}}" ], "timestamp": "2023-08-28T00:28:04+0000" }, From 6cb25ee5292c968db5679d0191664916ccaaf8f8 Mon Sep 17 00:00:00 2001 From: ltosti-tagomics Date: Tue, 31 Oct 2023 09:27:45 +0000 Subject: [PATCH 02/30] fix for bug #354 - dev branch --- conf/modules.config | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/conf/modules.config b/conf/modules.config index ad1d68ce..26f4cb88 100755 --- a/conf/modules.config +++ b/conf/modules.config @@ -418,6 +418,11 @@ process { path: { "${params.outdir}/methyldackel" }, mode: params.publish_dir_mode, pattern: "*.bedGraph" + ], + [ + path: { "${params.outdir}/methyldackel" }, + mode: params.publish_dir_mode, + pattern: "*.methylKit" ] ] } From 03880b0a03fd7fb6795b1235bb32d031f10300ef Mon Sep 17 00:00:00 2001 From: noe_c <57455039+noecochetel@users.noreply.github.com> Date: Fri, 3 Nov 2023 12:24:57 -0700 Subject: [PATCH 03/30] Update modules.config Replace simple quotes by double quotes for ignore_r1 parameters. --- conf/modules.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index ad1d68ce..3b71f551 100755 --- a/conf/modules.config +++ b/conf/modules.config @@ -209,8 +209,8 @@ process { params.comprehensive ? ' --comprehensive --merge_non_CpG' : '', params.meth_cutoff ? " --cutoff ${params.meth_cutoff}" : '', params.nomeseq ? '--CX' : '', - params.ignore_r1 > 0 ? '--ignore ${params.ignore_r1}' : '', - params.ignore_3prime_r1 > 0 ? '--ignore_3prime ${params.ignore_3prime_r1}' : '', + params.ignore_r1 > 0 ? "--ignore ${params.ignore_r1}" : '', + params.ignore_3prime_r1 > 0 ? "--ignore_3prime ${params.ignore_3prime_r1}" : '', meta.single_end ? '' : (params.no_overlap ? ' --no_overlap' : '--include_overlap'), meta.single_end ? '' : (params.ignore_r2 > 0 ? "--ignore_r2 ${params.ignore_r2}" : ""), meta.single_end ? '' : (params.ignore_3prime_r2 > 0 ? "--ignore_3prime_r2 ${params.ignore_3prime_r2}": "") From 3c6f816556ac6b96262b2682744298a07bf0f420 Mon Sep 17 00:00:00 2001 From: noe_c <57455039+noecochetel@users.noreply.github.com> Date: Fri, 3 Nov 2023 17:08:20 -0700 Subject: [PATCH 04/30] Update CHANGELOG.md Added a log for the fix --- CHANGELOG.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9cb2dab0..6b9cb5f1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,11 @@ # nf-core/methylseq +### Pipeline Updates + +### Bug fixes & refactoring + +- 🐛 fix `ignore_r1` and `ignore_3prime_r1` variable expansion #359 + ## [v2.5.0](https://github.com/nf-core/methylseq/releases/tag/2.5.0) - 2023-10-18 ### Pipeline Updates From bc6009747002638f4aea0b451f1bfb5df40fa392 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Mon, 6 Nov 2023 12:06:55 -0600 Subject: [PATCH 05/30] chore: Update CHANGELOG --- CHANGELOG.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9cb2dab0..27ff9ed2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,11 @@ # nf-core/methylseq +## Dev + +### Bug fixes & refactoring + +- 🛠 Copy methylKit-compatible files to publishDir [#357](https://github.com/nf-core/methylseq/pull/357) + ## [v2.5.0](https://github.com/nf-core/methylseq/releases/tag/2.5.0) - 2023-10-18 ### Pipeline Updates From 57f3e4cc5a2afd5d701fe6b592a82ff39ee7152f Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 20 Oct 2023 01:02:00 +0200 Subject: [PATCH 06/30] ci: Add scatter CI --- .github/workflows/ci.yml | 118 +++++++++++++++++++++++---------------- 1 file changed, 69 insertions(+), 49 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 699e5287..d48c2d84 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -21,67 +21,59 @@ concurrency: cancel-in-progress: true jobs: - define_nxf_versions: - name: Choose nextflow versions to test against depending on target branch - runs-on: ubuntu-latest + list: + name: List Tests + if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/methylseq') }}" outputs: - matrix: ${{ steps.nxf_versions.outputs.matrix }} + # Expose matched filters as job 'modules' output variable + tests: ${{ steps.list.outputs.tests }} + runs-on: ubuntu-latest steps: - - id: nxf_versions + - uses: actions/checkout@v3 + + - name: Setup Nextflow + uses: nf-core/setup-nextflow@v1 + + - name: Install nf-test + if: steps.cache-software.outputs.cache-hit != 'true' run: | - if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then - echo matrix='["latest-everything"]' | tee -a $GITHUB_OUTPUT - else - echo matrix='["latest-everything", "23.04.0"]' | tee -a $GITHUB_OUTPUT - fi + wget -qO- https://code.askimed.com/install/nf-test | bash + sudo mv nf-test /usr/local/bin/ + + - name: List nf-test + id: list + run: | + echo "tests=$(nf-test list --silent --format=json)" >> "$GITHUB_OUTPUT" test: - name: Run pipeline with test data - needs: define_nxf_versions + name: ${{ matrix.tags }} (${{ matrix.profile }}-${{ matrix.NXF_VER }}) + # Only run on push if this is the nf-core dev branch (merged PRs) + if: needs.list.outputs.tests != '[]' + needs: [list] runs-on: ubuntu-latest strategy: - fail-fast: false matrix: - NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }} - test_tags: - - "bismark" - - "bismark_hisat" - - "bwameth" - profile: - - "docker" - + NXF_VER: + - "23.04.0" + - "latest-everything" + profile: ["docker"] # TODO , "singularity", "conda"] + test: ["${{ fromJson(needs.list.outputs.tests) }}"] + exclude: + - test: "tests/subworkflows/local/grohmm/main.nf.test@3508b8c9" + - test: "tests/subworkflows/local/grohmm/main.nf.test@716555be" + - test: "tests/subworkflows/local/grohmm/main.nf.test@306b4b15" steps: - name: Check out pipeline code uses: actions/checkout@v3 - - name: Hash Github Workspace - id: hash_workspace - run: | - echo "digest=$(echo methylseq2_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT - - - name: Cache test data - id: cache-testdata + - name: Cache Nextflow installation + id: cache-software uses: actions/cache@v3 with: - path: test-datasets/ - key: ${{ steps.hash_workspace.outputs.digest }} - - - name: Check out test data - uses: actions/checkout@v3 - with: - repository: nf-core/test-datasets - ref: methylseq - path: test-datasets/ - - - name: Replace remote paths in samplesheets - run: | - for f in ./test-datasets/samplesheet/*csv; do - sed -i 's=https://github.com/nf-core/test-datasets/raw/methylseq/=./test-datasets/=g' $f - sed -i 's=https://raw.githubusercontent.com/nf-core/test-datasets/methylseq/=./test-datasets/=g' $f - echo "========== $f ============" - cat $f - echo "========================================" - done; + path: | + /usr/local/bin/nf-test + /home/runner/.nf-test/nf-test.jar + key: methylseq-${{ runner.os }}-${{ matrix.NXF_VER }} - name: Install Nextflow uses: nf-core/setup-nextflow@v1 @@ -89,13 +81,41 @@ jobs: version: "${{ matrix.NXF_VER }}" - name: Install nf-test + if: steps.cache-software.outputs.cache-hit != 'true' run: | - wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER + wget -qO- https://code.askimed.com/install/nf-test | bash sudo mv nf-test /usr/local/bin/ + - name: Set up Singularity + if: matrix.profile == 'singularity' + uses: eWaterCycle/setup-singularity@v5 + with: + singularity-version: 3.7.1 + + - name: Set up miniconda + if: matrix.profile == 'conda' + uses: conda-incubator/setup-miniconda@v2 + with: + auto-update-conda: true + channels: conda-forge,bioconda,defaults + python-version: ${{ matrix.python-version }} + + - name: Conda clean + if: matrix.profile == 'conda' + run: conda clean -a + - name: Run nf-test run: | - nf-test test --tag ${{ matrix.test_tags }} --profile "test,${{ matrix.profile }}" --junitxml=test.xml + nf-test test \ + --profile="test,${{ matrix.profile }}" \ + ${{ matrix.test }} \ + --junitxml=${{ matrix.test }}-${{ matrix.profile }}.xml + + - uses: actions/upload-artifact@v3 # upload test results + if: success() || failure() # run this step even if previous step failed + with: + name: test-results + path: ${{ matrix.test }}-${{ matrix.profile }}.xml - name: Output log on failure if: failure() From 7aca73b4f16998a5173da60525f646ee61570d1b Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 20 Oct 2023 02:11:03 +0200 Subject: [PATCH 07/30] ci: Bump nf-test --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index d48c2d84..907f22bc 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -14,7 +14,7 @@ on: env: NXF_ANSI_LOG: false - NFTEST_VER: "0.7.3" + NFTEST_VER: "0.8.1" concurrency: group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" From 23c48d5ea1b26f56078b53de94e095d1a8ca6933 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 20 Oct 2023 02:13:55 +0200 Subject: [PATCH 08/30] test: Mark bwameth index generation as failing --- tests/pipeline/bwameth/main.nf.test | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/pipeline/bwameth/main.nf.test b/tests/pipeline/bwameth/main.nf.test index 65b25dec..19f1c3c7 100644 --- a/tests/pipeline/bwameth/main.nf.test +++ b/tests/pipeline/bwameth/main.nf.test @@ -70,7 +70,7 @@ nextflow_pipeline { } then { - assert workflow.success + assert workflow.failed } } @@ -124,7 +124,7 @@ nextflow_pipeline { } then { - assert workflow.success + assert workflow.failed } } From 7d2146c19d2d8c9524e46fd26cc337d914b5aea3 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 20 Oct 2023 02:36:05 +0200 Subject: [PATCH 09/30] test: Mark all index tests as failing --- tests/pipeline/bismark/main.nf.test | 4 ++-- tests/pipeline/bismark_hisat/main.nf.test | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/pipeline/bismark/main.nf.test b/tests/pipeline/bismark/main.nf.test index 72af7acd..b81cbbfb 100644 --- a/tests/pipeline/bismark/main.nf.test +++ b/tests/pipeline/bismark/main.nf.test @@ -73,7 +73,7 @@ nextflow_pipeline { } then { - assert workflow.success + assert workflow.failed } } @@ -134,7 +134,7 @@ nextflow_pipeline { } then { - assert workflow.success + assert workflow.failed } } diff --git a/tests/pipeline/bismark_hisat/main.nf.test b/tests/pipeline/bismark_hisat/main.nf.test index e4bd6217..89fe8ff6 100644 --- a/tests/pipeline/bismark_hisat/main.nf.test +++ b/tests/pipeline/bismark_hisat/main.nf.test @@ -72,7 +72,7 @@ nextflow_pipeline { } then { - assert workflow.success + assert workflow.failed } } @@ -133,7 +133,7 @@ nextflow_pipeline { } then { - assert workflow.success + assert workflow.failed } } From 31b23b78e6c7496b9c34e84dabd12c527a5d2998 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Mon, 6 Nov 2023 13:17:38 -0600 Subject: [PATCH 10/30] build: nf-core modules install untar --- modules.json | 5 +++ modules/nf-core/untar/environment.yml | 8 ++++ modules/nf-core/untar/main.nf | 63 +++++++++++++++++++++++++++ modules/nf-core/untar/meta.yml | 46 +++++++++++++++++++ 4 files changed, 122 insertions(+) create mode 100644 modules/nf-core/untar/environment.yml create mode 100644 modules/nf-core/untar/main.nf create mode 100644 modules/nf-core/untar/meta.yml diff --git a/modules.json b/modules.json index 318b4e71..ffae7026 100644 --- a/modules.json +++ b/modules.json @@ -129,6 +129,11 @@ "branch": "master", "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["modules"] + }, + "untar": { + "branch": "master", + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "installed_by": ["modules"] } } } diff --git a/modules/nf-core/untar/environment.yml b/modules/nf-core/untar/environment.yml new file mode 100644 index 00000000..2d52ce64 --- /dev/null +++ b/modules/nf-core/untar/environment.yml @@ -0,0 +1,8 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - conda-forge::sed=4.7 + - conda-forge::grep=3.11 + - conda-forge::tar=1.34 diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf new file mode 100644 index 00000000..8a75bb95 --- /dev/null +++ b/modules/nf-core/untar/main.nf @@ -0,0 +1,63 @@ +process UNTAR { + tag "$archive" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : + 'nf-core/ubuntu:20.04' }" + + input: + tuple val(meta), path(archive) + + output: + tuple val(meta), path("$prefix"), emit: untar + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def args2 = task.ext.args2 ?: '' + prefix = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.baseName.toString().replaceFirst(/\.tar$/, "")) + + """ + mkdir $prefix + + ## Ensures --strip-components only applied when top level of tar contents is a directory + ## If just files or multiple directories, place all in prefix + if [[ \$(tar -taf ${archive} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then + tar \\ + -C $prefix --strip-components 1 \\ + -xavf \\ + $args \\ + $archive \\ + $args2 + else + tar \\ + -C $prefix \\ + -xavf \\ + $args \\ + $archive \\ + $args2 + fi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + untar: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//') + END_VERSIONS + """ + + stub: + prefix = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.toString().replaceFirst(/\.[^\.]+(.gz)?$/, "")) + """ + mkdir $prefix + touch ${prefix}/file.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + untar: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/untar/meta.yml b/modules/nf-core/untar/meta.yml new file mode 100644 index 00000000..a9a2110f --- /dev/null +++ b/modules/nf-core/untar/meta.yml @@ -0,0 +1,46 @@ +name: untar +description: Extract files. +keywords: + - untar + - uncompress + - extract +tools: + - untar: + description: | + Extract tar.gz files. + documentation: https://www.gnu.org/software/tar/manual/ + licence: ["GPL-3.0-or-later"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - archive: + type: file + description: File to be untar + pattern: "*.{tar}.{gz}" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - untar: + type: directory + description: Directory containing contents of archive + pattern: "*/" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@joseespinosa" + - "@drpatelh" + - "@matthdsm" + - "@jfy133" +maintainers: + - "@joseespinosa" + - "@drpatelh" + - "@matthdsm" + - "@jfy133" From fa6ffc4766d64694fb89d295e93c576b99f2ea26 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Mon, 6 Nov 2023 13:36:15 -0600 Subject: [PATCH 11/30] feat: Add untar for indexs --- subworkflows/local/prepare_genome.nf | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf index 8fa2cc6e..84e21ff5 100644 --- a/subworkflows/local/prepare_genome.nf +++ b/subworkflows/local/prepare_genome.nf @@ -2,6 +2,7 @@ // Prepare reference genome files // +include { UNTAR } from '../../modules/nf-core/untar/main' include { BISMARK_GENOMEPREPARATION } from '../../modules/nf-core/bismark/genomepreparation/main' include { BWAMETH_INDEX } from '../../modules/nf-core/bwameth/index/main' include { SAMTOOLS_FAIDX } from '../../modules/nf-core/samtools/faidx/main' @@ -27,7 +28,11 @@ workflow PREPARE_GENOME { * Generate bismark index if not supplied */ if (params.bismark_index) { - ch_bismark_index = Channel.value(file(params.bismark_index)) + if (params.bismark_index.endsWith('.gz')) { + ch_bismark_index = UNTAR ( [ [:], file(params.bismark_index) ] ).untar.map { it[1] } + } else { + ch_bismark_index = Channel.value(file(params.bismark_index)) + } } else { BISMARK_GENOMEPREPARATION(ch_fasta) ch_bismark_index = BISMARK_GENOMEPREPARATION.out.index @@ -42,7 +47,11 @@ workflow PREPARE_GENOME { * Generate bwameth index if not supplied */ if (params.bwa_meth_index) { - ch_bwameth_index = Channel.value(file(params.bwa_meth_index)) + if (params.bwa_meth_index.endsWith('.gz')) { + ch_bismark_index = UNTAR ( [ [:], file(params.bwa_meth_index) ] ).untar.map { it[1] } + } else { + ch_bismark_index = Channel.value(file(params.bwa_meth_index)) + } } else { BWAMETH_INDEX(ch_fasta) ch_bwameth_index = BWAMETH_INDEX.out.index From 0a7bcaccbc7b9476e27b09930882336991a33aff Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Mon, 6 Nov 2023 13:52:25 -0600 Subject: [PATCH 12/30] test: Remove tests depending on other tests --- tests/pipeline/bismark/main.nf.test | 23 ++++++++--------------- tests/pipeline/bismark_hisat/main.nf.test | 23 ++++++++--------------- tests/pipeline/bwameth/main.nf.test | 23 ++++++++--------------- 3 files changed, 24 insertions(+), 45 deletions(-) diff --git a/tests/pipeline/bismark/main.nf.test b/tests/pipeline/bismark/main.nf.test index b81cbbfb..bde39977 100644 --- a/tests/pipeline/bismark/main.nf.test +++ b/tests/pipeline/bismark/main.nf.test @@ -18,15 +18,6 @@ nextflow_pipeline { } then { - // issue #278: Clean up anything from previous runs - FileUtil.deleteDirectory(new File(".nf-test/indexes/")); - new File(".nf-test/indexes/").mkdirs() - // Copy the ref genome to a stable location for next tests - FileUtil.copyDirectory( - new File("$outputDir/bismark/reference_genome/BismarkIndex/").getAbsolutePath(), - new File(".nf-test/indexes/BismarkIndex/").getAbsolutePath() - ) - assertAll( { assert workflow.success }, { assert snapshot(path("$outputDir/bismark/deduplicated/Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bam"), @@ -65,15 +56,16 @@ nextflow_pipeline { when { params { aligner = "bismark" - // Generated by previous test - bismark_index = ".nf-test/indexes/BismarkIndex/" + bismark_index = "https://github.com/nf-core/test-datasets/raw/07ff447f2023e1e7b2e91396526601af485655fa/reference/BismarkIndex.tar.gz" cytosine_report = true outdir = "$outputDir" } } then { - assert workflow.failed + assertAll( + { assert workflow.success }, + ) } } @@ -126,15 +118,16 @@ nextflow_pipeline { aligner = "bismark" skip_trimming = true rrbs = true - // Generated by previous test - bismark_index = ".nf-test/indexes/BismarkIndex/" + bismark_index = "https://github.com/nf-core/test-datasets/raw/07ff447f2023e1e7b2e91396526601af485655fa/reference/BismarkIndex.tar.gz" cytosine_report = true outdir = "$outputDir" } } then { - assert workflow.failed + assertAll( + { assert workflow.success }, + ) } } diff --git a/tests/pipeline/bismark_hisat/main.nf.test b/tests/pipeline/bismark_hisat/main.nf.test index 89fe8ff6..ded63bd2 100644 --- a/tests/pipeline/bismark_hisat/main.nf.test +++ b/tests/pipeline/bismark_hisat/main.nf.test @@ -17,15 +17,6 @@ nextflow_pipeline { } then { - // Clean up anything from previous runs - FileUtil.deleteDirectory(new File(".nf-test/indexes/")); - new File(".nf-test/indexes/").mkdirs() - // Copy the ref genome to a stable location for next tests - FileUtil.copyDirectory( - new File("$outputDir/bismark_hisat/reference_genome/BismarkIndex/").getAbsolutePath(), - new File(".nf-test/indexes/BismarkIndex/").getAbsolutePath() - ) - assertAll( { assert workflow.success }, { assert snapshot(path("$outputDir/bismark_hisat/deduplicated/Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.bam"), @@ -64,15 +55,16 @@ nextflow_pipeline { when { params { aligner = "bismark_hisat" - // Generated by previous test - bismark_index = ".nf-test/indexes/BismarkIndex/" + bismark_index = "https://github.com/nf-core/test-datasets/raw/07ff447f2023e1e7b2e91396526601af485655fa/reference/BismarkIndex.tar.gz" local_alignment = true outdir = "$outputDir" } } then { - assert workflow.failed + assertAll( + { assert workflow.success }, + ) } } @@ -125,15 +117,16 @@ nextflow_pipeline { aligner = "bismark_hisat" skip_trimming = true rrbs = true - // Generated by previous test - bismark_index = ".nf-test/indexes/BismarkIndex/" + bismark_index = "https://github.com/nf-core/test-datasets/raw/07ff447f2023e1e7b2e91396526601af485655fa/reference/BismarkIndex.tar.gz" local_alignment = true outdir = "$outputDir" } } then { - assert workflow.failed + assertAll( + { assert workflow.success }, + ) } } diff --git a/tests/pipeline/bwameth/main.nf.test b/tests/pipeline/bwameth/main.nf.test index 19f1c3c7..4311ddc9 100644 --- a/tests/pipeline/bwameth/main.nf.test +++ b/tests/pipeline/bwameth/main.nf.test @@ -17,15 +17,6 @@ nextflow_pipeline { } then { - // Clean up anything from previous runs - FileUtil.deleteDirectory(new File(".nf-test/indexes/")); - new File(".nf-test/indexes/").mkdirs() - // Copy the ref genome to a stable location for next tests - FileUtil.copyDirectory( - new File("$outputDir/bwameth/reference_genome/bwameth/").getAbsolutePath(), - new File(".nf-test/indexes/bwameth/").getAbsolutePath() - ) - assertAll( { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_software_versions") }, @@ -62,15 +53,16 @@ nextflow_pipeline { when { params { aligner = "bwameth" - // Generated by previous test - bwa_meth_index = ".nf-test/indexes/bwameth/" + bwa_meth_index = "https://github.com/nf-core/test-datasets/raw/07ff447f2023e1e7b2e91396526601af485655fa/reference/bwameth.tar.gz" methyl_kit = true outdir = "$outputDir" } } then { - assert workflow.failed + assertAll( + { assert workflow.success }, + ) } } @@ -116,15 +108,16 @@ nextflow_pipeline { aligner = "bwameth" skip_trimming = true rrbs = true - // Generated by previous test - bwa_meth_index = ".nf-test/indexes/bwameth/" + bwa_meth_index = "https://github.com/nf-core/test-datasets/raw/07ff447f2023e1e7b2e91396526601af485655fa/reference/bwameth.tar.gz" methyl_kit = true outdir = "$outputDir" } } then { - assert workflow.failed + assertAll( + { assert workflow.success }, + ) } } From 98c4f8b16170ec041d55b0839e59a9376b106ca6 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Mon, 6 Nov 2023 14:14:39 -0600 Subject: [PATCH 13/30] test: Copy nf-test config from fetchngs https://github.com/nf-core/fetchngs/blob/a7ab1a20bab13b5ba16065071d593192592e3411/nf-test.config --- nf-test.config | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/nf-test.config b/nf-test.config index cd432d43..cb656b94 100644 --- a/nf-test.config +++ b/nf-test.config @@ -1,12 +1,12 @@ config { // location for all nf-tests - testsDir "tests" + testsDir "." // nf-test directory including temporary files for each test - workDir ".nf-test" + workDir "/tmp" // location of library folder that is added automatically to the classpath - libDir "tests/pipeline/lib/" + libDir "lib/" // location of an optional nextflow.config file specific for executing tests configFile "nextflow.config" From 0c464660d92f6d1e8ac9e8a9f16de297665aa62e Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Mon, 6 Nov 2023 14:20:38 -0600 Subject: [PATCH 14/30] ci: Don't upload test report --- .github/workflows/ci.yml | 10 ++-------- 1 file changed, 2 insertions(+), 8 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 907f22bc..0904c096 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -111,10 +111,10 @@ jobs: ${{ matrix.test }} \ --junitxml=${{ matrix.test }}-${{ matrix.profile }}.xml - - uses: actions/upload-artifact@v3 # upload test results + - name: Publish Test Report + uses: mikepenz/action-junit-report@v3 if: success() || failure() # run this step even if previous step failed with: - name: test-results path: ${{ matrix.test }}-${{ matrix.profile }}.xml - name: Output log on failure @@ -122,9 +122,3 @@ jobs: run: | sudo apt install bat > /dev/null batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/output/pipeline_info/software_versions.yml - - - name: Publish Test Report - uses: mikepenz/action-junit-report@v3 - if: always() # always run even if the previous step fails - with: - report_paths: test.xml From 5f8e463a1f0c099e661402c0c323a9959c1a4477 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 19 Dec 2023 19:04:49 +0000 Subject: [PATCH 15/30] Template update for nf-core/tools version 2.11 --- .github/CONTRIBUTING.md | 3 + .github/PULL_REQUEST_TEMPLATE.md | 1 + .github/workflows/ci.yml | 2 +- .github/workflows/fix-linting.yml | 4 +- .github/workflows/linting.yml | 12 +- .gitpod.yml | 4 +- CHANGELOG.md | 2 +- README.md | 17 +-- assets/multiqc_config.yml | 2 +- assets/slackreport.json | 2 +- conf/modules.config | 2 +- docs/usage.md | 4 +- lib/NfcoreTemplate.groovy | 32 ++--- modules.json | 6 +- .../dumpsoftwareversions/environment.yml | 7 ++ .../custom/dumpsoftwareversions/main.nf | 6 +- .../custom/dumpsoftwareversions/meta.yml | 7 +- .../dumpsoftwareversions/tests/main.nf.test | 38 ++++++ .../tests/main.nf.test.snap | 27 +++++ .../dumpsoftwareversions/tests/tags.yml | 2 + modules/nf-core/fastqc/environment.yml | 7 ++ modules/nf-core/fastqc/main.nf | 10 +- modules/nf-core/fastqc/meta.yml | 5 + modules/nf-core/fastqc/tests/main.nf.test | 109 ++++++++++++++++++ .../nf-core/fastqc/tests/main.nf.test.snap | 10 ++ modules/nf-core/fastqc/tests/tags.yml | 2 + modules/nf-core/multiqc/environment.yml | 7 ++ modules/nf-core/multiqc/main.nf | 8 +- modules/nf-core/multiqc/meta.yml | 11 +- modules/nf-core/multiqc/tests/main.nf.test | 63 ++++++++++ modules/nf-core/multiqc/tests/tags.yml | 2 + nextflow.config | 12 +- 32 files changed, 360 insertions(+), 66 deletions(-) create mode 100644 modules/nf-core/custom/dumpsoftwareversions/environment.yml create mode 100644 modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test create mode 100644 modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap create mode 100644 modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml create mode 100644 modules/nf-core/fastqc/environment.yml create mode 100644 modules/nf-core/fastqc/tests/main.nf.test create mode 100644 modules/nf-core/fastqc/tests/main.nf.test.snap create mode 100644 modules/nf-core/fastqc/tests/tags.yml create mode 100644 modules/nf-core/multiqc/environment.yml create mode 100644 modules/nf-core/multiqc/tests/main.nf.test create mode 100644 modules/nf-core/multiqc/tests/tags.yml diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 88e23a1a..38618636 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -27,6 +27,9 @@ If you're not used to this workflow with git, you can start with some [docs from ## Tests +You can optionally test your changes by running the pipeline locally. Then it is recommended to use the `debug` profile to +receive warnings about process selectors and other debug info. Example: `nextflow run . -profile debug,test,docker --outdir `. + When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests. Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then. diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 08cee127..1000a8aa 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -19,6 +19,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/meth - [ ] If necessary, also make a PR on the nf-core/methylseq _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] Make sure your code lints (`nf-core lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). +- [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. - [ ] Output Documentation in `docs/output.md` is updated. - [ ] `CHANGELOG.md` is updated. diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 0a7b78af..c8c61905 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -28,7 +28,7 @@ jobs: - "latest-everything" steps: - name: Check out pipeline code - uses: actions/checkout@v3 + uses: actions/checkout@v4 - name: Install Nextflow uses: nf-core/setup-nextflow@v1 diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml index a2f7f450..5430f37a 100644 --- a/.github/workflows/fix-linting.yml +++ b/.github/workflows/fix-linting.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-latest steps: # Use the @nf-core-bot token to check out so we can push later - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: token: ${{ secrets.nf_core_bot_auth_token }} @@ -24,7 +24,7 @@ jobs: env: GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} - - uses: actions/setup-node@v3 + - uses: actions/setup-node@v4 - name: Install Prettier run: npm install -g prettier @prettier/plugin-php diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index b8bdd214..905c58e4 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -14,9 +14,9 @@ jobs: EditorConfig: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - - uses: actions/setup-node@v3 + - uses: actions/setup-node@v4 - name: Install editorconfig-checker run: npm install -g editorconfig-checker @@ -27,9 +27,9 @@ jobs: Prettier: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - - uses: actions/setup-node@v3 + - uses: actions/setup-node@v4 - name: Install Prettier run: npm install -g prettier @@ -40,7 +40,7 @@ jobs: PythonBlack: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Check code lints with Black uses: psf/black@stable @@ -71,7 +71,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@v3 + uses: actions/checkout@v4 - name: Install Nextflow uses: nf-core/setup-nextflow@v1 diff --git a/.gitpod.yml b/.gitpod.yml index 25488dcc..acf72695 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -4,7 +4,9 @@ tasks: command: | pre-commit install --install-hooks nextflow self-update - + - name: unset JAVA_TOOL_OPTIONS + command: | + unset JAVA_TOOL_OPTIONS vscode: extensions: # based on nf-core.nf-core-extensionpack - codezombiech.gitignore # Language support for .gitignore files diff --git a/CHANGELOG.md b/CHANGELOG.md index 99290858..221e3238 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v2.5.0dev - [date] +## v2.6.0dev - [date] Initial release of nf-core/methylseq, created with the [nf-core](https://nf-co.re/) template. diff --git a/README.md b/README.md index 5f858c66..3fc9054b 100644 --- a/README.md +++ b/README.md @@ -30,11 +30,8 @@ ## Usage -:::note -If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how -to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) -with `-profile test` before running the workflow on actual data. -::: +> [!NOTE] +> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data. - + diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index c5e51cba..5d911554 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,5 +1,5 @@ report_comment: > - This report has been generated by the nf-core/methylseq + This report has been generated by the nf-core/methylseq analysis pipeline. For information about how to interpret these results, please see the documentation. report_section_order: diff --git a/assets/slackreport.json b/assets/slackreport.json index 3b5f9584..662a34bc 100644 --- a/assets/slackreport.json +++ b/assets/slackreport.json @@ -3,7 +3,7 @@ { "fallback": "Plain-text summary of the attachment.", "color": "<% if (success) { %>good<% } else { %>danger<%} %>", - "author_name": "nf-core/methylseq v${version} - ${runName}", + "author_name": "nf-core/methylseq ${version} - ${runName}", "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico", "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>", "fields": [ diff --git a/conf/modules.config b/conf/modules.config index 39e81386..d91c6aba 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -39,7 +39,7 @@ process { } withName: 'MULTIQC' { - ext.args = params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' + ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' } publishDir = [ path: { "${params.outdir}/multiqc" }, mode: params.publish_dir_mode, diff --git a/docs/usage.md b/docs/usage.md index a8037d24..ca9f5ae1 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -20,7 +20,7 @@ You will need to create a samplesheet with information about the samples you wou The `sample` identifiers have to be the same when you have re-sequenced the same sample more than once e.g. to increase sequencing depth. The pipeline will concatenate the raw reads before performing any downstream analysis. Below is an example for the same sample sequenced across 3 lanes: -```console +```csv title="samplesheet.csv" sample,fastq_1,fastq_2 CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz CONTROL_REP1,AEG588A1_S1_L003_R1_001.fastq.gz,AEG588A1_S1_L003_R2_001.fastq.gz @@ -33,7 +33,7 @@ The pipeline will auto-detect whether a sample is single- or paired-end using th A final samplesheet file consisting of both single- and paired-end data may look something like the one below. This is for 6 samples, where `TREATMENT_REP3` has been sequenced twice. -```console +```csv title="samplesheet.csv" sample,fastq_1,fastq_2 CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz CONTROL_REP2,AEG588A2_S2_L002_R1_001.fastq.gz,AEG588A2_S2_L002_R2_001.fastq.gz diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy index 01b8653d..e248e4c3 100755 --- a/lib/NfcoreTemplate.groovy +++ b/lib/NfcoreTemplate.groovy @@ -4,6 +4,7 @@ import org.yaml.snakeyaml.Yaml import groovy.json.JsonOutput +import nextflow.extension.FilesEx class NfcoreTemplate { @@ -141,12 +142,14 @@ class NfcoreTemplate { try { if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') } // Try to send HTML e-mail using sendmail + def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") + sendmail_tf.withWriter { w -> w << sendmail_html } [ 'sendmail', '-t' ].execute() << sendmail_html log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-" } catch (all) { // Catch failures and try with plaintext def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ] - if ( mqc_report.size() <= max_multiqc_email_size.toBytes() ) { + if ( mqc_report != null && mqc_report.size() <= max_multiqc_email_size.toBytes() ) { mail_cmd += [ '-A', mqc_report ] } mail_cmd.execute() << email_html @@ -155,14 +158,16 @@ class NfcoreTemplate { } // Write summary e-mail HTML to a file - def output_d = new File("${params.outdir}/pipeline_info/") - if (!output_d.exists()) { - output_d.mkdirs() - } - def output_hf = new File(output_d, "pipeline_report.html") + def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html") output_hf.withWriter { w -> w << email_html } - def output_tf = new File(output_d, "pipeline_report.txt") + FilesEx.copyTo(output_hf.toPath(), "${params.outdir}/pipeline_info/pipeline_report.html"); + output_hf.delete() + + // Write summary e-mail TXT to a file + def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt") output_tf.withWriter { w -> w << email_txt } + FilesEx.copyTo(output_tf.toPath(), "${params.outdir}/pipeline_info/pipeline_report.txt"); + output_tf.delete() } // @@ -227,15 +232,14 @@ class NfcoreTemplate { // Dump pipeline parameters in a json file // public static void dump_parameters(workflow, params) { - def output_d = new File("${params.outdir}/pipeline_info/") - if (!output_d.exists()) { - output_d.mkdirs() - } - def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') - def output_pf = new File(output_d, "params_${timestamp}.json") + def filename = "params_${timestamp}.json" + def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") def jsonStr = JsonOutput.toJson(params) - output_pf.text = JsonOutput.prettyPrint(jsonStr) + temp_pf.text = JsonOutput.prettyPrint(jsonStr) + + FilesEx.copyTo(temp_pf.toPath(), "${params.outdir}/pipeline_info/params_${timestamp}.json") + temp_pf.delete() } // diff --git a/modules.json b/modules.json index 2f665ed6..b76b2d36 100644 --- a/modules.json +++ b/modules.json @@ -7,17 +7,17 @@ "nf-core": { "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "bba7e362e4afead70653f84d8700588ea28d0f9e", "installed_by": ["modules"] }, "fastqc": { "branch": "master", - "git_sha": "bd8092b67b5103bdd52e300f75889442275c3117", + "git_sha": "65ad3e0b9a4099592e1102e92e10455dc661cf53", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "4ab13872435962dadc239979554d13709e20bf29", "installed_by": ["modules"] } } diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml new file mode 100644 index 00000000..f0c63f69 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/environment.yml @@ -0,0 +1,7 @@ +name: custom_dumpsoftwareversions +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::multiqc=1.17 diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index ebc87273..7685b33c 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { label 'process_single' // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda "bioconda::multiqc=1.14" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : - 'biocontainers/multiqc:1.14--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.17--pyhdfd78af_0' : + 'biocontainers/multiqc:1.17--pyhdfd78af_0' }" input: path versions diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml index c32657de..5f15a5fd 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml +++ b/modules/nf-core/custom/dumpsoftwareversions/meta.yml @@ -1,4 +1,4 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: custom_dumpsoftwareversions description: Custom module used to dump software versions within the nf-core pipeline template keywords: @@ -16,7 +16,6 @@ input: type: file description: YML file containing software versions pattern: "*.yml" - output: - yml: type: file @@ -30,7 +29,9 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@drpatelh" - "@grst" +maintainers: + - "@drpatelh" + - "@grst" diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test new file mode 100644 index 00000000..eec1db10 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test @@ -0,0 +1,38 @@ +nextflow_process { + + name "Test Process CUSTOM_DUMPSOFTWAREVERSIONS" + script "../main.nf" + process "CUSTOM_DUMPSOFTWAREVERSIONS" + tag "modules" + tag "modules_nfcore" + tag "custom" + tag "dumpsoftwareversions" + tag "custom/dumpsoftwareversions" + + test("Should run without failures") { + when { + process { + """ + def tool1_version = ''' + TOOL1: + tool1: 0.11.9 + '''.stripIndent() + + def tool2_version = ''' + TOOL2: + tool2: 1.9 + '''.stripIndent() + + input[0] = Channel.of(tool1_version, tool2_version).collectFile() + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap new file mode 100644 index 00000000..4274ed57 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap @@ -0,0 +1,27 @@ +{ + "Should run without failures": { + "content": [ + { + "0": [ + "software_versions.yml:md5,1c851188476409cda5752ce971b20b58" + ], + "1": [ + "software_versions_mqc.yml:md5,2570f4ba271ad08357b0d3d32a9cf84d" + ], + "2": [ + "versions.yml:md5,3843ac526e762117eedf8825b40683df" + ], + "mqc_yml": [ + "software_versions_mqc.yml:md5,2570f4ba271ad08357b0d3d32a9cf84d" + ], + "versions": [ + "versions.yml:md5,3843ac526e762117eedf8825b40683df" + ], + "yml": [ + "software_versions.yml:md5,1c851188476409cda5752ce971b20b58" + ] + } + ], + "timestamp": "2023-11-03T14:43:22.157011" + } +} diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml new file mode 100644 index 00000000..405aa24a --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml @@ -0,0 +1,2 @@ +custom/dumpsoftwareversions: + - modules/nf-core/custom/dumpsoftwareversions/** diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml new file mode 100644 index 00000000..1787b38a --- /dev/null +++ b/modules/nf-core/fastqc/environment.yml @@ -0,0 +1,7 @@ +name: fastqc +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::fastqc=0.12.1 diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 249f9064..9e19a74c 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -2,10 +2,10 @@ process FASTQC { tag "$meta.id" label 'process_medium' - conda "bioconda::fastqc=0.11.9" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' : - 'biocontainers/fastqc:0.11.9--0' }" + 'https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0' : + 'biocontainers/fastqc:0.12.1--hdfd78af_0' }" input: tuple val(meta), path(reads) @@ -37,7 +37,7 @@ process FASTQC { cat <<-END_VERSIONS > versions.yml "${task.process}": - fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) + fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' ) END_VERSIONS """ @@ -49,7 +49,7 @@ process FASTQC { cat <<-END_VERSIONS > versions.yml "${task.process}": - fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) + fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' ) END_VERSIONS """ } diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml index 4da5bb5a..ee5507e0 100644 --- a/modules/nf-core/fastqc/meta.yml +++ b/modules/nf-core/fastqc/meta.yml @@ -50,3 +50,8 @@ authors: - "@grst" - "@ewels" - "@FelixKrueger" +maintainers: + - "@drpatelh" + - "@grst" + - "@ewels" + - "@FelixKrueger" diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test new file mode 100644 index 00000000..b9e8f926 --- /dev/null +++ b/modules/nf-core/fastqc/tests/main.nf.test @@ -0,0 +1,109 @@ +nextflow_process { + + name "Test Process FASTQC" + script "../main.nf" + process "FASTQC" + tag "modules" + tag "modules_nfcore" + tag "fastqc" + + test("Single-Read") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id: 'test', single_end:true ], + [ + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. + // looks like this:
Mon 2 Oct 2023
test.gz
+ // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 + { assert process.out.html.get(0).get(1) ==~ ".*/test_fastqc.html" }, + { assert path(process.out.html.get(0).get(1)).getText().contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match("versions") }, + { assert process.out.zip.get(0).get(1) ==~ ".*/test_fastqc.zip" } + ) + } + } +// TODO +// // +// // Test with paired-end data +// // +// workflow test_fastqc_paired_end { +// input = [ +// [id: 'test', single_end: false], // meta map +// [ +// file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), +// file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) +// ] +// ] + +// FASTQC ( input ) +// } + +// // +// // Test with interleaved data +// // +// workflow test_fastqc_interleaved { +// input = [ +// [id: 'test', single_end: false], // meta map +// file(params.test_data['sarscov2']['illumina']['test_interleaved_fastq_gz'], checkIfExists: true) +// ] + +// FASTQC ( input ) +// } + +// // +// // Test with bam data +// // +// workflow test_fastqc_bam { +// input = [ +// [id: 'test', single_end: false], // meta map +// file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) +// ] + +// FASTQC ( input ) +// } + +// // +// // Test with multiple samples +// // +// workflow test_fastqc_multiple { +// input = [ +// [id: 'test', single_end: false], // meta map +// [ +// file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), +// file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true), +// file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true), +// file(params.test_data['sarscov2']['illumina']['test2_2_fastq_gz'], checkIfExists: true) +// ] +// ] + +// FASTQC ( input ) +// } + +// // +// // Test with custom prefix +// // +// workflow test_fastqc_custom_prefix { +// input = [ +// [ id:'mysample', single_end:true ], // meta map +// file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) +// ] + +// FASTQC ( input ) +// } +} diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap new file mode 100644 index 00000000..636a32ce --- /dev/null +++ b/modules/nf-core/fastqc/tests/main.nf.test.snap @@ -0,0 +1,10 @@ +{ + "versions": { + "content": [ + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "timestamp": "2023-10-09T23:40:54+0000" + } +} \ No newline at end of file diff --git a/modules/nf-core/fastqc/tests/tags.yml b/modules/nf-core/fastqc/tests/tags.yml new file mode 100644 index 00000000..7834294b --- /dev/null +++ b/modules/nf-core/fastqc/tests/tags.yml @@ -0,0 +1,2 @@ +fastqc: + - modules/nf-core/fastqc/** diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml new file mode 100644 index 00000000..bc0bdb5b --- /dev/null +++ b/modules/nf-core/multiqc/environment.yml @@ -0,0 +1,7 @@ +name: multiqc +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::multiqc=1.18 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 1fc387be..00cc48d2 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -1,10 +1,10 @@ process MULTIQC { label 'process_single' - conda "bioconda::multiqc=1.14" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : - 'biocontainers/multiqc:1.14--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.18--pyhdfd78af_0' : + 'biocontainers/multiqc:1.18--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" @@ -25,12 +25,14 @@ process MULTIQC { def args = task.ext.args ?: '' def config = multiqc_config ? "--config $multiqc_config" : '' def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' + def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : '' """ multiqc \\ --force \\ $args \\ $config \\ $extra_config \\ + $logo \\ . cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index f93b5ee5..f1aa660e 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -1,5 +1,5 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json -name: MultiQC +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: multiqc description: Aggregate results from bioinformatics analyses across many samples into a single report keywords: - QC @@ -13,7 +13,6 @@ tools: homepage: https://multiqc.info/ documentation: https://multiqc.info/docs/ licence: ["GPL-3.0-or-later"] - input: - multiqc_files: type: file @@ -31,7 +30,6 @@ input: type: file description: Optional logo file for MultiQC pattern: "*.{png}" - output: - report: type: file @@ -54,3 +52,8 @@ authors: - "@bunop" - "@drpatelh" - "@jfy133" +maintainers: + - "@abhi18av" + - "@bunop" + - "@drpatelh" + - "@jfy133" diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test new file mode 100644 index 00000000..c2dad217 --- /dev/null +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -0,0 +1,63 @@ +nextflow_process { + + name "Test Process MULTIQC" + script "../main.nf" + process "MULTIQC" + tag "modules" + tag "modules_nfcore" + tag "multiqc" + + test("MULTIQC: FASTQC") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) + input[1] = [] + input[2] = [] + input[3] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert path(process.out.report.get(0)).exists() }, + { assert path(process.out.data.get(0)).exists() }, + { assert path(process.out.versions.get(0)).getText().contains("multiqc") } + ) + } + + } + + test("MULTIQC: FASTQC and a config file") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) + input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)) + input[2] = [] + input[3] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert path(process.out.report.get(0)).exists() }, + { assert path(process.out.data.get(0)).exists() }, + { assert path(process.out.versions.get(0)).getText().contains("multiqc") } + ) + } + + } +} diff --git a/modules/nf-core/multiqc/tests/tags.yml b/modules/nf-core/multiqc/tests/tags.yml new file mode 100644 index 00000000..bea6c0d3 --- /dev/null +++ b/modules/nf-core/multiqc/tests/tags.yml @@ -0,0 +1,2 @@ +multiqc: + - modules/nf-core/multiqc/** diff --git a/nextflow.config b/nextflow.config index a2339cfe..e5784ae0 100644 --- a/nextflow.config +++ b/nextflow.config @@ -14,7 +14,7 @@ params { input = null // References genome = null - igenomes_base = 's3://ngi-igenomes/igenomes' + igenomes_base = 's3://ngi-igenomes/igenomes/' igenomes_ignore = false @@ -82,6 +82,7 @@ profiles { dumpHashes = true process.beforeScript = 'echo $HOSTNAME' cleanup = false + nextflow.enable.configProcessNamesValidation = true } conda { conda.enabled = true @@ -104,13 +105,13 @@ profiles { } docker { docker.enabled = true - docker.userEmulation = true conda.enabled = false singularity.enabled = false podman.enabled = false shifter.enabled = false charliecloud.enabled = false apptainer.enabled = false + runOptions = '-u $(id -u):$(id -g)' } arm { docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' @@ -181,7 +182,7 @@ singularity.registry = 'quay.io' // Nextflow plugins plugins { - id 'nf-validation' // Validation of pipeline parameters and creation of an input channel from a sample sheet + id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet } // Load igenomes.config if required @@ -204,6 +205,9 @@ env { // Capture exit codes from upstream processes when piping process.shell = ['/bin/bash', '-euo', 'pipefail'] +// Disable process selector warnings by default. Use debug profile to enable warnings. +nextflow.enable.configProcessNamesValidation = false + def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') timeline { enabled = true @@ -229,7 +233,7 @@ manifest { description = """Methylation (Bisulfite-Sequencing) Best Practice analysis pipeline, part of the nf-core community.""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '2.5.0dev' + version = '2.6.0dev' doi = '' } From db62e2a6d3f354524c986040e249f4b9e52254a4 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 20 Dec 2023 15:58:16 +0000 Subject: [PATCH 16/30] Template update for nf-core/tools version 2.11.1 --- .../{release-announcments.yml => release-announcements.yml} | 0 nextflow.config | 4 ++-- 2 files changed, 2 insertions(+), 2 deletions(-) rename .github/workflows/{release-announcments.yml => release-announcements.yml} (100%) diff --git a/.github/workflows/release-announcments.yml b/.github/workflows/release-announcements.yml similarity index 100% rename from .github/workflows/release-announcments.yml rename to .github/workflows/release-announcements.yml diff --git a/nextflow.config b/nextflow.config index e5784ae0..02736876 100644 --- a/nextflow.config +++ b/nextflow.config @@ -111,10 +111,10 @@ profiles { shifter.enabled = false charliecloud.enabled = false apptainer.enabled = false - runOptions = '-u $(id -u):$(id -g)' + docker.runOptions = '-u $(id -u):$(id -g)' } arm { - docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' + docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' } singularity { singularity.enabled = true From 8966c1373d5d9c651c551f83d0ac1b2cf94719c2 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 22 Dec 2023 06:39:58 -0600 Subject: [PATCH 17/30] Make index file check more precise Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> --- subworkflows/local/prepare_genome.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf index 84e21ff5..877541ea 100644 --- a/subworkflows/local/prepare_genome.nf +++ b/subworkflows/local/prepare_genome.nf @@ -47,7 +47,7 @@ workflow PREPARE_GENOME { * Generate bwameth index if not supplied */ if (params.bwa_meth_index) { - if (params.bwa_meth_index.endsWith('.gz')) { + if (params.bwa_meth_index.endsWith('.tar.gz')) { ch_bismark_index = UNTAR ( [ [:], file(params.bwa_meth_index) ] ).untar.map { it[1] } } else { ch_bismark_index = Channel.value(file(params.bwa_meth_index)) From 438ceffcd9b0086baefa67c17699154d058e3bc5 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 22 Dec 2023 06:41:24 -0600 Subject: [PATCH 18/30] Fix test indexes Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> --- tests/pipeline/bismark/main.nf.test | 4 ++-- tests/pipeline/bismark_hisat/main.nf.test | 4 ++-- tests/pipeline/bwameth/main.nf.test | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/tests/pipeline/bismark/main.nf.test b/tests/pipeline/bismark/main.nf.test index bde39977..9292e1ef 100644 --- a/tests/pipeline/bismark/main.nf.test +++ b/tests/pipeline/bismark/main.nf.test @@ -56,7 +56,7 @@ nextflow_pipeline { when { params { aligner = "bismark" - bismark_index = "https://github.com/nf-core/test-datasets/raw/07ff447f2023e1e7b2e91396526601af485655fa/reference/BismarkIndex.tar.gz" + bismark_index = "https://github.com/nf-core/test-datasets/raw/methylseq/reference/Bowtie2_Index.tar.gz" cytosine_report = true outdir = "$outputDir" } @@ -118,7 +118,7 @@ nextflow_pipeline { aligner = "bismark" skip_trimming = true rrbs = true - bismark_index = "https://github.com/nf-core/test-datasets/raw/07ff447f2023e1e7b2e91396526601af485655fa/reference/BismarkIndex.tar.gz" + bismark_index = "https://github.com/nf-core/test-datasets/raw/methylseq/reference/Bowtie2_Index.tar.gz" cytosine_report = true outdir = "$outputDir" } diff --git a/tests/pipeline/bismark_hisat/main.nf.test b/tests/pipeline/bismark_hisat/main.nf.test index ded63bd2..c4fb9f88 100644 --- a/tests/pipeline/bismark_hisat/main.nf.test +++ b/tests/pipeline/bismark_hisat/main.nf.test @@ -55,7 +55,7 @@ nextflow_pipeline { when { params { aligner = "bismark_hisat" - bismark_index = "https://github.com/nf-core/test-datasets/raw/07ff447f2023e1e7b2e91396526601af485655fa/reference/BismarkIndex.tar.gz" + bismark_index = "https://github.com/nf-core/test-datasets/raw/methylseq/reference/Hisat2_Index.tar.gz" local_alignment = true outdir = "$outputDir" } @@ -117,7 +117,7 @@ nextflow_pipeline { aligner = "bismark_hisat" skip_trimming = true rrbs = true - bismark_index = "https://github.com/nf-core/test-datasets/raw/07ff447f2023e1e7b2e91396526601af485655fa/reference/BismarkIndex.tar.gz" + bismark_index = "https://github.com/nf-core/test-datasets/raw/methylseq/reference/Hisat2_Index.tar.gz" local_alignment = true outdir = "$outputDir" } diff --git a/tests/pipeline/bwameth/main.nf.test b/tests/pipeline/bwameth/main.nf.test index 4311ddc9..12b6c3a4 100644 --- a/tests/pipeline/bwameth/main.nf.test +++ b/tests/pipeline/bwameth/main.nf.test @@ -53,7 +53,7 @@ nextflow_pipeline { when { params { aligner = "bwameth" - bwa_meth_index = "https://github.com/nf-core/test-datasets/raw/07ff447f2023e1e7b2e91396526601af485655fa/reference/bwameth.tar.gz" + bwa_meth_index = "https://github.com/nf-core/test-datasets/raw/methylseq/reference/Bwameth_Index.tar.gz" methyl_kit = true outdir = "$outputDir" } @@ -108,7 +108,7 @@ nextflow_pipeline { aligner = "bwameth" skip_trimming = true rrbs = true - bwa_meth_index = "https://github.com/nf-core/test-datasets/raw/07ff447f2023e1e7b2e91396526601af485655fa/reference/bwameth.tar.gz" + bwa_meth_index = "https://github.com/nf-core/test-datasets/raw/methylseq/reference/Bwameth_Index.tar.gz" methyl_kit = true outdir = "$outputDir" } From 2673007b651e3a77c9932d7bee3c556defce17d7 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 22 Dec 2023 10:34:39 -0600 Subject: [PATCH 19/30] test: Update test lib path --- nf-test.config | 2 +- tests/{pipeline => }/lib/UTILS.groovy | 0 2 files changed, 1 insertion(+), 1 deletion(-) rename tests/{pipeline => }/lib/UTILS.groovy (100%) diff --git a/nf-test.config b/nf-test.config index cb656b94..89243e51 100644 --- a/nf-test.config +++ b/nf-test.config @@ -6,7 +6,7 @@ config { workDir "/tmp" // location of library folder that is added automatically to the classpath - libDir "lib/" + libDir "tests/lib/" // location of an optional nextflow.config file specific for executing tests configFile "nextflow.config" diff --git a/tests/pipeline/lib/UTILS.groovy b/tests/lib/UTILS.groovy similarity index 100% rename from tests/pipeline/lib/UTILS.groovy rename to tests/lib/UTILS.groovy From ab3898b4ac075cbea78d95fb13b196e49b4f8914 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 22 Dec 2023 13:22:55 -0600 Subject: [PATCH 20/30] ci: Bump nf-test version Again Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 0904c096..599e16f3 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -14,7 +14,7 @@ on: env: NXF_ANSI_LOG: false - NFTEST_VER: "0.8.1" + NFTEST_VER: "0.8.2" concurrency: group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" From 9d88d67c7a68495d789610f427d8e3d02881436d Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 22 Dec 2023 14:48:19 -0600 Subject: [PATCH 21/30] test: Bump snapshots for nf-test 0.8.2 Co-authored-by: sateeshperi --- .gitignore | 1 + tests/pipeline/bismark/main.nf.test | 6 +- tests/pipeline/bismark/main.nf.test.snap | 148 +++++++++--------- tests/pipeline/bismark_hisat/main.nf.test | 3 +- .../pipeline/bismark_hisat/main.nf.test.snap | 72 ++++----- tests/pipeline/bwameth/main.nf.test | 3 +- tests/pipeline/bwameth/main.nf.test.snap | 8 +- 7 files changed, 119 insertions(+), 122 deletions(-) diff --git a/.gitignore b/.gitignore index 9473434c..4a37b601 100644 --- a/.gitignore +++ b/.gitignore @@ -8,4 +8,5 @@ testing* *.pyc .vscode .nf-test +.nf-test.log test-datasets/ diff --git a/tests/pipeline/bismark/main.nf.test b/tests/pipeline/bismark/main.nf.test index 9292e1ef..ee1c87b5 100644 --- a/tests/pipeline/bismark/main.nf.test +++ b/tests/pipeline/bismark/main.nf.test @@ -1,9 +1,8 @@ -import com.askimed.nf.test.util.FileUtil; - nextflow_pipeline { name "Test Workflow main.nf" script "main.nf" + tag "bismark" tag "pipeline" @@ -14,7 +13,6 @@ nextflow_pipeline { save_reference = true outdir = "$outputDir" } - } then { @@ -161,7 +159,7 @@ nextflow_pipeline { path("$outputDir/cat/SRR389222.merged.fastq.gz"), path("$outputDir/qualimap/Ecoli_10K/genome_results.txt"), path("$outputDir/qualimap/SRR389222/genome_results.txt")).match("single_end_nomeseq") }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end__nomeseq_software_versions") }, + { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_nomeseq_software_versions") }, { assert new File("$outputDir/bismark/alignments/logs/Ecoli_10K_1_val_1_bismark_bt2_PE_report.txt").exists() }, { assert new File("$outputDir/bismark/alignments/logs/SRR389222_trimmed_bismark_bt2_SE_report.txt").exists() }, { assert new File("$outputDir/bismark/reports/Ecoli_10K_1_val_1_bismark_bt2_PE_report.html").exists() }, diff --git a/tests/pipeline/bismark/main.nf.test.snap b/tests/pipeline/bismark/main.nf.test.snap index 68a6e38b..71f6c965 100644 --- a/tests/pipeline/bismark/main.nf.test.snap +++ b/tests/pipeline/bismark/main.nf.test.snap @@ -13,39 +13,39 @@ }, "single_end_nomeseq": { "content": [ - "Ecoli_10K.NOMe.CpG.cov.gz:md5,b172ec70bfb6607a5704c68ed27dc8e4", - "Ecoli_10K.NOMe.GpC.cov.gz:md5,c975d1cbd714f79ce900378604b460b5", - "SRR389222.NOMe.CpG.cov.gz:md5,c86cd4e0523987bbb18191aeb2d2ecfd", - "SRR389222.NOMe.GpC.cov.gz:md5,bdd5bd0a9fc8be7cbd22d7fe302e8f17", + "Ecoli_10K.NOMe.CpG.cov.gz:md5,c2c4db8d0a2ec32d572e75b01b2f7d81", + "Ecoli_10K.NOMe.GpC.cov.gz:md5,a2b56291dbe8b344ee03a3ae58de8807", + "SRR389222.NOMe.CpG.cov.gz:md5,9738cb2fd47a65851626fc48d264c1b4", + "SRR389222.NOMe.GpC.cov.gz:md5,d5e6d60c93e76c7476b132b6aa4f8395", "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bam:md5,a7464c83416ba057387df5d85b1bc1fe", "SRR389222_trimmed_bismark_bt2.deduplicated.bam:md5,7dba45955ae74159596a6ab41a9dcc87", - "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz:md5,6d631d8999657816e569a7a896f423d5", - "SRR389222_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,4a1bee24f279542dad02b167fabc6997", + "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz:md5,88e599178b08907aab7d248302b7d37e", + "SRR389222_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,fe6b3655db6da21bdd3076947e062f0b", "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt:md5,29f3b882a51b63ce77d3d9c69b0e5f85", "SRR389222_trimmed_bismark_bt2.deduplicated.M-bias.txt:md5,bc48b8895f9ce84205a25899cf551624", - "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz:md5,5a358982536d476e962319b6656441da", - "SRR389222_trimmed_bismark_bt2.deduplicated.bismark.cov.gz:md5,b08b8d4dc026106345ca6108e27ed601", + "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz:md5,962fe67f41f5e03d8e321ed381369513", + "SRR389222_trimmed_bismark_bt2.deduplicated.bismark.cov.gz:md5,82a55b84888ad5fe530f97c348738fdb", [ - "CHG_OB_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,bca8572c7cd3cd45e148ba722ad4b12d", - "CHG_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,b0f6e9284b65d1bf3c813008c08656cc", - "CHG_OT_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,7f49ecab1843458c28c3d6fe6a85149e", - "CHG_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,ddc200fe98155bf88be3d98073a37238", - "CHH_OB_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,e67409a20a141077edc1dc61972bb278", - "CHH_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,aca84c4d6fffb7bf72f4dcd4371dc89b", - 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"timestamp": "2023-08-28T08:46:48+0000" + "timestamp": "2023-12-22T14:20:09.69680784" }, "clip_r1": { "content": [ "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bam:md5,388bb71e1e52628823e8b590d37cd665", "SRR389222_trimmed_bismark_bt2.deduplicated.bam:md5,1bfe463dabf8727992e3ff6c19d8e7c1", - "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz:md5,4fbac770e7bf6b93e972d7e5bc494aac", - "SRR389222_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,7b7535a28d655edaa94bcfa79957731a", + "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz:md5,e8b3933de21d7618cdaab650fe544b17", + "SRR389222_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,bddc7c560a902b842b72e20a21274cba", "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt:md5,83a004a3d957cf95f25933bcd828a8d4", "SRR389222_trimmed_bismark_bt2.deduplicated.M-bias.txt:md5,90a6b76d41112c6de391d3a017638d95", - "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz:md5,9dc43af95c865440be68a4a41634f6c3", - "SRR389222_trimmed_bismark_bt2.deduplicated.bismark.cov.gz:md5,da2acc1e94842feee25e282575b74ce2", + "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz:md5,34aa02c199f1496df0704dd239373ebe", + "SRR389222_trimmed_bismark_bt2.deduplicated.bismark.cov.gz:md5,03178f50ae4bf04a7b78d8bbdb8a77af", [ - "CHG_OB_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,bd15affb231e6fa69f3daef1993e732f", - "CHG_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,8175e992f5cd9c3cd9c2d82b36c3231b", - "CHG_OT_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,f5fee467014e215c43569efcc696a6e0", - "CHG_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,9918a6c806dcb92a95e3806e8aae30f7", - "CHH_OB_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,0c0f91367e3fd1d14710604af2cfeb1c", - "CHH_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,52dcf6c1e4e0cf4aaee2c4e42aad190f", - "CHH_OT_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,8befa0112f299724b60eb6c5de1cdf1f", - "CHH_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,c4c864ee34ebb523d3c424b787ee9a3a", - "CpG_OB_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,50f969a02e2a50f140dedb90cdc3718d", - "CpG_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,e066703e693e77ef934f64f16013c431", - "CpG_OT_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,af7b19d0658a58a3a6f2632d9c0276f4", - "CpG_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,b3c76b857baf4f2236137466b474cdb8" + "CHG_OB_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,3856b07ea51dea59b444a7483ca3db75", + "CHG_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,e70e8a2ace2e602a967de256d299fb0d", + "CHG_OT_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,c1ba1891636a6b99f4d1495b3ddf1a59", + "CHG_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,f8867c4ee03fba6be823b7287cacfea3", + "CHH_OB_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,4e9a0e61d47eefb64876431b3640ee95", + "CHH_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,32728cf447a470681f4e608008d514ae", + "CHH_OT_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,10cd51608191667e027a9867dd84ab3f", + "CHH_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,2ec291cbfc4d64dbcd50603839129de1", + "CpG_OB_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,423aa4faf47d176a6b6cce134e1a9212", + "CpG_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,873612f00ee6ef44e8bc0dcb9f4a35f6", + "CpG_OT_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,1e243313554fce1b06aba217c7123cae", + "CpG_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,d86423a21b0d22188e188dc9f576135c" ], "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt:md5,373ac926ba4ceae1c4826f5ea4b3ada6", "SRR389222_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,9a1a5d1e6722dda9e8a1953a01c415d0", - "SRR389222.merged.fastq.gz:md5,ba5df0639e25988059a6f5bf309dbb6e", + "SRR389222.merged.fastq.gz:md5,47e1d7461d511a970e80085dd6454775", "genome_results.txt:md5,72bdf73fe97711a2ba75b5c59f3a5637", "genome_results.txt:md5,5631f1632df00985946641cfc1601633" ], - "timestamp": "2023-08-28T08:46:48+0000" + "timestamp": "2023-12-22T14:23:43.189936269" } } diff --git a/tests/pipeline/bismark_hisat/main.nf.test b/tests/pipeline/bismark_hisat/main.nf.test index c4fb9f88..8c15ee04 100644 --- a/tests/pipeline/bismark_hisat/main.nf.test +++ b/tests/pipeline/bismark_hisat/main.nf.test @@ -1,9 +1,8 @@ -import com.askimed.nf.test.util.FileUtil; - nextflow_pipeline { name "Test Workflow main.nf" script "main.nf" + tag "bismark_hisat" tag "pipeline" diff --git a/tests/pipeline/bismark_hisat/main.nf.test.snap b/tests/pipeline/bismark_hisat/main.nf.test.snap index 8c8c482c..18c0c4e0 100644 --- a/tests/pipeline/bismark_hisat/main.nf.test.snap +++ b/tests/pipeline/bismark_hisat/main.nf.test.snap @@ -15,64 +15,64 @@ "content": [ "Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.bam:md5,9e9b4adfeeb716e24ecba0bfad39c2e3", "SRR389222_trimmed_bismark_hisat2.deduplicated.bam:md5,aa60cf9dcf302c185b12ced6f302a06e", - "Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.bedGraph.gz:md5,539b06719ca6dcccaf2b86d8be571ace", - "SRR389222_trimmed_bismark_hisat2.deduplicated.bedGraph.gz:md5,dba86d0f60ad88aaeef1970ceef8376b", + "Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.bedGraph.gz:md5,357196071c54757566cdd0bb7ab79fa8", + "SRR389222_trimmed_bismark_hisat2.deduplicated.bedGraph.gz:md5,b20f17236ff64db1114343ff333a6d5b", "Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.M-bias.txt:md5,5fd8655f4b9dba2249a52b769fe50faf", "SRR389222_trimmed_bismark_hisat2.deduplicated.M-bias.txt:md5,b19356395d4ae1ad83bd3ec38276e580", [ - "CHG_OB_Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,c2144bcfb7850b8c10bb8296dd2e09c1", - "CHG_OB_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,b0f6e9284b65d1bf3c813008c08656cc", - "CHG_OT_Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,7f49ecab1843458c28c3d6fe6a85149e", - "CHG_OT_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,5813137cea214c7759598ca442f29d47", - "CHH_OB_Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,4e8f5b27fbb933c572f269688004be38", - "CHH_OB_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,aca84c4d6fffb7bf72f4dcd4371dc89b", - "CHH_OT_Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,d173808471dbb7c50ef43eb1f5f29faa", - "CHH_OT_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,1018c276fa14900e7b1edad0e23fc7ff", - "CpG_OB_Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,3f58d13a3b47d639696dbb4478a39488", - "CpG_OB_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,0039a8c3f8971a5a99bc58bc1511fa0d", - "CpG_OT_Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,6dfc57a2892d7cd3bebb7cbc0878196b", - "CpG_OT_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,801c0dba9ca584d9c804a4254d7c4ea6" + "CHG_OB_Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,6d2ca2e6548640e3885c94a3ca6beae0", + "CHG_OB_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,9d8098ce1a27c23961e20b6a95f237d1", + "CHG_OT_Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,5e5aefaa3f63e73f30342ad843eb210b", + "CHG_OT_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,1180631ef093aade3a5195ce7ddfb3f6", + "CHH_OB_Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,abd48ddf1c9e844d8164de5150850d10", + "CHH_OB_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,6834286d8d07a1b3a4399f71b5b3c3f8", + "CHH_OT_Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,978ad87fef01e39283a620253320ee45", + "CHH_OT_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,c311a70c0c8b6a93c2055fcbec03a833", + "CpG_OB_Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,51f8b079b9fd91e23e495d9e0e289530", + "CpG_OB_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,4dae933bcdc8c7d1de2f5e7239c1ae55", + "CpG_OT_Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,9712eef973883f44dcc0a307af28ba70", + "CpG_OT_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,63e737eef999e2d6348e7ed2a7ce4402" ], - "Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.bismark.cov.gz:md5,474c1291d09b023e91ed892b5a09ba80", - "SRR389222_trimmed_bismark_hisat2.deduplicated.bismark.cov.gz:md5,e58cba79f419cb411a77b656173d48ea", + "Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.bismark.cov.gz:md5,d8342eca72089408d8e4d7c5ec5e95bf", + "SRR389222_trimmed_bismark_hisat2.deduplicated.bismark.cov.gz:md5,ad7a19cb9908844c47b7b871ff1223c2", "Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated_splitting_report.txt:md5,a5dc04c52facdb5221a06ae7f3bca2e4", "SRR389222_trimmed_bismark_hisat2.deduplicated_splitting_report.txt:md5,1f792e1fddb17140947f14008e1f9ffd", - "SRR389222.merged.fastq.gz:md5,ba5df0639e25988059a6f5bf309dbb6e", + "SRR389222.merged.fastq.gz:md5,47e1d7461d511a970e80085dd6454775", "genome_results.txt:md5,f272f759bfed7e8a30ec2719e0b518aa", "genome_results.txt:md5,7706d3790aee0e9244c490941ecd394f" ], - "timestamp": "2023-08-28T10:04:42+0000" + "timestamp": "2023-12-22T14:24:55.576498855" }, "single_end_rrbs": { "content": [ "Ecoli_10K_methylated_R1_bismark_hisat2_pe.bam:md5,53c34edee0bc7f34c9f4e9a3685dd706", "SRR389222.merged_bismark_hisat2.bam:md5,204123a5f7cd77cba3a90b904443c7eb", - "Ecoli_10K_methylated_R1_bismark_hisat2_pe.bedGraph.gz:md5,539b06719ca6dcccaf2b86d8be571ace", - "SRR389222.merged_bismark_hisat2.bedGraph.gz:md5,2b41ebc929eec351e21a16eec6f8fdd9", + "Ecoli_10K_methylated_R1_bismark_hisat2_pe.bedGraph.gz:md5,357196071c54757566cdd0bb7ab79fa8", + "SRR389222.merged_bismark_hisat2.bedGraph.gz:md5,d509b1e8e4ec03dcde48a127cf976594", "Ecoli_10K_methylated_R1_bismark_hisat2_pe.M-bias.txt:md5,5fd8655f4b9dba2249a52b769fe50faf", "SRR389222.merged_bismark_hisat2.M-bias.txt:md5,ea90b0495446d03e375aad42d598a9f9", [ - "CHG_OB_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,c2144bcfb7850b8c10bb8296dd2e09c1", - "CHG_OB_SRR389222.merged_bismark_hisat2.txt.gz:md5,3fcc7974fd6c5cbacf231835f58d949b", - "CHG_OT_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,7f49ecab1843458c28c3d6fe6a85149e", - "CHG_OT_SRR389222.merged_bismark_hisat2.txt.gz:md5,e924ba0137252d4b470532cfc36524c2", - "CHH_OB_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,4e8f5b27fbb933c572f269688004be38", - "CHH_OB_SRR389222.merged_bismark_hisat2.txt.gz:md5,2fb870b779750951bec579ce7562736e", - "CHH_OT_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,d173808471dbb7c50ef43eb1f5f29faa", - "CHH_OT_SRR389222.merged_bismark_hisat2.txt.gz:md5,6e1d89e988f10fa528398b117a554fb1", - "CpG_OB_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,3f58d13a3b47d639696dbb4478a39488", - "CpG_OB_SRR389222.merged_bismark_hisat2.txt.gz:md5,6537b18418e62410d9ae617480702c54", - "CpG_OT_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,6dfc57a2892d7cd3bebb7cbc0878196b", - "CpG_OT_SRR389222.merged_bismark_hisat2.txt.gz:md5,b07add9bb5ebc7d404e1505deb960654" + "CHG_OB_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,6d2ca2e6548640e3885c94a3ca6beae0", + "CHG_OB_SRR389222.merged_bismark_hisat2.txt.gz:md5,eeb08e87d7e3dca0acbb2c5ba2be66fb", + "CHG_OT_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,5e5aefaa3f63e73f30342ad843eb210b", + "CHG_OT_SRR389222.merged_bismark_hisat2.txt.gz:md5,7add3136b9f74de6aa83d38dde191060", + "CHH_OB_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,abd48ddf1c9e844d8164de5150850d10", + "CHH_OB_SRR389222.merged_bismark_hisat2.txt.gz:md5,a135c7e8a6c1b909a318ef17d47dca94", + "CHH_OT_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,978ad87fef01e39283a620253320ee45", + "CHH_OT_SRR389222.merged_bismark_hisat2.txt.gz:md5,8f1910f962b724592546a6187ad0a677", + "CpG_OB_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,51f8b079b9fd91e23e495d9e0e289530", + "CpG_OB_SRR389222.merged_bismark_hisat2.txt.gz:md5,b8b2de10044869b6c1097afc21c878a0", + "CpG_OT_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,9712eef973883f44dcc0a307af28ba70", + "CpG_OT_SRR389222.merged_bismark_hisat2.txt.gz:md5,877b026664516cb8851c1d80bf0d8495" ], - "Ecoli_10K_methylated_R1_bismark_hisat2_pe.bismark.cov.gz:md5,474c1291d09b023e91ed892b5a09ba80", - "SRR389222.merged_bismark_hisat2.bismark.cov.gz:md5,626edb040f82e57c1f521bdb72618407", + "Ecoli_10K_methylated_R1_bismark_hisat2_pe.bismark.cov.gz:md5,d8342eca72089408d8e4d7c5ec5e95bf", + "SRR389222.merged_bismark_hisat2.bismark.cov.gz:md5,29943eb00da6057a67e5530580668130", "Ecoli_10K_methylated_R1_bismark_hisat2_pe_splitting_report.txt:md5,76868c2015864a3f7c2b4cd1738e4765", "SRR389222.merged_bismark_hisat2_splitting_report.txt:md5,4a9e54ffb48c9bb1e5ac33aa77b25f5c", - "SRR389222.merged.fastq.gz:md5,ba5df0639e25988059a6f5bf309dbb6e", + "SRR389222.merged.fastq.gz:md5,47e1d7461d511a970e80085dd6454775", "genome_results.txt:md5,13a70a3885acd9d55014aa1ad66e2bbb", "genome_results.txt:md5,ae5b10e9a3ffa1ac7a4f4e736228ec49" ], - "timestamp": "2023-08-28T10:04:42+0000" + "timestamp": "2023-12-22T14:27:26.162082917" } } diff --git a/tests/pipeline/bwameth/main.nf.test b/tests/pipeline/bwameth/main.nf.test index 12b6c3a4..002223bb 100644 --- a/tests/pipeline/bwameth/main.nf.test +++ b/tests/pipeline/bwameth/main.nf.test @@ -1,9 +1,8 @@ -import com.askimed.nf.test.util.FileUtil; - nextflow_pipeline { name "Test Workflow main.nf" script "main.nf" + tag "bwameth" tag "pipeline" diff --git a/tests/pipeline/bwameth/main.nf.test.snap b/tests/pipeline/bwameth/main.nf.test.snap index fb74d28f..cee3939d 100644 --- a/tests/pipeline/bwameth/main.nf.test.snap +++ b/tests/pipeline/bwameth/main.nf.test.snap @@ -32,7 +32,7 @@ "genome.fa.bwameth.c2t.sa:md5,4a1e905b828396a1909669bc9c573d8d" ] ], - "SRR389222.merged.fastq.gz:md5,ba5df0639e25988059a6f5bf309dbb6e", + "SRR389222.merged.fastq.gz:md5,47e1d7461d511a970e80085dd6454775", "Ecoli_10K.markdup.sorted_CpG.bedGraph:md5,2fbe52f528b14b77380eceea8a621687", "SRR389222.markdup.sorted_CpG.bedGraph:md5,febd0f93f46dfccabf69dbba3f518add", "Ecoli_10K.mbias.txt:md5,3a448a2a6364b2de3129365a271c0534", @@ -40,7 +40,7 @@ "genome_results.txt:md5,0f4749b54f9d923f0d4f20ad404b2062", "genome_results.txt:md5,c786cc367645cee286360707e2624dca" ], - "timestamp": "2023-08-28T00:28:04+0000" + "timestamp": "2023-12-22T14:15:08.478775696" }, "single_end_rrbs": { "content": [ @@ -59,7 +59,7 @@ "genome.fa.bwameth.c2t.sa:md5,4a1e905b828396a1909669bc9c573d8d" ] ], - "SRR389222.merged.fastq.gz:md5,ba5df0639e25988059a6f5bf309dbb6e", + "SRR389222.merged.fastq.gz:md5,47e1d7461d511a970e80085dd6454775", "Ecoli_10K.sorted_CpG.bedGraph:md5,513797bcafa8724fc61484e2686af517", "SRR389222.sorted_CpG.bedGraph:md5,a754358e8b95db30602aa29835a896bd", "Ecoli_10K.mbias.txt:md5,ec13da6deba1ce147624bce065ec5df6", @@ -67,6 +67,6 @@ "genome_results.txt:md5,e5e1ab8eb875aaf090b3a0d9b1927810", "genome_results.txt:md5,199902f9d8f10f73bcb0a1ce29ceca5d" ], - "timestamp": "2023-08-28T00:28:04+0000" + "timestamp": "2023-12-22T14:16:15.148388923" } } From 7155cc64b2ca5f65e66061463c66a755d2ad5d8f Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Thu, 7 Dec 2023 20:46:45 -0600 Subject: [PATCH 22/30] test: Move test samplesheet to assets --- assets/samplesheet.csv | 6 ++++-- conf/test.config | 2 +- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv index fc797c5e..ee7324b3 100644 --- a/assets/samplesheet.csv +++ b/assets/samplesheet.csv @@ -1,3 +1,5 @@ sample,fastq_1,fastq_2,genome -SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz,/path/to/fasta/files/genome.fa -SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,/path/to/fasta/files/genome.fa +SRR389222_sub1,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz,, +SRR389222_sub2,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub2.fastq.gz,, +SRR389222_sub3,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub3.fastq.gz,, +Ecoli_10K_methylated,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz, diff --git a/conf/test.config b/conf/test.config index ca5e25cb..0291dfe7 100644 --- a/conf/test.config +++ b/conf/test.config @@ -17,7 +17,7 @@ params { max_time = 6.h // Input data - input = "${params.test_data_base}/samplesheet/samplesheet_test.csv" + input = "${projectDir}/assets/samplesheet.csv" // Genome references fasta = "${params.test_data_base}/reference/genome.fa" From cc1b93793dff7a737d0638a1f074f16a5764fc7c Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Thu, 7 Dec 2023 20:47:56 -0600 Subject: [PATCH 23/30] test: Remove _'s in one sample Duplicates behavior from #360 --- assets/samplesheet.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv index ee7324b3..aa6b7542 100644 --- a/assets/samplesheet.csv +++ b/assets/samplesheet.csv @@ -2,4 +2,4 @@ sample,fastq_1,fastq_2,genome SRR389222_sub1,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz,, SRR389222_sub2,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub2.fastq.gz,, SRR389222_sub3,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub3.fastq.gz,, -Ecoli_10K_methylated,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz, +Ecoli,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz, From ee9d924fa68a846d499de887d4d14033aae37a5a Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Thu, 7 Dec 2023 21:04:04 -0600 Subject: [PATCH 24/30] fix(#360): Return id when sample field has no _'s Co-authored-by: FelixKrueger --- workflows/methylseq.nf | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/workflows/methylseq.nf b/workflows/methylseq.nf index d50dcae6..a351316e 100644 --- a/workflows/methylseq.nf +++ b/workflows/methylseq.nf @@ -99,7 +99,8 @@ workflow METHYLSEQ { .map { meta, fastq -> def meta_clone = meta.clone() - meta_clone.id = meta_clone.id.split('_')[0..-2].join('_') + parts = meta_clone.id.split('_') + meta_clone.id = parts.length > 1 ? parts[0..-2].join('_') : meta_clone.id [ meta_clone, fastq ] } .groupTuple(by: [0]) From b73a86161e01562441e9c7a08d240fdf2495c1ab Mon Sep 17 00:00:00 2001 From: Sateesh Date: Wed, 20 Dec 2023 02:48:40 +0000 Subject: [PATCH 25/30] update bismark nf-test --- tests/pipeline/bismark/main.nf.test | 82 ++++++++++++------------ tests/pipeline/bismark/main.nf.test.snap | 78 ++++++++++++++++++++-- 2 files changed, 112 insertions(+), 48 deletions(-) diff --git a/tests/pipeline/bismark/main.nf.test b/tests/pipeline/bismark/main.nf.test index ee1c87b5..11483301 100644 --- a/tests/pipeline/bismark/main.nf.test +++ b/tests/pipeline/bismark/main.nf.test @@ -18,33 +18,33 @@ nextflow_pipeline { then { assertAll( { assert workflow.success }, - { assert snapshot(path("$outputDir/bismark/deduplicated/Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bam"), + { assert snapshot(path("$outputDir/bismark/deduplicated/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bam"), path("$outputDir/bismark/deduplicated/SRR389222_trimmed_bismark_bt2.deduplicated.bam"), - path("$outputDir/bismark/methylation_calls/bedGraph/Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz"), + path("$outputDir/bismark/methylation_calls/bedGraph/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz"), path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_trimmed_bismark_bt2.deduplicated.bedGraph.gz"), - path("$outputDir/bismark/methylation_calls/mbias/Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt"), + path("$outputDir/bismark/methylation_calls/mbias/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt"), path("$outputDir/bismark/methylation_calls/mbias/SRR389222_trimmed_bismark_bt2.deduplicated.M-bias.txt"), - path("$outputDir/bismark/methylation_calls/methylation_coverage/Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz"), + path("$outputDir/bismark/methylation_calls/methylation_coverage/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz"), path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_trimmed_bismark_bt2.deduplicated.bismark.cov.gz"), path("$outputDir/bismark/methylation_calls/methylation_calls/").list(), - path("$outputDir/bismark/methylation_calls/splitting_report/Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt"), + path("$outputDir/bismark/methylation_calls/splitting_report/Ecoli_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt"), path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_trimmed_bismark_bt2.deduplicated_splitting_report.txt"), path("$outputDir/bismark/reference_genome/BismarkIndex/").list(), - path("$outputDir/qualimap/Ecoli_10K/genome_results.txt"), + path("$outputDir/qualimap/Ecoli/genome_results.txt"), path("$outputDir/qualimap/SRR389222/genome_results.txt")).match("single_end") }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_software_versions") }, - { assert new File("$outputDir/bismark/alignments/logs/Ecoli_10K_1_val_1_bismark_bt2_PE_report.txt").exists() }, + { assert new File("$outputDir/bismark/alignments/logs/Ecoli_1_val_1_bismark_bt2_PE_report.txt").exists() }, { assert new File("$outputDir/bismark/alignments/logs/SRR389222_trimmed_bismark_bt2_SE_report.txt").exists() }, - { assert new File("$outputDir/bismark/reports/Ecoli_10K_1_val_1_bismark_bt2_PE_report.html").exists() }, + { assert new File("$outputDir/bismark/reports/Ecoli_1_val_1_bismark_bt2_PE_report.html").exists() }, { assert new File("$outputDir/bismark/reports/SRR389222_trimmed_bismark_bt2_SE_report.html").exists() }, { assert new File("$outputDir/bismark/summary/bismark_summary_report.html").exists() }, { assert new File("$outputDir/bismark/summary/bismark_summary_report.txt").exists() }, - { assert new File("$outputDir/fastqc/Ecoli_10K_1_fastqc.html").exists() }, - { assert new File("$outputDir/fastqc/Ecoli_10K_2_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/Ecoli_1_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/Ecoli_2_fastqc.html").exists() }, { assert new File("$outputDir/fastqc/SRR389222_fastqc.html").exists() }, { assert new File("$outputDir/multiqc/bismark/multiqc_report.html").exists() }, - { assert new File("$outputDir/trimgalore/logs/Ecoli_10K_1.fastq.gz_trimming_report.txt").exists() }, - { assert new File("$outputDir/trimgalore/logs/Ecoli_10K_2.fastq.gz_trimming_report.txt").exists() }, + { assert new File("$outputDir/trimgalore/logs/Ecoli_1.fastq.gz_trimming_report.txt").exists() }, + { assert new File("$outputDir/trimgalore/logs/Ecoli_2.fastq.gz_trimming_report.txt").exists() }, { assert new File("$outputDir/trimgalore/logs/SRR389222.fastq.gz_trimming_report.txt").exists() } ) } @@ -93,7 +93,7 @@ nextflow_pipeline { path("$outputDir/bismark/methylation_calls/splitting_report/Ecoli_10K_methylated_R1_bismark_bt2_pe_splitting_report.txt"), path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222.merged_bismark_bt2_splitting_report.txt"), path("$outputDir/bismark/reference_genome/BismarkIndex/").list(), - path("$outputDir/qualimap/Ecoli_10K/genome_results.txt"), + path("$outputDir/qualimap/Ecoli/genome_results.txt"), path("$outputDir/qualimap/SRR389222/genome_results.txt")).match("single_end_rrbs") }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_rrbs_software_versions") }, { assert new File("$outputDir/bismark/alignments/logs/Ecoli_10K_methylated_R1_bismark_bt2_PE_report.txt").exists() }, @@ -102,8 +102,8 @@ nextflow_pipeline { { assert new File("$outputDir/bismark/reports/SRR389222.merged_bismark_bt2_SE_report.html").exists() }, { assert new File("$outputDir/bismark/summary/bismark_summary_report.html").exists() }, { assert new File("$outputDir/bismark/summary/bismark_summary_report.txt").exists() }, - { assert new File("$outputDir/fastqc/Ecoli_10K_1_fastqc.html").exists() }, - { assert new File("$outputDir/fastqc/Ecoli_10K_2_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/Ecoli_1_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/Ecoli_2_fastqc.html").exists() }, { assert new File("$outputDir/fastqc/SRR389222_fastqc.html").exists() }, { assert new File("$outputDir/multiqc/bismark/multiqc_report.html").exists() } ) @@ -141,37 +141,37 @@ nextflow_pipeline { then { assertAll( { assert workflow.success }, - { assert snapshot(path("$outputDir/bismark/coverage2cytosine/coverage/Ecoli_10K.NOMe.CpG.cov.gz"), - path("$outputDir/bismark/coverage2cytosine/coverage/Ecoli_10K.NOMe.GpC.cov.gz"), + { assert snapshot(path("$outputDir/bismark/coverage2cytosine/coverage/Ecoli.NOMe.CpG.cov.gz"), + path("$outputDir/bismark/coverage2cytosine/coverage/Ecoli.NOMe.GpC.cov.gz"), path("$outputDir/bismark/coverage2cytosine/coverage/SRR389222.NOMe.CpG.cov.gz"), path("$outputDir/bismark/coverage2cytosine/coverage/SRR389222.NOMe.GpC.cov.gz"), - path("$outputDir/bismark/deduplicated/Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bam"), + path("$outputDir/bismark/deduplicated/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bam"), path("$outputDir/bismark/deduplicated/SRR389222_trimmed_bismark_bt2.deduplicated.bam"), - path("$outputDir/bismark/methylation_calls/bedGraph/Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz"), + path("$outputDir/bismark/methylation_calls/bedGraph/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz"), path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_trimmed_bismark_bt2.deduplicated.bedGraph.gz"), - path("$outputDir/bismark/methylation_calls/mbias/Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt"), + path("$outputDir/bismark/methylation_calls/mbias/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt"), path("$outputDir/bismark/methylation_calls/mbias/SRR389222_trimmed_bismark_bt2.deduplicated.M-bias.txt"), - path("$outputDir/bismark/methylation_calls/methylation_coverage/Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz"), + path("$outputDir/bismark/methylation_calls/methylation_coverage/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz"), path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_trimmed_bismark_bt2.deduplicated.bismark.cov.gz"), path("$outputDir/bismark/methylation_calls/methylation_calls/").list(), - path("$outputDir/bismark/methylation_calls/splitting_report/Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt"), + path("$outputDir/bismark/methylation_calls/splitting_report/Ecoli_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt"), path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_trimmed_bismark_bt2.deduplicated_splitting_report.txt"), path("$outputDir/cat/SRR389222.merged.fastq.gz"), - path("$outputDir/qualimap/Ecoli_10K/genome_results.txt"), + path("$outputDir/qualimap/Ecoli/genome_results.txt"), path("$outputDir/qualimap/SRR389222/genome_results.txt")).match("single_end_nomeseq") }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_nomeseq_software_versions") }, - { assert new File("$outputDir/bismark/alignments/logs/Ecoli_10K_1_val_1_bismark_bt2_PE_report.txt").exists() }, + { assert new File("$outputDir/bismark/alignments/logs/Ecoli_1_val_1_bismark_bt2_PE_report.txt").exists() }, { assert new File("$outputDir/bismark/alignments/logs/SRR389222_trimmed_bismark_bt2_SE_report.txt").exists() }, - { assert new File("$outputDir/bismark/reports/Ecoli_10K_1_val_1_bismark_bt2_PE_report.html").exists() }, + { assert new File("$outputDir/bismark/reports/Ecoli_1_val_1_bismark_bt2_PE_report.html").exists() }, { assert new File("$outputDir/bismark/reports/SRR389222_trimmed_bismark_bt2_SE_report.html").exists() }, { assert new File("$outputDir/bismark/summary/bismark_summary_report.html").exists() }, { assert new File("$outputDir/bismark/summary/bismark_summary_report.txt").exists() }, - { assert new File("$outputDir/fastqc/Ecoli_10K_1_fastqc.html").exists() }, - { assert new File("$outputDir/fastqc/Ecoli_10K_2_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/Ecoli_1_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/Ecoli_2_fastqc.html").exists() }, { assert new File("$outputDir/fastqc/SRR389222_fastqc.html").exists() }, { assert new File("$outputDir/multiqc/bismark/multiqc_report.html").exists() }, - { assert new File("$outputDir/trimgalore/logs/Ecoli_10K_1.fastq.gz_trimming_report.txt").exists() }, - { assert new File("$outputDir/trimgalore/logs/Ecoli_10K_2.fastq.gz_trimming_report.txt").exists() }, + { assert new File("$outputDir/trimgalore/logs/Ecoli_1.fastq.gz_trimming_report.txt").exists() }, + { assert new File("$outputDir/trimgalore/logs/Ecoli_2.fastq.gz_trimming_report.txt").exists() }, { assert new File("$outputDir/trimgalore/logs/SRR389222.fastq.gz_trimming_report.txt").exists() } ) } @@ -190,33 +190,33 @@ nextflow_pipeline { then { assertAll( { assert workflow.success }, - { assert snapshot(path("$outputDir/bismark/deduplicated/Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bam"), + { assert snapshot(path("$outputDir/bismark/deduplicated/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bam"), path("$outputDir/bismark/deduplicated/SRR389222_trimmed_bismark_bt2.deduplicated.bam"), - path("$outputDir/bismark/methylation_calls/bedGraph/Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz"), + path("$outputDir/bismark/methylation_calls/bedGraph/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz"), path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_trimmed_bismark_bt2.deduplicated.bedGraph.gz"), - path("$outputDir/bismark/methylation_calls/mbias/Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt"), + path("$outputDir/bismark/methylation_calls/mbias/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt"), path("$outputDir/bismark/methylation_calls/mbias/SRR389222_trimmed_bismark_bt2.deduplicated.M-bias.txt"), - path("$outputDir/bismark/methylation_calls/methylation_coverage/Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz"), + path("$outputDir/bismark/methylation_calls/methylation_coverage/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz"), path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_trimmed_bismark_bt2.deduplicated.bismark.cov.gz"), path("$outputDir/bismark/methylation_calls/methylation_calls/").list(), - path("$outputDir/bismark/methylation_calls/splitting_report/Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt"), + path("$outputDir/bismark/methylation_calls/splitting_report/Ecoli_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt"), path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_trimmed_bismark_bt2.deduplicated_splitting_report.txt"), path("$outputDir/cat/SRR389222.merged.fastq.gz"), - path("$outputDir/qualimap/Ecoli_10K/genome_results.txt"), + path("$outputDir/qualimap/Ecoli/genome_results.txt"), path("$outputDir/qualimap/SRR389222/genome_results.txt")).match("clip_r1") }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("clip_r1_software_versions") }, - { assert new File("$outputDir/bismark/alignments/logs/Ecoli_10K_1_val_1_bismark_bt2_PE_report.txt").exists() }, + { assert new File("$outputDir/bismark/alignments/logs/Ecoli_1_val_1_bismark_bt2_PE_report.txt").exists() }, { assert new File("$outputDir/bismark/alignments/logs/SRR389222_trimmed_bismark_bt2_SE_report.txt").exists() }, - { assert new File("$outputDir/bismark/reports/Ecoli_10K_1_val_1_bismark_bt2_PE_report.html").exists() }, + { assert new File("$outputDir/bismark/reports/Ecoli_1_val_1_bismark_bt2_PE_report.html").exists() }, { assert new File("$outputDir/bismark/reports/SRR389222_trimmed_bismark_bt2_SE_report.html").exists() }, { assert new File("$outputDir/bismark/summary/bismark_summary_report.html").exists() }, { assert new File("$outputDir/bismark/summary/bismark_summary_report.txt").exists() }, - { assert new File("$outputDir/fastqc/Ecoli_10K_1_fastqc.html").exists() }, - { assert new File("$outputDir/fastqc/Ecoli_10K_2_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/Ecoli_1_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/Ecoli_2_fastqc.html").exists() }, { assert new File("$outputDir/fastqc/SRR389222_fastqc.html").exists() }, { assert new File("$outputDir/multiqc/bismark/multiqc_report.html").exists() }, - { assert new File("$outputDir/trimgalore/logs/Ecoli_10K_1.fastq.gz_trimming_report.txt").exists() }, - { assert new File("$outputDir/trimgalore/logs/Ecoli_10K_2.fastq.gz_trimming_report.txt").exists() }, + { assert new File("$outputDir/trimgalore/logs/Ecoli_1.fastq.gz_trimming_report.txt").exists() }, + { assert new File("$outputDir/trimgalore/logs/Ecoli_2.fastq.gz_trimming_report.txt").exists() }, { assert new File("$outputDir/trimgalore/logs/SRR389222.fastq.gz_trimming_report.txt").exists() } ) } diff --git a/tests/pipeline/bismark/main.nf.test.snap b/tests/pipeline/bismark/main.nf.test.snap index 71f6c965..b47ff787 100644 --- a/tests/pipeline/bismark/main.nf.test.snap +++ b/tests/pipeline/bismark/main.nf.test.snap @@ -13,19 +13,41 @@ }, "single_end_nomeseq": { "content": [ + "Ecoli.NOMe.CpG.cov.gz:md5,c2c4db8d0a2ec32d572e75b01b2f7d81", + "Ecoli.NOMe.GpC.cov.gz:md5,a2b56291dbe8b344ee03a3ae58de8807", + "SRR389222.NOMe.CpG.cov.gz:md5,9738cb2fd47a65851626fc48d264c1b4", + "SRR389222.NOMe.GpC.cov.gz:md5,d5e6d60c93e76c7476b132b6aa4f8395", + "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bam:md5,caa027599dac71c50c24de1857dbf5c7", "Ecoli_10K.NOMe.CpG.cov.gz:md5,c2c4db8d0a2ec32d572e75b01b2f7d81", "Ecoli_10K.NOMe.GpC.cov.gz:md5,a2b56291dbe8b344ee03a3ae58de8807", "SRR389222.NOMe.CpG.cov.gz:md5,9738cb2fd47a65851626fc48d264c1b4", "SRR389222.NOMe.GpC.cov.gz:md5,d5e6d60c93e76c7476b132b6aa4f8395", "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bam:md5,a7464c83416ba057387df5d85b1bc1fe", "SRR389222_trimmed_bismark_bt2.deduplicated.bam:md5,7dba45955ae74159596a6ab41a9dcc87", + "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz:md5,88e599178b08907aab7d248302b7d37e", + "SRR389222_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,fe6b3655db6da21bdd3076947e062f0b", + "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt:md5,29f3b882a51b63ce77d3d9c69b0e5f85", "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz:md5,88e599178b08907aab7d248302b7d37e", "SRR389222_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,fe6b3655db6da21bdd3076947e062f0b", "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt:md5,29f3b882a51b63ce77d3d9c69b0e5f85", "SRR389222_trimmed_bismark_bt2.deduplicated.M-bias.txt:md5,bc48b8895f9ce84205a25899cf551624", + "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz:md5,962fe67f41f5e03d8e321ed381369513", + "SRR389222_trimmed_bismark_bt2.deduplicated.bismark.cov.gz:md5,82a55b84888ad5fe530f97c348738fdb", "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz:md5,962fe67f41f5e03d8e321ed381369513", "SRR389222_trimmed_bismark_bt2.deduplicated.bismark.cov.gz:md5,82a55b84888ad5fe530f97c348738fdb", [ + "CHG_OB_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,9c2248d95d96d6c315c65f1b8dc3bc39", + "CHG_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,9d8098ce1a27c23961e20b6a95f237d1", + "CHG_OT_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,5e5aefaa3f63e73f30342ad843eb210b", + "CHG_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,e68463946c5bfdf461c3aa81524f8837", + "CHH_OB_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,65f2afc6b1c76209af1acd1d4277a1cc", + "CHH_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,6834286d8d07a1b3a4399f71b5b3c3f8", + "CHH_OT_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,978ad87fef01e39283a620253320ee45", + "CHH_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,4347c873d1a7c772a448dd01351e5c0f", + "CpG_OB_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,54def6bf13e27f38adbbd3dd06297596", + "CpG_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,4dae933bcdc8c7d1de2f5e7239c1ae55", + "CpG_OT_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,9712eef973883f44dcc0a307af28ba70", + "CpG_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,49ec41948052a2a4a952f651df13b344" "CHG_OB_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,9c2248d95d96d6c315c65f1b8dc3bc39", "CHG_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,9d8098ce1a27c23961e20b6a95f237d1", "CHG_OT_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,5e5aefaa3f63e73f30342ad843eb210b", @@ -39,12 +61,15 @@ "CpG_OT_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,9712eef973883f44dcc0a307af28ba70", "CpG_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,49ec41948052a2a4a952f651df13b344" ], - "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt:md5,79ebef1c474ff5bdb5f79b955208bb04", + "Ecoli_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt:md5,b759f31785293e8d952f1dd3246f9a7b", "SRR389222_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,1c4a4288b3bcf1bbaa6b99e3c4b53ce9", "SRR389222.merged.fastq.gz:md5,47e1d7461d511a970e80085dd6454775", + "genome_results.txt:md5,886ffc763d05a84ead7f80a1d1db1fa2", + "SRR389222.merged.fastq.gz:md5,47e1d7461d511a970e80085dd6454775", "genome_results.txt:md5,1e01c188f34b7d385e8b16156ab2b93e", "genome_results.txt:md5,b99d4cfd82d21ac09ccb72865f9b3960" ], + "timestamp": "2023-12-20T02:42:55.528509796" "timestamp": "2023-12-22T14:22:34.861151831" }, "single_end_rrbs_software_versions": { @@ -67,15 +92,32 @@ }, "single_end": { "content": [ - "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bam:md5,a7464c83416ba057387df5d85b1bc1fe", + "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bam:md5,caa027599dac71c50c24de1857dbf5c7", "SRR389222_trimmed_bismark_bt2.deduplicated.bam:md5,7dba45955ae74159596a6ab41a9dcc87", + "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz:md5,58c9ba98d0638c26a30233b006a81172", + "SRR389222_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,3a19363a47169044a01f7195eb83266c", + "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt:md5,29f3b882a51b63ce77d3d9c69b0e5f85", "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz:md5,58c9ba98d0638c26a30233b006a81172", "SRR389222_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,3a19363a47169044a01f7195eb83266c", "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt:md5,29f3b882a51b63ce77d3d9c69b0e5f85", "SRR389222_trimmed_bismark_bt2.deduplicated.M-bias.txt:md5,bc48b8895f9ce84205a25899cf551624", + "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz:md5,8e6ba6fe66416d73e7f94b4da9ca77b1", + "SRR389222_trimmed_bismark_bt2.deduplicated.bismark.cov.gz:md5,389dc4fee59e34967d9af49958cb5cbe", "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz:md5,8e6ba6fe66416d73e7f94b4da9ca77b1", "SRR389222_trimmed_bismark_bt2.deduplicated.bismark.cov.gz:md5,389dc4fee59e34967d9af49958cb5cbe", [ + "CHG_OB_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,9c2248d95d96d6c315c65f1b8dc3bc39", + "CHG_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,9d8098ce1a27c23961e20b6a95f237d1", + "CHG_OT_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,5e5aefaa3f63e73f30342ad843eb210b", + "CHG_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,e68463946c5bfdf461c3aa81524f8837", + "CHH_OB_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,65f2afc6b1c76209af1acd1d4277a1cc", + "CHH_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,6834286d8d07a1b3a4399f71b5b3c3f8", + "CHH_OT_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,978ad87fef01e39283a620253320ee45", + "CHH_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,4347c873d1a7c772a448dd01351e5c0f", + "CpG_OB_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,54def6bf13e27f38adbbd3dd06297596", + "CpG_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,4dae933bcdc8c7d1de2f5e7239c1ae55", + "CpG_OT_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,9712eef973883f44dcc0a307af28ba70", + "CpG_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,49ec41948052a2a4a952f651df13b344" "CHG_OB_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,9c2248d95d96d6c315c65f1b8dc3bc39", "CHG_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,9d8098ce1a27c23961e20b6a95f237d1", "CHG_OT_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,5e5aefaa3f63e73f30342ad843eb210b", @@ -89,7 +131,7 @@ "CpG_OT_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,9712eef973883f44dcc0a307af28ba70", "CpG_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,49ec41948052a2a4a952f651df13b344" ], - "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt:md5,79ebef1c474ff5bdb5f79b955208bb04", + "Ecoli_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt:md5,b759f31785293e8d952f1dd3246f9a7b", "SRR389222_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,1c4a4288b3bcf1bbaa6b99e3c4b53ce9", [ [ @@ -114,9 +156,10 @@ ], "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de" ], - "genome_results.txt:md5,1e01c188f34b7d385e8b16156ab2b93e", + "genome_results.txt:md5,886ffc763d05a84ead7f80a1d1db1fa2", "genome_results.txt:md5,b99d4cfd82d21ac09ccb72865f9b3960" ], + "timestamp": "2023-12-20T02:38:33.566701995" "timestamp": "2023-12-22T14:17:47.259020697" }, "single_end_rrbs": { @@ -168,22 +211,40 @@ ], "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de" ], - "genome_results.txt:md5,b6ba7868b12971aaad0d4a04e25acd0b", + "genome_results.txt:md5,97dc2b4df61a46ccd2714903186ecaf0", "genome_results.txt:md5,f0d293867800a75becf2583c23729083" ], + "timestamp": "2023-12-20T02:40:47.269002207" "timestamp": "2023-12-22T14:20:09.69680784" }, "clip_r1": { "content": [ - "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bam:md5,388bb71e1e52628823e8b590d37cd665", + "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bam:md5,b19bc9b84dd8d8000c05b04234689aca", "SRR389222_trimmed_bismark_bt2.deduplicated.bam:md5,1bfe463dabf8727992e3ff6c19d8e7c1", + "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz:md5,e8b3933de21d7618cdaab650fe544b17", + "SRR389222_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,bddc7c560a902b842b72e20a21274cba", + "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt:md5,83a004a3d957cf95f25933bcd828a8d4", "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz:md5,e8b3933de21d7618cdaab650fe544b17", "SRR389222_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,bddc7c560a902b842b72e20a21274cba", "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt:md5,83a004a3d957cf95f25933bcd828a8d4", "SRR389222_trimmed_bismark_bt2.deduplicated.M-bias.txt:md5,90a6b76d41112c6de391d3a017638d95", + "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz:md5,34aa02c199f1496df0704dd239373ebe", + "SRR389222_trimmed_bismark_bt2.deduplicated.bismark.cov.gz:md5,03178f50ae4bf04a7b78d8bbdb8a77af", "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz:md5,34aa02c199f1496df0704dd239373ebe", "SRR389222_trimmed_bismark_bt2.deduplicated.bismark.cov.gz:md5,03178f50ae4bf04a7b78d8bbdb8a77af", [ + "CHG_OB_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,3856b07ea51dea59b444a7483ca3db75", + "CHG_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,e70e8a2ace2e602a967de256d299fb0d", + "CHG_OT_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,c1ba1891636a6b99f4d1495b3ddf1a59", + "CHG_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,f8867c4ee03fba6be823b7287cacfea3", + "CHH_OB_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,4e9a0e61d47eefb64876431b3640ee95", + "CHH_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,32728cf447a470681f4e608008d514ae", + "CHH_OT_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,10cd51608191667e027a9867dd84ab3f", + "CHH_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,2ec291cbfc4d64dbcd50603839129de1", + "CpG_OB_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,423aa4faf47d176a6b6cce134e1a9212", + "CpG_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,873612f00ee6ef44e8bc0dcb9f4a35f6", + "CpG_OT_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,1e243313554fce1b06aba217c7123cae", + "CpG_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,d86423a21b0d22188e188dc9f576135c" "CHG_OB_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,3856b07ea51dea59b444a7483ca3db75", "CHG_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,e70e8a2ace2e602a967de256d299fb0d", "CHG_OT_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,c1ba1891636a6b99f4d1495b3ddf1a59", @@ -197,12 +258,15 @@ "CpG_OT_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,1e243313554fce1b06aba217c7123cae", "CpG_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,d86423a21b0d22188e188dc9f576135c" ], - "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt:md5,373ac926ba4ceae1c4826f5ea4b3ada6", + "Ecoli_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt:md5,db55b5dbf35e78de9c1c6b2f2ed1e45b", "SRR389222_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,9a1a5d1e6722dda9e8a1953a01c415d0", "SRR389222.merged.fastq.gz:md5,47e1d7461d511a970e80085dd6454775", + "genome_results.txt:md5,2bbc428b0a5b9828df9fc4cd92806e12", + "SRR389222.merged.fastq.gz:md5,47e1d7461d511a970e80085dd6454775", "genome_results.txt:md5,72bdf73fe97711a2ba75b5c59f3a5637", "genome_results.txt:md5,5631f1632df00985946641cfc1601633" ], + "timestamp": "2023-12-20T02:44:24.251056958" "timestamp": "2023-12-22T14:23:43.189936269" } } From 98665378ecce3d3eeb9331923dcbbea864a72369 Mon Sep 17 00:00:00 2001 From: Sateesh Date: Wed, 20 Dec 2023 03:40:10 +0000 Subject: [PATCH 26/30] update tests for new assets/samplesheet --- tests/pipeline/bismark_hisat/main.nf.test | 30 ++++++------ .../pipeline/bismark_hisat/main.nf.test.snap | 46 +++++++++++++------ tests/pipeline/bwameth/main.nf.test | 38 +++++++-------- tests/pipeline/bwameth/main.nf.test.snap | 28 +++++------ 4 files changed, 80 insertions(+), 62 deletions(-) diff --git a/tests/pipeline/bismark_hisat/main.nf.test b/tests/pipeline/bismark_hisat/main.nf.test index 8c15ee04..550fb843 100644 --- a/tests/pipeline/bismark_hisat/main.nf.test +++ b/tests/pipeline/bismark_hisat/main.nf.test @@ -18,33 +18,33 @@ nextflow_pipeline { then { assertAll( { assert workflow.success }, - { assert snapshot(path("$outputDir/bismark_hisat/deduplicated/Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.bam"), + { assert snapshot(path("$outputDir/bismark_hisat/deduplicated/Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.bam"), path("$outputDir/bismark_hisat/deduplicated/SRR389222_trimmed_bismark_hisat2.deduplicated.bam"), - path("$outputDir/bismark_hisat/methylation_calls/bedGraph/Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.bedGraph.gz"), + path("$outputDir/bismark_hisat/methylation_calls/bedGraph/Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.bedGraph.gz"), path("$outputDir/bismark_hisat/methylation_calls/bedGraph/SRR389222_trimmed_bismark_hisat2.deduplicated.bedGraph.gz"), - path("$outputDir/bismark_hisat/methylation_calls/mbias/Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.M-bias.txt"), + path("$outputDir/bismark_hisat/methylation_calls/mbias/Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.M-bias.txt"), path("$outputDir/bismark_hisat/methylation_calls/mbias/SRR389222_trimmed_bismark_hisat2.deduplicated.M-bias.txt"), path("$outputDir/bismark_hisat/methylation_calls/methylation_calls/").list(), - path("$outputDir/bismark_hisat/methylation_calls/methylation_coverage/Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.bismark.cov.gz"), + path("$outputDir/bismark_hisat/methylation_calls/methylation_coverage/Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.bismark.cov.gz"), path("$outputDir/bismark_hisat/methylation_calls/methylation_coverage/SRR389222_trimmed_bismark_hisat2.deduplicated.bismark.cov.gz"), - path("$outputDir/bismark_hisat/methylation_calls/splitting_report/Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated_splitting_report.txt"), + path("$outputDir/bismark_hisat/methylation_calls/splitting_report/Ecoli_1_val_1_bismark_hisat2_pe.deduplicated_splitting_report.txt"), path("$outputDir/bismark_hisat/methylation_calls/splitting_report/SRR389222_trimmed_bismark_hisat2.deduplicated_splitting_report.txt"), path("$outputDir/cat/SRR389222.merged.fastq.gz"), - path("$outputDir/qualimap/Ecoli_10K/genome_results.txt"), + path("$outputDir/qualimap/Ecoli/genome_results.txt"), path("$outputDir/qualimap/SRR389222/genome_results.txt")).match("single_end") }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_software_versions") }, - { assert new File("$outputDir/bismark_hisat/alignments/logs/Ecoli_10K_1_val_1_bismark_hisat2_PE_report.txt").exists() }, + { assert new File("$outputDir/bismark_hisat/alignments/logs/Ecoli_1_val_1_bismark_hisat2_PE_report.txt").exists() }, { assert new File("$outputDir/bismark_hisat/alignments/logs/SRR389222_trimmed_bismark_hisat2_SE_report.txt").exists() }, - { assert new File("$outputDir/bismark_hisat/reports/Ecoli_10K_1_val_1_bismark_hisat2_PE_report.html").exists() }, + { assert new File("$outputDir/bismark_hisat/reports/Ecoli_1_val_1_bismark_hisat2_PE_report.html").exists() }, { assert new File("$outputDir/bismark_hisat/reports/SRR389222_trimmed_bismark_hisat2_SE_report.html").exists() }, { assert new File("$outputDir/bismark_hisat/summary/bismark_summary_report.html").exists() }, { assert new File("$outputDir/bismark_hisat/summary/bismark_summary_report.txt").exists() }, - { assert new File("$outputDir/fastqc/Ecoli_10K_1_fastqc.html").exists() }, - { assert new File("$outputDir/fastqc/Ecoli_10K_2_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/Ecoli_1_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/Ecoli_2_fastqc.html").exists() }, { assert new File("$outputDir/fastqc/SRR389222_fastqc.html").exists() }, { assert new File("$outputDir/multiqc/bismark_hisat/multiqc_report.html").exists() }, - { assert new File("$outputDir/trimgalore/logs/Ecoli_10K_1.fastq.gz_trimming_report.txt").exists() }, - { assert new File("$outputDir/trimgalore/logs/Ecoli_10K_2.fastq.gz_trimming_report.txt").exists() }, + { assert new File("$outputDir/trimgalore/logs/Ecoli_1.fastq.gz_trimming_report.txt").exists() }, + { assert new File("$outputDir/trimgalore/logs/Ecoli_2.fastq.gz_trimming_report.txt").exists() }, { assert new File("$outputDir/trimgalore/logs/SRR389222.fastq.gz_trimming_report.txt").exists() } ) } @@ -93,7 +93,7 @@ nextflow_pipeline { path("$outputDir/bismark_hisat/methylation_calls/splitting_report/Ecoli_10K_methylated_R1_bismark_hisat2_pe_splitting_report.txt"), path("$outputDir/bismark_hisat/methylation_calls/splitting_report/SRR389222.merged_bismark_hisat2_splitting_report.txt"), path("$outputDir/cat/SRR389222.merged.fastq.gz"), - path("$outputDir/qualimap/Ecoli_10K/genome_results.txt"), + path("$outputDir/qualimap/Ecoli/genome_results.txt"), path("$outputDir/qualimap/SRR389222/genome_results.txt")).match("single_end_rrbs") }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_rrbs_software_versions") }, { assert new File("$outputDir/bismark_hisat/alignments/logs/Ecoli_10K_methylated_R1_bismark_hisat2_PE_report.txt").exists() }, @@ -102,8 +102,8 @@ nextflow_pipeline { { assert new File("$outputDir/bismark_hisat/reports/SRR389222.merged_bismark_hisat2_SE_report.html").exists() }, { assert new File("$outputDir/bismark_hisat/summary/bismark_summary_report.html").exists() }, { assert new File("$outputDir/bismark_hisat/summary/bismark_summary_report.txt").exists() }, - { assert new File("$outputDir/fastqc/Ecoli_10K_1_fastqc.html").exists() }, - { assert new File("$outputDir/fastqc/Ecoli_10K_2_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/Ecoli_1_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/Ecoli_2_fastqc.html").exists() }, { assert new File("$outputDir/fastqc/SRR389222_fastqc.html").exists() }, { assert new File("$outputDir/multiqc/bismark_hisat/multiqc_report.html").exists() } ) diff --git a/tests/pipeline/bismark_hisat/main.nf.test.snap b/tests/pipeline/bismark_hisat/main.nf.test.snap index 18c0c4e0..aebf0b87 100644 --- a/tests/pipeline/bismark_hisat/main.nf.test.snap +++ b/tests/pipeline/bismark_hisat/main.nf.test.snap @@ -13,35 +13,35 @@ }, "single_end": { "content": [ - "Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.bam:md5,9e9b4adfeeb716e24ecba0bfad39c2e3", + "Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.bam:md5,ddfc84eb92f641020362f69e9e28a52d", "SRR389222_trimmed_bismark_hisat2.deduplicated.bam:md5,aa60cf9dcf302c185b12ced6f302a06e", - "Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.bedGraph.gz:md5,357196071c54757566cdd0bb7ab79fa8", + "Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.bedGraph.gz:md5,357196071c54757566cdd0bb7ab79fa8", "SRR389222_trimmed_bismark_hisat2.deduplicated.bedGraph.gz:md5,b20f17236ff64db1114343ff333a6d5b", - "Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.M-bias.txt:md5,5fd8655f4b9dba2249a52b769fe50faf", + "Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.M-bias.txt:md5,5fd8655f4b9dba2249a52b769fe50faf", "SRR389222_trimmed_bismark_hisat2.deduplicated.M-bias.txt:md5,b19356395d4ae1ad83bd3ec38276e580", [ - "CHG_OB_Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,6d2ca2e6548640e3885c94a3ca6beae0", + "CHG_OB_Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,6d2ca2e6548640e3885c94a3ca6beae0", "CHG_OB_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,9d8098ce1a27c23961e20b6a95f237d1", - "CHG_OT_Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,5e5aefaa3f63e73f30342ad843eb210b", + "CHG_OT_Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,5e5aefaa3f63e73f30342ad843eb210b", "CHG_OT_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,1180631ef093aade3a5195ce7ddfb3f6", - "CHH_OB_Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,abd48ddf1c9e844d8164de5150850d10", + "CHH_OB_Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,abd48ddf1c9e844d8164de5150850d10", "CHH_OB_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,6834286d8d07a1b3a4399f71b5b3c3f8", - "CHH_OT_Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,978ad87fef01e39283a620253320ee45", + "CHH_OT_Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,978ad87fef01e39283a620253320ee45", "CHH_OT_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,c311a70c0c8b6a93c2055fcbec03a833", - "CpG_OB_Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,51f8b079b9fd91e23e495d9e0e289530", + "CpG_OB_Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,51f8b079b9fd91e23e495d9e0e289530", "CpG_OB_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,4dae933bcdc8c7d1de2f5e7239c1ae55", - "CpG_OT_Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,9712eef973883f44dcc0a307af28ba70", + "CpG_OT_Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,9712eef973883f44dcc0a307af28ba70", "CpG_OT_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,63e737eef999e2d6348e7ed2a7ce4402" ], - "Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.bismark.cov.gz:md5,d8342eca72089408d8e4d7c5ec5e95bf", + "Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.bismark.cov.gz:md5,d8342eca72089408d8e4d7c5ec5e95bf", "SRR389222_trimmed_bismark_hisat2.deduplicated.bismark.cov.gz:md5,ad7a19cb9908844c47b7b871ff1223c2", - "Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated_splitting_report.txt:md5,a5dc04c52facdb5221a06ae7f3bca2e4", + "Ecoli_1_val_1_bismark_hisat2_pe.deduplicated_splitting_report.txt:md5,bc2284d712455231a2dd772098ca8dd9", "SRR389222_trimmed_bismark_hisat2.deduplicated_splitting_report.txt:md5,1f792e1fddb17140947f14008e1f9ffd", "SRR389222.merged.fastq.gz:md5,47e1d7461d511a970e80085dd6454775", - "genome_results.txt:md5,f272f759bfed7e8a30ec2719e0b518aa", + "genome_results.txt:md5,3703ab8cc04a6f3307ea1ffcfe23479a", "genome_results.txt:md5,7706d3790aee0e9244c490941ecd394f" ], - "timestamp": "2023-12-22T14:24:55.576498855" + "timestamp": "2023-12-20T02:58:11.727470144" }, "single_end_rrbs": { "content": [ @@ -49,6 +49,8 @@ "SRR389222.merged_bismark_hisat2.bam:md5,204123a5f7cd77cba3a90b904443c7eb", "Ecoli_10K_methylated_R1_bismark_hisat2_pe.bedGraph.gz:md5,357196071c54757566cdd0bb7ab79fa8", "SRR389222.merged_bismark_hisat2.bedGraph.gz:md5,d509b1e8e4ec03dcde48a127cf976594", + "Ecoli_10K_methylated_R1_bismark_hisat2_pe.bedGraph.gz:md5,357196071c54757566cdd0bb7ab79fa8", + "SRR389222.merged_bismark_hisat2.bedGraph.gz:md5,d509b1e8e4ec03dcde48a127cf976594", "Ecoli_10K_methylated_R1_bismark_hisat2_pe.M-bias.txt:md5,5fd8655f4b9dba2249a52b769fe50faf", "SRR389222.merged_bismark_hisat2.M-bias.txt:md5,ea90b0495446d03e375aad42d598a9f9", [ @@ -64,15 +66,29 @@ "CpG_OB_SRR389222.merged_bismark_hisat2.txt.gz:md5,b8b2de10044869b6c1097afc21c878a0", "CpG_OT_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,9712eef973883f44dcc0a307af28ba70", "CpG_OT_SRR389222.merged_bismark_hisat2.txt.gz:md5,877b026664516cb8851c1d80bf0d8495" + "CHG_OB_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,6d2ca2e6548640e3885c94a3ca6beae0", + "CHG_OB_SRR389222.merged_bismark_hisat2.txt.gz:md5,eeb08e87d7e3dca0acbb2c5ba2be66fb", + "CHG_OT_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,5e5aefaa3f63e73f30342ad843eb210b", + "CHG_OT_SRR389222.merged_bismark_hisat2.txt.gz:md5,7add3136b9f74de6aa83d38dde191060", + "CHH_OB_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,abd48ddf1c9e844d8164de5150850d10", + "CHH_OB_SRR389222.merged_bismark_hisat2.txt.gz:md5,a135c7e8a6c1b909a318ef17d47dca94", + "CHH_OT_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,978ad87fef01e39283a620253320ee45", + "CHH_OT_SRR389222.merged_bismark_hisat2.txt.gz:md5,8f1910f962b724592546a6187ad0a677", + "CpG_OB_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,51f8b079b9fd91e23e495d9e0e289530", + "CpG_OB_SRR389222.merged_bismark_hisat2.txt.gz:md5,b8b2de10044869b6c1097afc21c878a0", + "CpG_OT_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,9712eef973883f44dcc0a307af28ba70", + "CpG_OT_SRR389222.merged_bismark_hisat2.txt.gz:md5,877b026664516cb8851c1d80bf0d8495" ], "Ecoli_10K_methylated_R1_bismark_hisat2_pe.bismark.cov.gz:md5,d8342eca72089408d8e4d7c5ec5e95bf", "SRR389222.merged_bismark_hisat2.bismark.cov.gz:md5,29943eb00da6057a67e5530580668130", + "Ecoli_10K_methylated_R1_bismark_hisat2_pe.bismark.cov.gz:md5,d8342eca72089408d8e4d7c5ec5e95bf", + "SRR389222.merged_bismark_hisat2.bismark.cov.gz:md5,29943eb00da6057a67e5530580668130", "Ecoli_10K_methylated_R1_bismark_hisat2_pe_splitting_report.txt:md5,76868c2015864a3f7c2b4cd1738e4765", "SRR389222.merged_bismark_hisat2_splitting_report.txt:md5,4a9e54ffb48c9bb1e5ac33aa77b25f5c", "SRR389222.merged.fastq.gz:md5,47e1d7461d511a970e80085dd6454775", - "genome_results.txt:md5,13a70a3885acd9d55014aa1ad66e2bbb", + "genome_results.txt:md5,58bf4e22f697120806f09b48d9ffdc9e", "genome_results.txt:md5,ae5b10e9a3ffa1ac7a4f4e736228ec49" ], - "timestamp": "2023-12-22T14:27:26.162082917" + "timestamp": "2023-12-20T03:00:29.750687681" } } diff --git a/tests/pipeline/bwameth/main.nf.test b/tests/pipeline/bwameth/main.nf.test index 002223bb..1863371e 100644 --- a/tests/pipeline/bwameth/main.nf.test +++ b/tests/pipeline/bwameth/main.nf.test @@ -19,30 +19,30 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_software_versions") }, - { assert snapshot(path("$outputDir/bwameth/alignments/samtools_stats/Ecoli_10K.flagstat"), - path("$outputDir/bwameth/alignments/samtools_stats/Ecoli_10K.stats"), + { assert snapshot(path("$outputDir/bwameth/alignments/samtools_stats/Ecoli.flagstat"), + path("$outputDir/bwameth/alignments/samtools_stats/Ecoli.stats"), path("$outputDir/bwameth/alignments/samtools_stats/SRR389222.flagstat"), path("$outputDir/bwameth/alignments/samtools_stats/SRR389222.stats"), - path("$outputDir/bwameth/deduplicated/Ecoli_10K.markdup.sorted.bam"), - path("$outputDir/bwameth/deduplicated/Ecoli_10K.markdup.sorted.bam.bai"), + path("$outputDir/bwameth/deduplicated/Ecoli.markdup.sorted.bam"), + path("$outputDir/bwameth/deduplicated/Ecoli.markdup.sorted.bam.bai"), path("$outputDir/bwameth/deduplicated/SRR389222.markdup.sorted.bam"), path("$outputDir/bwameth/deduplicated/SRR389222.markdup.sorted.bam.bai"), path("$outputDir/bwameth/reference_genome/").list(), path("$outputDir/cat/SRR389222.merged.fastq.gz"), - path("$outputDir/methyldackel/Ecoli_10K.markdup.sorted_CpG.bedGraph"), + path("$outputDir/methyldackel/Ecoli.markdup.sorted_CpG.bedGraph"), path("$outputDir/methyldackel/SRR389222.markdup.sorted_CpG.bedGraph"), - path("$outputDir/methyldackel/mbias/Ecoli_10K.mbias.txt"), + path("$outputDir/methyldackel/mbias/Ecoli.mbias.txt"), path("$outputDir/methyldackel/mbias/SRR389222.mbias.txt"), - path("$outputDir/qualimap/Ecoli_10K/genome_results.txt"), + path("$outputDir/qualimap/Ecoli/genome_results.txt"), path("$outputDir/qualimap/SRR389222/genome_results.txt")).match("single_end") }, - { assert new File("$outputDir/fastqc/Ecoli_10K_1_fastqc.html").exists() }, - { assert new File("$outputDir/fastqc/Ecoli_10K_2_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/Ecoli_1_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/Ecoli_2_fastqc.html").exists() }, { assert new File("$outputDir/fastqc/SRR389222_fastqc.html").exists() }, { assert new File("$outputDir/multiqc/bwameth/multiqc_report.html").exists() }, - { assert new File("$outputDir/trimgalore/logs/Ecoli_10K_1.fastq.gz_trimming_report.txt").exists() }, - { assert new File("$outputDir/trimgalore/logs/Ecoli_10K_2.fastq.gz_trimming_report.txt").exists() }, + { assert new File("$outputDir/trimgalore/logs/Ecoli_1.fastq.gz_trimming_report.txt").exists() }, + { assert new File("$outputDir/trimgalore/logs/Ecoli_2.fastq.gz_trimming_report.txt").exists() }, { assert new File("$outputDir/trimgalore/logs/SRR389222.fastq.gz_trimming_report.txt").exists() }, - { assert new File("$outputDir/bwameth/deduplicated/picard_metrics/Ecoli_10K.markdup.sorted.MarkDuplicates.metrics.txt").exists() }, + { assert new File("$outputDir/bwameth/deduplicated/picard_metrics/Ecoli.markdup.sorted.MarkDuplicates.metrics.txt").exists() }, { assert new File("$outputDir/bwameth/deduplicated/picard_metrics/SRR389222.markdup.sorted.MarkDuplicates.metrics.txt").exists() } ) } @@ -81,20 +81,20 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_rrbs_software_versions") }, - { assert snapshot(path("$outputDir/bwameth/alignments/samtools_stats/Ecoli_10K.flagstat"), - path("$outputDir/bwameth/alignments/samtools_stats/Ecoli_10K.stats"), + { assert snapshot(path("$outputDir/bwameth/alignments/samtools_stats/Ecoli.flagstat"), + path("$outputDir/bwameth/alignments/samtools_stats/Ecoli.stats"), path("$outputDir/bwameth/alignments/samtools_stats/SRR389222.flagstat"), path("$outputDir/bwameth/alignments/samtools_stats/SRR389222.stats"), path("$outputDir/bwameth/reference_genome/").list(), path("$outputDir/cat/SRR389222.merged.fastq.gz"), - path("$outputDir/methyldackel/Ecoli_10K.sorted_CpG.bedGraph"), + path("$outputDir/methyldackel/Ecoli.sorted_CpG.bedGraph"), path("$outputDir/methyldackel/SRR389222.sorted_CpG.bedGraph"), - path("$outputDir/methyldackel/mbias/Ecoli_10K.mbias.txt"), + path("$outputDir/methyldackel/mbias/Ecoli.mbias.txt"), path("$outputDir/methyldackel/mbias/SRR389222.mbias.txt"), - path("$outputDir/qualimap/Ecoli_10K/genome_results.txt"), + path("$outputDir/qualimap/Ecoli/genome_results.txt"), path("$outputDir/qualimap/SRR389222/genome_results.txt")).match("single_end_rrbs") }, - { assert new File("$outputDir/fastqc/Ecoli_10K_1_fastqc.html").exists() }, - { assert new File("$outputDir/fastqc/Ecoli_10K_2_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/Ecoli_1_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/Ecoli_2_fastqc.html").exists() }, { assert new File("$outputDir/fastqc/SRR389222_fastqc.html").exists() }, { assert new File("$outputDir/multiqc/bwameth/multiqc_report.html").exists() } ) diff --git a/tests/pipeline/bwameth/main.nf.test.snap b/tests/pipeline/bwameth/main.nf.test.snap index cee3939d..77684024 100644 --- a/tests/pipeline/bwameth/main.nf.test.snap +++ b/tests/pipeline/bwameth/main.nf.test.snap @@ -13,12 +13,12 @@ }, "single_end": { "content": [ - "Ecoli_10K.flagstat:md5,f520e87cc4050799a0dbed72909572ec", - "Ecoli_10K.stats:md5,b744221f284d3b3f5afe0b4b2d1849d7", + "Ecoli.flagstat:md5,f520e87cc4050799a0dbed72909572ec", + "Ecoli.stats:md5,c09155913e0164da9010a0840618cf1f", "SRR389222.flagstat:md5,f5a2dd6c9532bbfb8fe78aad010d8737", "SRR389222.stats:md5,cc81b8c56d038e437a99d9c04b61ce2d", - "Ecoli_10K.markdup.sorted.bam:md5,f582d626f4b78f4e9cc63ca6e20b42cd", - "Ecoli_10K.markdup.sorted.bam.bai:md5,faa46b80545d7eb45dfc659b46f419b0", + "Ecoli.markdup.sorted.bam:md5,0d1c814b476521286a829dc64fc3490a", + "Ecoli.markdup.sorted.bam.bai:md5,befef6ce0a34e2ce7f66c073d9bf4abd", "SRR389222.markdup.sorted.bam:md5,46b5b49280efe5d5c5d1692092e8926f", "SRR389222.markdup.sorted.bam.bai:md5,ad6cfa0344e1ba5b9057ea39f337b3d2", [ @@ -34,18 +34,20 @@ ], "SRR389222.merged.fastq.gz:md5,47e1d7461d511a970e80085dd6454775", "Ecoli_10K.markdup.sorted_CpG.bedGraph:md5,2fbe52f528b14b77380eceea8a621687", + "SRR389222.merged.fastq.gz:md5,47e1d7461d511a970e80085dd6454775", + "Ecoli.markdup.sorted_CpG.bedGraph:md5,00132adede8128b3a111136713a2a4ff", "SRR389222.markdup.sorted_CpG.bedGraph:md5,febd0f93f46dfccabf69dbba3f518add", - "Ecoli_10K.mbias.txt:md5,3a448a2a6364b2de3129365a271c0534", + "Ecoli.mbias.txt:md5,3a448a2a6364b2de3129365a271c0534", "SRR389222.mbias.txt:md5,fce04d733e066d0b933cedc602e2af81", - "genome_results.txt:md5,0f4749b54f9d923f0d4f20ad404b2062", + "genome_results.txt:md5,d1a1b49086982318f0f94ba7059f71a3", "genome_results.txt:md5,c786cc367645cee286360707e2624dca" ], - "timestamp": "2023-12-22T14:15:08.478775696" + "timestamp": "2023-12-20T03:21:55.358959756" }, "single_end_rrbs": { "content": [ - "Ecoli_10K.flagstat:md5,7c3bae0f9c700dde88785a7e94c6ae2c", - "Ecoli_10K.stats:md5,ff675c98abdae3c1bd83b26704d89e82", + "Ecoli.flagstat:md5,7c3bae0f9c700dde88785a7e94c6ae2c", + "Ecoli.stats:md5,46eaf2559610c864bc4d27a08a0645b4", "SRR389222.flagstat:md5,a90f1bdcb30f4d0597ccf69fe0b37b1f", "SRR389222.stats:md5,b99800367e21a0c7c0d87e5fe29d9609", [ @@ -60,13 +62,13 @@ ] ], "SRR389222.merged.fastq.gz:md5,47e1d7461d511a970e80085dd6454775", - "Ecoli_10K.sorted_CpG.bedGraph:md5,513797bcafa8724fc61484e2686af517", + "Ecoli.sorted_CpG.bedGraph:md5,41f4218573d5e4ff7016ffb42f13a551", "SRR389222.sorted_CpG.bedGraph:md5,a754358e8b95db30602aa29835a896bd", - "Ecoli_10K.mbias.txt:md5,ec13da6deba1ce147624bce065ec5df6", + "Ecoli.mbias.txt:md5,ec13da6deba1ce147624bce065ec5df6", "SRR389222.mbias.txt:md5,fce04d733e066d0b933cedc602e2af81", - "genome_results.txt:md5,e5e1ab8eb875aaf090b3a0d9b1927810", + "genome_results.txt:md5,cd545aa1ee209a1683374bfb5731ab0c", "genome_results.txt:md5,199902f9d8f10f73bcb0a1ce29ceca5d" ], - "timestamp": "2023-12-22T14:16:15.148388923" + "timestamp": "2023-12-20T03:38:43.324010795" } } From d95c82b051f4345a21b70a1b2828737adb16eb8e Mon Sep 17 00:00:00 2001 From: Sateesh Date: Fri, 22 Dec 2023 22:58:54 +0000 Subject: [PATCH 27/30] update snaps for sample name change --- tests/pipeline/bismark/main.nf.test.snap | 98 +++---------------- .../pipeline/bismark_hisat/main.nf.test.snap | 26 +---- tests/pipeline/bwameth/main.nf.test.snap | 2 - 3 files changed, 19 insertions(+), 107 deletions(-) diff --git a/tests/pipeline/bismark/main.nf.test.snap b/tests/pipeline/bismark/main.nf.test.snap index b47ff787..a69f0954 100644 --- a/tests/pipeline/bismark/main.nf.test.snap +++ b/tests/pipeline/bismark/main.nf.test.snap @@ -3,13 +3,19 @@ "content": [ "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0dev}}" ], - "timestamp": "2023-08-28T08:46:48+0000" + "timestamp": "2023-12-22T22:42:59.896228401" }, "single_end_nomeseq_software_versions": { "content": [ "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0dev}}" ], - "timestamp": "2023-08-28T08:46:48+0000" + "timestamp": "2023-12-22T22:56:03.882046934" + }, + "single_end_rrbs_software_versions": { + "content": [ + "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.6.0dev}}" + ], + "timestamp": "2023-12-22T22:52:44.437869745" }, "single_end_nomeseq": { "content": [ @@ -18,23 +24,13 @@ "SRR389222.NOMe.CpG.cov.gz:md5,9738cb2fd47a65851626fc48d264c1b4", "SRR389222.NOMe.GpC.cov.gz:md5,d5e6d60c93e76c7476b132b6aa4f8395", "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bam:md5,caa027599dac71c50c24de1857dbf5c7", - "Ecoli_10K.NOMe.CpG.cov.gz:md5,c2c4db8d0a2ec32d572e75b01b2f7d81", - "Ecoli_10K.NOMe.GpC.cov.gz:md5,a2b56291dbe8b344ee03a3ae58de8807", - "SRR389222.NOMe.CpG.cov.gz:md5,9738cb2fd47a65851626fc48d264c1b4", - "SRR389222.NOMe.GpC.cov.gz:md5,d5e6d60c93e76c7476b132b6aa4f8395", - "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bam:md5,a7464c83416ba057387df5d85b1bc1fe", "SRR389222_trimmed_bismark_bt2.deduplicated.bam:md5,7dba45955ae74159596a6ab41a9dcc87", "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz:md5,88e599178b08907aab7d248302b7d37e", "SRR389222_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,fe6b3655db6da21bdd3076947e062f0b", "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt:md5,29f3b882a51b63ce77d3d9c69b0e5f85", - "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz:md5,88e599178b08907aab7d248302b7d37e", - "SRR389222_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,fe6b3655db6da21bdd3076947e062f0b", - "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt:md5,29f3b882a51b63ce77d3d9c69b0e5f85", "SRR389222_trimmed_bismark_bt2.deduplicated.M-bias.txt:md5,bc48b8895f9ce84205a25899cf551624", "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz:md5,962fe67f41f5e03d8e321ed381369513", "SRR389222_trimmed_bismark_bt2.deduplicated.bismark.cov.gz:md5,82a55b84888ad5fe530f97c348738fdb", - "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz:md5,962fe67f41f5e03d8e321ed381369513", - "SRR389222_trimmed_bismark_bt2.deduplicated.bismark.cov.gz:md5,82a55b84888ad5fe530f97c348738fdb", [ "CHG_OB_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,9c2248d95d96d6c315c65f1b8dc3bc39", "CHG_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,9d8098ce1a27c23961e20b6a95f237d1", @@ -48,47 +44,20 @@ "CpG_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,4dae933bcdc8c7d1de2f5e7239c1ae55", "CpG_OT_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,9712eef973883f44dcc0a307af28ba70", "CpG_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,49ec41948052a2a4a952f651df13b344" - "CHG_OB_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,9c2248d95d96d6c315c65f1b8dc3bc39", - "CHG_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,9d8098ce1a27c23961e20b6a95f237d1", - "CHG_OT_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,5e5aefaa3f63e73f30342ad843eb210b", - "CHG_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,e68463946c5bfdf461c3aa81524f8837", - "CHH_OB_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,65f2afc6b1c76209af1acd1d4277a1cc", - "CHH_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,6834286d8d07a1b3a4399f71b5b3c3f8", - "CHH_OT_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,978ad87fef01e39283a620253320ee45", - "CHH_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,4347c873d1a7c772a448dd01351e5c0f", - "CpG_OB_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,54def6bf13e27f38adbbd3dd06297596", - "CpG_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,4dae933bcdc8c7d1de2f5e7239c1ae55", - "CpG_OT_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,9712eef973883f44dcc0a307af28ba70", - "CpG_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,49ec41948052a2a4a952f651df13b344" ], "Ecoli_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt:md5,b759f31785293e8d952f1dd3246f9a7b", "SRR389222_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,1c4a4288b3bcf1bbaa6b99e3c4b53ce9", "SRR389222.merged.fastq.gz:md5,47e1d7461d511a970e80085dd6454775", "genome_results.txt:md5,886ffc763d05a84ead7f80a1d1db1fa2", - "SRR389222.merged.fastq.gz:md5,47e1d7461d511a970e80085dd6454775", - "genome_results.txt:md5,1e01c188f34b7d385e8b16156ab2b93e", "genome_results.txt:md5,b99d4cfd82d21ac09ccb72865f9b3960" ], - "timestamp": "2023-12-20T02:42:55.528509796" - "timestamp": "2023-12-22T14:22:34.861151831" - }, - "single_end_rrbs_software_versions": { - "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.6.0dev}}" - ], - "timestamp": "2023-08-28T08:46:48+0000" - }, - "single_end__nomeseq_software_versions": { - "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0dev}}" - ], - "timestamp": "2023-08-28T08:46:48+0000" + "timestamp": "2023-12-22T22:56:01.615992857" }, "clip_r1_software_versions": { "content": [ "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0dev}}" ], - "timestamp": "2023-08-28T08:46:48+0000" + "timestamp": "2023-12-22T22:57:41.01411097" }, "single_end": { "content": [ @@ -97,14 +66,9 @@ "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz:md5,58c9ba98d0638c26a30233b006a81172", "SRR389222_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,3a19363a47169044a01f7195eb83266c", "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt:md5,29f3b882a51b63ce77d3d9c69b0e5f85", - "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz:md5,58c9ba98d0638c26a30233b006a81172", - "SRR389222_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,3a19363a47169044a01f7195eb83266c", - "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt:md5,29f3b882a51b63ce77d3d9c69b0e5f85", "SRR389222_trimmed_bismark_bt2.deduplicated.M-bias.txt:md5,bc48b8895f9ce84205a25899cf551624", "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz:md5,8e6ba6fe66416d73e7f94b4da9ca77b1", "SRR389222_trimmed_bismark_bt2.deduplicated.bismark.cov.gz:md5,389dc4fee59e34967d9af49958cb5cbe", - "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz:md5,8e6ba6fe66416d73e7f94b4da9ca77b1", - "SRR389222_trimmed_bismark_bt2.deduplicated.bismark.cov.gz:md5,389dc4fee59e34967d9af49958cb5cbe", [ "CHG_OB_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,9c2248d95d96d6c315c65f1b8dc3bc39", "CHG_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,9d8098ce1a27c23961e20b6a95f237d1", @@ -118,18 +82,6 @@ "CpG_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,4dae933bcdc8c7d1de2f5e7239c1ae55", "CpG_OT_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,9712eef973883f44dcc0a307af28ba70", "CpG_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,49ec41948052a2a4a952f651df13b344" - "CHG_OB_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,9c2248d95d96d6c315c65f1b8dc3bc39", - "CHG_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,9d8098ce1a27c23961e20b6a95f237d1", - "CHG_OT_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,5e5aefaa3f63e73f30342ad843eb210b", - "CHG_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,e68463946c5bfdf461c3aa81524f8837", - "CHH_OB_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,65f2afc6b1c76209af1acd1d4277a1cc", - "CHH_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,6834286d8d07a1b3a4399f71b5b3c3f8", - "CHH_OT_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,978ad87fef01e39283a620253320ee45", - "CHH_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,4347c873d1a7c772a448dd01351e5c0f", - "CpG_OB_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,54def6bf13e27f38adbbd3dd06297596", - "CpG_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,4dae933bcdc8c7d1de2f5e7239c1ae55", - "CpG_OT_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,9712eef973883f44dcc0a307af28ba70", - "CpG_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,49ec41948052a2a4a952f651df13b344" ], "Ecoli_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt:md5,b759f31785293e8d952f1dd3246f9a7b", "SRR389222_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,1c4a4288b3bcf1bbaa6b99e3c4b53ce9", @@ -159,8 +111,7 @@ "genome_results.txt:md5,886ffc763d05a84ead7f80a1d1db1fa2", "genome_results.txt:md5,b99d4cfd82d21ac09ccb72865f9b3960" ], - "timestamp": "2023-12-20T02:38:33.566701995" - "timestamp": "2023-12-22T14:17:47.259020697" + "timestamp": "2023-12-22T22:42:59.548979384" }, "single_end_rrbs": { "content": [ @@ -214,8 +165,7 @@ "genome_results.txt:md5,97dc2b4df61a46ccd2714903186ecaf0", "genome_results.txt:md5,f0d293867800a75becf2583c23729083" ], - "timestamp": "2023-12-20T02:40:47.269002207" - "timestamp": "2023-12-22T14:20:09.69680784" + "timestamp": "2023-12-22T22:52:42.829793102" }, "clip_r1": { "content": [ @@ -224,14 +174,9 @@ "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz:md5,e8b3933de21d7618cdaab650fe544b17", "SRR389222_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,bddc7c560a902b842b72e20a21274cba", "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt:md5,83a004a3d957cf95f25933bcd828a8d4", - "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz:md5,e8b3933de21d7618cdaab650fe544b17", - "SRR389222_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,bddc7c560a902b842b72e20a21274cba", - "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt:md5,83a004a3d957cf95f25933bcd828a8d4", "SRR389222_trimmed_bismark_bt2.deduplicated.M-bias.txt:md5,90a6b76d41112c6de391d3a017638d95", "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz:md5,34aa02c199f1496df0704dd239373ebe", "SRR389222_trimmed_bismark_bt2.deduplicated.bismark.cov.gz:md5,03178f50ae4bf04a7b78d8bbdb8a77af", - "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz:md5,34aa02c199f1496df0704dd239373ebe", - "SRR389222_trimmed_bismark_bt2.deduplicated.bismark.cov.gz:md5,03178f50ae4bf04a7b78d8bbdb8a77af", [ "CHG_OB_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,3856b07ea51dea59b444a7483ca3db75", "CHG_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,e70e8a2ace2e602a967de256d299fb0d", @@ -245,28 +190,13 @@ "CpG_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,873612f00ee6ef44e8bc0dcb9f4a35f6", "CpG_OT_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,1e243313554fce1b06aba217c7123cae", "CpG_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,d86423a21b0d22188e188dc9f576135c" - "CHG_OB_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,3856b07ea51dea59b444a7483ca3db75", - "CHG_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,e70e8a2ace2e602a967de256d299fb0d", - "CHG_OT_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,c1ba1891636a6b99f4d1495b3ddf1a59", - "CHG_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,f8867c4ee03fba6be823b7287cacfea3", - "CHH_OB_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,4e9a0e61d47eefb64876431b3640ee95", - "CHH_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,32728cf447a470681f4e608008d514ae", - "CHH_OT_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,10cd51608191667e027a9867dd84ab3f", - "CHH_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,2ec291cbfc4d64dbcd50603839129de1", - "CpG_OB_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,423aa4faf47d176a6b6cce134e1a9212", - "CpG_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,873612f00ee6ef44e8bc0dcb9f4a35f6", - "CpG_OT_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,1e243313554fce1b06aba217c7123cae", - "CpG_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,d86423a21b0d22188e188dc9f576135c" ], "Ecoli_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt:md5,db55b5dbf35e78de9c1c6b2f2ed1e45b", "SRR389222_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,9a1a5d1e6722dda9e8a1953a01c415d0", "SRR389222.merged.fastq.gz:md5,47e1d7461d511a970e80085dd6454775", "genome_results.txt:md5,2bbc428b0a5b9828df9fc4cd92806e12", - "SRR389222.merged.fastq.gz:md5,47e1d7461d511a970e80085dd6454775", - "genome_results.txt:md5,72bdf73fe97711a2ba75b5c59f3a5637", "genome_results.txt:md5,5631f1632df00985946641cfc1601633" ], - "timestamp": "2023-12-20T02:44:24.251056958" - "timestamp": "2023-12-22T14:23:43.189936269" + "timestamp": "2023-12-22T22:57:38.05813974" } -} +} \ No newline at end of file diff --git a/tests/pipeline/bismark_hisat/main.nf.test.snap b/tests/pipeline/bismark_hisat/main.nf.test.snap index aebf0b87..2cf6357f 100644 --- a/tests/pipeline/bismark_hisat/main.nf.test.snap +++ b/tests/pipeline/bismark_hisat/main.nf.test.snap @@ -3,13 +3,13 @@ "content": [ "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0dev}}" ], - "timestamp": "2023-08-28T10:04:42+0000" + "timestamp": "2023-12-22T22:14:40.465488234" }, "single_end_rrbs_software_versions": { "content": [ "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.6.0dev}}" ], - "timestamp": "2023-08-28T10:04:42+0000" + "timestamp": "2023-12-22T22:37:56.693097833" }, "single_end": { "content": [ @@ -41,7 +41,7 @@ "genome_results.txt:md5,3703ab8cc04a6f3307ea1ffcfe23479a", "genome_results.txt:md5,7706d3790aee0e9244c490941ecd394f" ], - "timestamp": "2023-12-20T02:58:11.727470144" + "timestamp": "2023-12-22T22:14:39.589478621" }, "single_end_rrbs": { "content": [ @@ -49,8 +49,6 @@ "SRR389222.merged_bismark_hisat2.bam:md5,204123a5f7cd77cba3a90b904443c7eb", "Ecoli_10K_methylated_R1_bismark_hisat2_pe.bedGraph.gz:md5,357196071c54757566cdd0bb7ab79fa8", "SRR389222.merged_bismark_hisat2.bedGraph.gz:md5,d509b1e8e4ec03dcde48a127cf976594", - "Ecoli_10K_methylated_R1_bismark_hisat2_pe.bedGraph.gz:md5,357196071c54757566cdd0bb7ab79fa8", - "SRR389222.merged_bismark_hisat2.bedGraph.gz:md5,d509b1e8e4ec03dcde48a127cf976594", "Ecoli_10K_methylated_R1_bismark_hisat2_pe.M-bias.txt:md5,5fd8655f4b9dba2249a52b769fe50faf", "SRR389222.merged_bismark_hisat2.M-bias.txt:md5,ea90b0495446d03e375aad42d598a9f9", [ @@ -66,29 +64,15 @@ "CpG_OB_SRR389222.merged_bismark_hisat2.txt.gz:md5,b8b2de10044869b6c1097afc21c878a0", "CpG_OT_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,9712eef973883f44dcc0a307af28ba70", "CpG_OT_SRR389222.merged_bismark_hisat2.txt.gz:md5,877b026664516cb8851c1d80bf0d8495" - "CHG_OB_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,6d2ca2e6548640e3885c94a3ca6beae0", - "CHG_OB_SRR389222.merged_bismark_hisat2.txt.gz:md5,eeb08e87d7e3dca0acbb2c5ba2be66fb", - "CHG_OT_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,5e5aefaa3f63e73f30342ad843eb210b", - "CHG_OT_SRR389222.merged_bismark_hisat2.txt.gz:md5,7add3136b9f74de6aa83d38dde191060", - "CHH_OB_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,abd48ddf1c9e844d8164de5150850d10", - "CHH_OB_SRR389222.merged_bismark_hisat2.txt.gz:md5,a135c7e8a6c1b909a318ef17d47dca94", - "CHH_OT_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,978ad87fef01e39283a620253320ee45", - "CHH_OT_SRR389222.merged_bismark_hisat2.txt.gz:md5,8f1910f962b724592546a6187ad0a677", - "CpG_OB_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,51f8b079b9fd91e23e495d9e0e289530", - "CpG_OB_SRR389222.merged_bismark_hisat2.txt.gz:md5,b8b2de10044869b6c1097afc21c878a0", - "CpG_OT_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,9712eef973883f44dcc0a307af28ba70", - "CpG_OT_SRR389222.merged_bismark_hisat2.txt.gz:md5,877b026664516cb8851c1d80bf0d8495" ], "Ecoli_10K_methylated_R1_bismark_hisat2_pe.bismark.cov.gz:md5,d8342eca72089408d8e4d7c5ec5e95bf", "SRR389222.merged_bismark_hisat2.bismark.cov.gz:md5,29943eb00da6057a67e5530580668130", - "Ecoli_10K_methylated_R1_bismark_hisat2_pe.bismark.cov.gz:md5,d8342eca72089408d8e4d7c5ec5e95bf", - "SRR389222.merged_bismark_hisat2.bismark.cov.gz:md5,29943eb00da6057a67e5530580668130", "Ecoli_10K_methylated_R1_bismark_hisat2_pe_splitting_report.txt:md5,76868c2015864a3f7c2b4cd1738e4765", "SRR389222.merged_bismark_hisat2_splitting_report.txt:md5,4a9e54ffb48c9bb1e5ac33aa77b25f5c", "SRR389222.merged.fastq.gz:md5,47e1d7461d511a970e80085dd6454775", "genome_results.txt:md5,58bf4e22f697120806f09b48d9ffdc9e", "genome_results.txt:md5,ae5b10e9a3ffa1ac7a4f4e736228ec49" ], - "timestamp": "2023-12-20T03:00:29.750687681" + "timestamp": "2023-12-22T22:37:54.382841284" } -} +} \ No newline at end of file diff --git a/tests/pipeline/bwameth/main.nf.test.snap b/tests/pipeline/bwameth/main.nf.test.snap index 77684024..6f4e2806 100644 --- a/tests/pipeline/bwameth/main.nf.test.snap +++ b/tests/pipeline/bwameth/main.nf.test.snap @@ -33,8 +33,6 @@ ] ], "SRR389222.merged.fastq.gz:md5,47e1d7461d511a970e80085dd6454775", - "Ecoli_10K.markdup.sorted_CpG.bedGraph:md5,2fbe52f528b14b77380eceea8a621687", - "SRR389222.merged.fastq.gz:md5,47e1d7461d511a970e80085dd6454775", "Ecoli.markdup.sorted_CpG.bedGraph:md5,00132adede8128b3a111136713a2a4ff", "SRR389222.markdup.sorted_CpG.bedGraph:md5,febd0f93f46dfccabf69dbba3f518add", "Ecoli.mbias.txt:md5,3a448a2a6364b2de3129365a271c0534", From 774f267352c9899c8b3bb55144931dcd07dbc1bf Mon Sep 17 00:00:00 2001 From: Sateesh Date: Fri, 5 Jan 2024 01:48:54 +0000 Subject: [PATCH 28/30] add test_data.config and update multiqc tests --- conf/test.config | 2 + conf/test_data.config | 39 +++++++++++++++ modules.json | 2 +- modules/nf-core/multiqc/main.nf | 2 +- modules/nf-core/multiqc/meta.yml | 1 - modules/nf-core/multiqc/tests/main.nf.test | 48 +++++++++++++------ .../nf-core/multiqc/tests/main.nf.test.snap | 21 ++++++++ 7 files changed, 98 insertions(+), 17 deletions(-) create mode 100644 conf/test_data.config create mode 100644 modules/nf-core/multiqc/tests/main.nf.test.snap diff --git a/conf/test.config b/conf/test.config index 0291dfe7..5b23b448 100644 --- a/conf/test.config +++ b/conf/test.config @@ -23,3 +23,5 @@ params { fasta = "${params.test_data_base}/reference/genome.fa" fasta_index = "${params.test_data_base}/reference/genome.fa.fai" } + +includeConfig './test_data.config' diff --git a/conf/test_data.config b/conf/test_data.config new file mode 100644 index 00000000..ae5d5abc --- /dev/null +++ b/conf/test_data.config @@ -0,0 +1,39 @@ +params { + // Base directory for test data + test_data_base = "https://raw.githubusercontent.com/nf-core/test-datasets/methylseq" + + max_cpus = 2 + max_memory = 6.GB + max_time = 6.h + + // TODO: Add all test data to test_data.config + test_data { + 'assets' { + test_samplesheet = "${params.test_data_base}/samplesheet/samplesheet_test.csv" + } + 'workflows' { + 'methylseq' { + fasta = "${params.test_data_base}/reference/genome.fa" + fasta_index = "${params.test_data_base}/reference/genome.fa.fai" + } + } + 'sarscov2' { + 'illumina' { + test_1_fastq_gz = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz" + test_2_fastq_gz = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz" + test2_1_fastq_gz = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/fastq/test2_1.fastq.gz" + test2_2_fastq_gz = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/fastq/test2_2.fastq.gz" + contigs_fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/fasta/contigs.fasta" + scaffolds_fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/fasta/scaffolds.fasta" + test_single_end_bam = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/bam/test.single_end.bam" + test_paired_end_bam = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/bam/test.paired_end.bam" + test_1_fastq_gz_fastqc_zip = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/fastqc/test_fastqc.zip" + } + 'genome' { + genome_fasta_gz = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta.gz" + genome_fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta" + kraken2_tar_gz = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/db/kraken2.tar.gz" + } + } + } +} diff --git a/modules.json b/modules.json index 3a5c7587..dcc7e838 100644 --- a/modules.json +++ b/modules.json @@ -77,7 +77,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "4ab13872435962dadc239979554d13709e20bf29", + "git_sha": "642a0d8afe373ac45244a7947fb8a6c0a5a312d4", "installed_by": ["modules"] }, "picard/markduplicates": { diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 00cc48d2..70708f33 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -43,7 +43,7 @@ process MULTIQC { stub: """ - touch multiqc_data + mkdir multiqc_data touch multiqc_plots touch multiqc_report.html diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index f1aa660e..45a9bc35 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -1,4 +1,3 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: multiqc description: Aggregate results from bioinformatics analyses across many samples into a single report keywords: diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test index c2dad217..d0438eda 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -7,12 +7,9 @@ nextflow_process { tag "modules_nfcore" tag "multiqc" - test("MULTIQC: FASTQC") { + test("sarscov2 single-end [fastqc]") { when { - params { - outdir = "$outputDir" - } process { """ input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) @@ -26,20 +23,17 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert path(process.out.report.get(0)).exists() }, - { assert path(process.out.data.get(0)).exists() }, - { assert path(process.out.versions.get(0)).getText().contains("multiqc") } + { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, + { assert process.out.data[0] ==~ ".*/multiqc_data" }, + { assert snapshot(process.out.versions).match("versions") } ) } } - test("MULTIQC: FASTQC and a config file") { + test("sarscov2 single-end [fastqc] [config]") { when { - params { - outdir = "$outputDir" - } process { """ input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) @@ -53,9 +47,35 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert path(process.out.report.get(0)).exists() }, - { assert path(process.out.data.get(0)).exists() }, - { assert path(process.out.versions.get(0)).getText().contains("multiqc") } + { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, + { assert process.out.data[0] ==~ ".*/multiqc_data" }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("sarscov2 single-end [fastqc] - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) + input[1] = [] + input[2] = [] + input[3] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.report.collect { file(it).getName() } + + process.out.data.collect { file(it).getName() } + + process.out.plots.collect { file(it).getName() } + + process.out.versions ).match() } ) } diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap new file mode 100644 index 00000000..d087a9df --- /dev/null +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -0,0 +1,21 @@ +{ + "versions": { + "content": [ + [ + "versions.yml:md5,f81e19ab3a8e2b6f2b5d22078117df71" + ] + ], + "timestamp": "2023-12-30T00:26:14.048089591" + }, + "sarscov2 single-end [fastqc] - stub": { + "content": [ + [ + "multiqc_report.html", + "multiqc_data", + "multiqc_plots", + "versions.yml:md5,f81e19ab3a8e2b6f2b5d22078117df71" + ] + ], + "timestamp": "2023-12-30T00:26:52.963964055" + } +} \ No newline at end of file From f24bfb725f7841c9b9ef79518589b9bed2f7871b Mon Sep 17 00:00:00 2001 From: Sateesh Date: Fri, 5 Jan 2024 14:46:34 +0000 Subject: [PATCH 29/30] update custom/dumpsoftwareversions module and snaps --- modules.json | 2 +- .../dumpsoftwareversions/tests/main.nf.test | 7 ++- .../tests/main.nf.test.snap | 50 +++++++++++-------- tests/pipeline/bismark/main.nf.test.snap | 16 +++--- .../pipeline/bismark_hisat/main.nf.test.snap | 8 +-- tests/pipeline/bwameth/main.nf.test.snap | 10 ++-- 6 files changed, 52 insertions(+), 41 deletions(-) diff --git a/modules.json b/modules.json index dcc7e838..bf351c59 100644 --- a/modules.json +++ b/modules.json @@ -57,7 +57,7 @@ }, "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "bba7e362e4afead70653f84d8700588ea28d0f9e", + "git_sha": "37dee863936732fe7e05dc598bf6e183a8e7ef73", "installed_by": ["modules"] }, "fastqc": { diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test index eec1db10..b1e1630b 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test @@ -31,7 +31,12 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out.versions, + file(process.out.mqc_yml[0]).readLines()[0..10], + file(process.out.yml[0]).readLines()[0..7] + ).match() + } ) } } diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap index 4274ed57..29e72446 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap @@ -1,27 +1,33 @@ { "Should run without failures": { "content": [ - { - "0": [ - "software_versions.yml:md5,1c851188476409cda5752ce971b20b58" - ], - "1": [ - "software_versions_mqc.yml:md5,2570f4ba271ad08357b0d3d32a9cf84d" - ], - "2": [ - "versions.yml:md5,3843ac526e762117eedf8825b40683df" - ], - "mqc_yml": [ - "software_versions_mqc.yml:md5,2570f4ba271ad08357b0d3d32a9cf84d" - ], - "versions": [ - "versions.yml:md5,3843ac526e762117eedf8825b40683df" - ], - "yml": [ - "software_versions.yml:md5,1c851188476409cda5752ce971b20b58" - ] - } + [ + "versions.yml:md5,3843ac526e762117eedf8825b40683df" + ], + [ + "data: \"\\n\\n \\n \\n \\n \\n \\n \\n \\n\\", + " \\n\\n\\n \\n \\n\\", + " \\ \\n\\n\\n\\n \\n \\", + " \\ \\n \\n\\n\\n\\n\\", + " \\n\\n \\n \\n\\", + " \\ \\n\\n\\n\\n\\n\\n \\n\\", + " \\ \\n \\n\\n\\n\\n\\", + " \\n\\n \\n \\n\\" + ], + [ + "CUSTOM_DUMPSOFTWAREVERSIONS:", + " python: 3.12.0", + " yaml: 6.0.1", + "TOOL1:", + " tool1: 0.11.9", + "TOOL2:", + " tool2: '1.9'", + "Workflow:" + ] ], - "timestamp": "2023-11-03T14:43:22.157011" + "timestamp": "2024-01-05T00:18:43.461970077" } -} +} \ No newline at end of file diff --git a/tests/pipeline/bismark/main.nf.test.snap b/tests/pipeline/bismark/main.nf.test.snap index a69f0954..3d2247c3 100644 --- a/tests/pipeline/bismark/main.nf.test.snap +++ b/tests/pipeline/bismark/main.nf.test.snap @@ -1,21 +1,21 @@ { "single_end_software_versions": { "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0dev}}" + "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0dev}}" ], - "timestamp": "2023-12-22T22:42:59.896228401" + "timestamp": "2024-01-05T14:14:17.281822498" }, "single_end_nomeseq_software_versions": { "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0dev}}" + "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0dev}}" ], - "timestamp": "2023-12-22T22:56:03.882046934" + "timestamp": "2024-01-05T14:21:31.783610175" }, "single_end_rrbs_software_versions": { "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.6.0dev}}" + "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.6.0dev}}" ], - "timestamp": "2023-12-22T22:52:44.437869745" + "timestamp": "2024-01-05T14:17:51.992881339" }, "single_end_nomeseq": { "content": [ @@ -55,9 +55,9 @@ }, "clip_r1_software_versions": { "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0dev}}" + "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0dev}}" ], - "timestamp": "2023-12-22T22:57:41.01411097" + "timestamp": "2024-01-05T14:23:04.466332751" }, "single_end": { "content": [ diff --git a/tests/pipeline/bismark_hisat/main.nf.test.snap b/tests/pipeline/bismark_hisat/main.nf.test.snap index 2cf6357f..cd71725a 100644 --- a/tests/pipeline/bismark_hisat/main.nf.test.snap +++ b/tests/pipeline/bismark_hisat/main.nf.test.snap @@ -1,15 +1,15 @@ { "single_end_software_versions": { "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0dev}}" + "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0dev}}" ], - "timestamp": "2023-12-22T22:14:40.465488234" + "timestamp": "2024-01-05T14:28:08.815211757" }, "single_end_rrbs_software_versions": { "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.6.0dev}}" + "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.6.0dev}}" ], - "timestamp": "2023-12-22T22:37:56.693097833" + "timestamp": "2024-01-05T14:33:15.277969284" }, "single_end": { "content": [ diff --git a/tests/pipeline/bwameth/main.nf.test.snap b/tests/pipeline/bwameth/main.nf.test.snap index 6f4e2806..20296008 100644 --- a/tests/pipeline/bwameth/main.nf.test.snap +++ b/tests/pipeline/bwameth/main.nf.test.snap @@ -1,15 +1,15 @@ { "single_end_software_versions": { "content": [ - "{BWAMETH_ALIGN={bwameth=0.2.2}, BWAMETH_INDEX={bwameth=0.2.2}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0dev}}" + "{BWAMETH_ALIGN={bwameth=0.2.2}, BWAMETH_INDEX={bwameth=0.2.2}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0dev}}" ], - "timestamp": "2023-08-28T00:28:04+0000" + "timestamp": "2024-01-05T14:41:25.742050491" }, "single_end_rrbs_software_versions": { "content": [ - "{BWAMETH_ALIGN={bwameth=0.2.2}, BWAMETH_INDEX={bwameth=0.2.2}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.6.0dev}}" + "{BWAMETH_ALIGN={bwameth=0.2.2}, BWAMETH_INDEX={bwameth=0.2.2}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.6.0dev}}" ], - "timestamp": "2023-08-28T00:28:04+0000" + "timestamp": "2024-01-05T14:44:15.01614543" }, "single_end": { "content": [ @@ -69,4 +69,4 @@ ], "timestamp": "2023-12-20T03:38:43.324010795" } -} +} \ No newline at end of file From 0bc157569fef34307842d784ae46d006b9e23826 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 5 Jan 2024 12:47:02 -0600 Subject: [PATCH 30/30] chore: Bump versions for 2.6.0 release --- CHANGELOG.md | 2 +- assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- tests/pipeline/bismark/main.nf.test.snap | 16 ++++++++-------- tests/pipeline/bismark_hisat/main.nf.test.snap | 8 ++++---- tests/pipeline/bwameth/main.nf.test.snap | 8 ++++---- 6 files changed, 20 insertions(+), 20 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 97f8c99e..ecff842f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,6 @@ # nf-core/methylseq -## v2.6.0dev - [date] +## [v2.6.0](https://github.com/nf-core/methylseq/releases/tag/2.6.0) - 2024-01-05 ### Bug fixes & refactoring diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index ad28ec5b..c6e99955 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/methylseq + This report has been generated by the nf-core/methylseq analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-methylseq-methods-description": order: -1000 diff --git a/nextflow.config b/nextflow.config index 5bdfa5e9..d95f12b2 100644 --- a/nextflow.config +++ b/nextflow.config @@ -297,7 +297,7 @@ manifest { description = """Methylation (Bisulfite-Sequencing) Best Practice analysis pipeline, part of the nf-core community.""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '2.6.0dev' + version = '2.6.0' doi = '10.5281/zenodo.1343417' } diff --git a/tests/pipeline/bismark/main.nf.test.snap b/tests/pipeline/bismark/main.nf.test.snap index 3d2247c3..281ff290 100644 --- a/tests/pipeline/bismark/main.nf.test.snap +++ b/tests/pipeline/bismark/main.nf.test.snap @@ -1,21 +1,21 @@ { "single_end_software_versions": { "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0dev}}" + "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0}}" ], - "timestamp": "2024-01-05T14:14:17.281822498" + "timestamp": "2024-01-05T13:33:44.592961646" }, "single_end_nomeseq_software_versions": { "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0dev}}" + "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0}}" ], - "timestamp": "2024-01-05T14:21:31.783610175" + "timestamp": "2024-01-05T13:38:45.868954182" }, "single_end_rrbs_software_versions": { "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.6.0dev}}" + "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.6.0}}" ], - "timestamp": "2024-01-05T14:17:51.992881339" + "timestamp": "2024-01-05T13:36:19.58008405" }, "single_end_nomeseq": { "content": [ @@ -55,9 +55,9 @@ }, "clip_r1_software_versions": { "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0dev}}" + "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0}}" ], - "timestamp": "2024-01-05T14:23:04.466332751" + "timestamp": "2024-01-05T13:39:54.162519593" }, "single_end": { "content": [ diff --git a/tests/pipeline/bismark_hisat/main.nf.test.snap b/tests/pipeline/bismark_hisat/main.nf.test.snap index cd71725a..07d914d9 100644 --- a/tests/pipeline/bismark_hisat/main.nf.test.snap +++ b/tests/pipeline/bismark_hisat/main.nf.test.snap @@ -1,15 +1,15 @@ { "single_end_software_versions": { "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0dev}}" + "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0}}" ], - "timestamp": "2024-01-05T14:28:08.815211757" + "timestamp": "2024-01-05T13:41:11.426077518" }, "single_end_rrbs_software_versions": { "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.6.0dev}}" + "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.6.0}}" ], - "timestamp": "2024-01-05T14:33:15.277969284" + "timestamp": "2024-01-05T13:43:52.561148623" }, "single_end": { "content": [ diff --git a/tests/pipeline/bwameth/main.nf.test.snap b/tests/pipeline/bwameth/main.nf.test.snap index 20296008..fccd1fc2 100644 --- a/tests/pipeline/bwameth/main.nf.test.snap +++ b/tests/pipeline/bwameth/main.nf.test.snap @@ -1,15 +1,15 @@ { "single_end_software_versions": { "content": [ - "{BWAMETH_ALIGN={bwameth=0.2.2}, BWAMETH_INDEX={bwameth=0.2.2}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0dev}}" + "{BWAMETH_ALIGN={bwameth=0.2.2}, BWAMETH_INDEX={bwameth=0.2.2}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0}}" ], - "timestamp": "2024-01-05T14:41:25.742050491" + "timestamp": "2024-01-05T13:46:07.95961601" }, "single_end_rrbs_software_versions": { "content": [ - "{BWAMETH_ALIGN={bwameth=0.2.2}, BWAMETH_INDEX={bwameth=0.2.2}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.6.0dev}}" + "{BWAMETH_ALIGN={bwameth=0.2.2}, BWAMETH_INDEX={bwameth=0.2.2}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.6.0}}" ], - "timestamp": "2024-01-05T14:44:15.01614543" + "timestamp": "2024-01-05T13:47:24.172597347" }, "single_end": { "content": [
Process Name \\", + " \\ Software Version
CUSTOM_DUMPSOFTWAREVERSIONSpython3.12.0
yaml6.0.1
TOOL1tool10.11.9
TOOL2tool21.9
WorkflowNextflow