From 57f3e4cc5a2afd5d701fe6b592a82ff39ee7152f Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 20 Oct 2023 01:02:00 +0200 Subject: [PATCH 01/14] 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 02/14] 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 03/14] 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 04/14] 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 05/14] 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 06/14] 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 07/14] 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 08/14] 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 09/14] 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 8966c1373d5d9c651c551f83d0ac1b2cf94719c2 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 22 Dec 2023 06:39:58 -0600 Subject: [PATCH 10/14] 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 11/14] 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 = "$outputDir" } From 2673007b651e3a77c9932d7bee3c556defce17d7 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 22 Dec 2023 10:34:39 -0600 Subject: [PATCH 12/14] test: Update test lib path --- nf-test.config | 2 +- tests/{pipeline => }/lib/UTILS.groovy | 0 2 files changed, 1 insertion(+), 1 deletion(-) rename tests/{pipeline => }/lib/UTILS.groovy (100%) diff --git a/nf-test.config b/nf-test.config index cb656b94..89243e51 100644 --- a/nf-test.config +++ b/nf-test.config @@ -6,7 +6,7 @@ config { workDir "/tmp" // location of library folder that is added automatically to the classpath - libDir "lib/" + libDir "tests/lib/" // location of an optional nextflow.config file specific for executing tests configFile "nextflow.config" diff --git a/tests/pipeline/lib/UTILS.groovy b/tests/lib/UTILS.groovy similarity index 100% rename from tests/pipeline/lib/UTILS.groovy rename to tests/lib/UTILS.groovy From ab3898b4ac075cbea78d95fb13b196e49b4f8914 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 22 Dec 2023 13:22:55 -0600 Subject: [PATCH 13/14] ci: Bump nf-test version Again Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 0904c096..599e16f3 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -14,7 +14,7 @@ on: env: NXF_ANSI_LOG: false - NFTEST_VER: "0.8.1" + NFTEST_VER: "0.8.2" concurrency: group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" From 9d88d67c7a68495d789610f427d8e3d02881436d Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 22 Dec 2023 14:48:19 -0600 Subject: [PATCH 14/14] test: Bump snapshots for nf-test 0.8.2 Co-authored-by: sateeshperi --- .gitignore | 1 + tests/pipeline/bismark/main.nf.test | 6 +- tests/pipeline/bismark/main.nf.test.snap | 148 +++++++++--------- tests/pipeline/bismark_hisat/main.nf.test | 3 +- .../pipeline/bismark_hisat/main.nf.test.snap | 72 ++++----- tests/pipeline/bwameth/main.nf.test | 3 +- tests/pipeline/bwameth/main.nf.test.snap | 8 +- 7 files changed, 119 insertions(+), 122 deletions(-) diff --git a/.gitignore b/.gitignore index 9473434c..4a37b601 100644 --- a/.gitignore +++ b/.gitignore @@ -8,4 +8,5 @@ testing* *.pyc .vscode .nf-test +.nf-test.log test-datasets/ diff --git a/tests/pipeline/bismark/main.nf.test b/tests/pipeline/bismark/main.nf.test index 9292e1ef..ee1c87b5 100644 --- a/tests/pipeline/bismark/main.nf.test +++ b/tests/pipeline/bismark/main.nf.test @@ -1,9 +1,8 @@ -import com.askimed.nf.test.util.FileUtil; - nextflow_pipeline { name "Test Workflow main.nf" script "main.nf" + tag "bismark" tag "pipeline" @@ -14,7 +13,6 @@ nextflow_pipeline { save_reference = true outdir = "$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", - "CHH_OT_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,d173808471dbb7c50ef43eb1f5f29faa", - "CHH_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,a23e78b714eb1ef1810714d29557c620", - "CpG_OB_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,c3d32d42c00d94ea8322487aa0a20787", - "CpG_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,0039a8c3f8971a5a99bc58bc1511fa0d", - "CpG_OT_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,6dfc57a2892d7cd3bebb7cbc0878196b", - "CpG_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,288062a6b71f04688afad75dcd2230f9" + "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_10K_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt:md5,79ebef1c474ff5bdb5f79b955208bb04", "SRR389222_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,1c4a4288b3bcf1bbaa6b99e3c4b53ce9", - "SRR389222.merged.fastq.gz:md5,ba5df0639e25988059a6f5bf309dbb6e", + "SRR389222.merged.fastq.gz:md5,47e1d7461d511a970e80085dd6454775", "genome_results.txt:md5,1e01c188f34b7d385e8b16156ab2b93e", "genome_results.txt:md5,b99d4cfd82d21ac09ccb72865f9b3960" ], - "timestamp": "2023-08-28T08:46:48+0000" + "timestamp": "2023-12-22T14:22:34.861151831" }, "single_end_rrbs_software_versions": { "content": [ @@ -69,25 +69,25 @@ "content": [ "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:md5,66af42e52cdcaf5ceabddb33c9045a4d", - "SRR389222_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,60bf00418d5e2ede8740e3cba6c6ef61", + "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_10K_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz:md5,ef5178734cdbba3326e22f8459b4db48", - "SRR389222_trimmed_bismark_bt2.deduplicated.bismark.cov.gz:md5,0bb6dd26908e239f695105230564b59b", + "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_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", - "CHH_OT_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,d173808471dbb7c50ef43eb1f5f29faa", - "CHH_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,a23e78b714eb1ef1810714d29557c620", - "CpG_OB_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,c3d32d42c00d94ea8322487aa0a20787", - "CpG_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,0039a8c3f8971a5a99bc58bc1511fa0d", - "CpG_OT_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,6dfc57a2892d7cd3bebb7cbc0878196b", - "CpG_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,288062a6b71f04688afad75dcd2230f9" + "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_10K_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt:md5,79ebef1c474ff5bdb5f79b955208bb04", "SRR389222_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,1c4a4288b3bcf1bbaa6b99e3c4b53ce9", @@ -117,31 +117,31 @@ "genome_results.txt:md5,1e01c188f34b7d385e8b16156ab2b93e", "genome_results.txt:md5,b99d4cfd82d21ac09ccb72865f9b3960" ], - "timestamp": "2023-08-28T08:46:48+0000" + "timestamp": "2023-12-22T14:17:47.259020697" }, "single_end_rrbs": { "content": [ "Ecoli_10K_methylated_R1_bismark_bt2_pe.bam:md5,1497e3a06ee045cb82f834ddb4bcfe88", "SRR389222.merged_bismark_bt2.bam:md5,c3e94ff13a934e0c78ebb6d40f7c8230", - "Ecoli_10K_methylated_R1_bismark_bt2_pe.bedGraph.gz:md5,66af42e52cdcaf5ceabddb33c9045a4d", - "SRR389222.merged_bismark_bt2.bedGraph.gz:md5,5d87f42769268bceb35b3341aa4dc92f", + "Ecoli_10K_methylated_R1_bismark_bt2_pe.bedGraph.gz:md5,58c9ba98d0638c26a30233b006a81172", + "SRR389222.merged_bismark_bt2.bedGraph.gz:md5,c154fe825d9bb867c9efcf55d6cb7e94", "Ecoli_10K_methylated_R1_bismark_bt2_pe.M-bias.txt:md5,29f3b882a51b63ce77d3d9c69b0e5f85", "SRR389222.merged_bismark_bt2.M-bias.txt:md5,514f544046333337f0f74b7386b8afa6", - "Ecoli_10K_methylated_R1_bismark_bt2_pe.bismark.cov.gz:md5,ef5178734cdbba3326e22f8459b4db48", - "SRR389222.merged_bismark_bt2.bismark.cov.gz:md5,b46638fd5f36fa4bce5f4f7b7247d995", + "Ecoli_10K_methylated_R1_bismark_bt2_pe.bismark.cov.gz:md5,8e6ba6fe66416d73e7f94b4da9ca77b1", + "SRR389222.merged_bismark_bt2.bismark.cov.gz:md5,d4a5b741ca46b486bf165ede18baadd0", [ - "CHG_OB_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz:md5,bca8572c7cd3cd45e148ba722ad4b12d", - "CHG_OB_SRR389222.merged_bismark_bt2.txt.gz:md5,3fcc7974fd6c5cbacf231835f58d949b", - "CHG_OT_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz:md5,7f49ecab1843458c28c3d6fe6a85149e", - "CHG_OT_SRR389222.merged_bismark_bt2.txt.gz:md5,d80c75d6eb49f629c9f5f4c2e63588aa", - "CHH_OB_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz:md5,e67409a20a141077edc1dc61972bb278", - "CHH_OB_SRR389222.merged_bismark_bt2.txt.gz:md5,2fb870b779750951bec579ce7562736e", - "CHH_OT_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz:md5,d173808471dbb7c50ef43eb1f5f29faa", - "CHH_OT_SRR389222.merged_bismark_bt2.txt.gz:md5,8fea7767cfe903f9671a506feaa7a8a6", - "CpG_OB_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz:md5,c3d32d42c00d94ea8322487aa0a20787", - "CpG_OB_SRR389222.merged_bismark_bt2.txt.gz:md5,6537b18418e62410d9ae617480702c54", - "CpG_OT_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz:md5,6dfc57a2892d7cd3bebb7cbc0878196b", - "CpG_OT_SRR389222.merged_bismark_bt2.txt.gz:md5,3450512dc718e26edf13ff870cf3b159" + "CHG_OB_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz:md5,9c2248d95d96d6c315c65f1b8dc3bc39", + "CHG_OB_SRR389222.merged_bismark_bt2.txt.gz:md5,eeb08e87d7e3dca0acbb2c5ba2be66fb", + "CHG_OT_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz:md5,5e5aefaa3f63e73f30342ad843eb210b", + "CHG_OT_SRR389222.merged_bismark_bt2.txt.gz:md5,930f995efd5204b5b04a548afdef1a6e", + "CHH_OB_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz:md5,65f2afc6b1c76209af1acd1d4277a1cc", + "CHH_OB_SRR389222.merged_bismark_bt2.txt.gz:md5,a135c7e8a6c1b909a318ef17d47dca94", + "CHH_OT_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz:md5,978ad87fef01e39283a620253320ee45", + "CHH_OT_SRR389222.merged_bismark_bt2.txt.gz:md5,2a356ae7fe7774f140f11ed5d935f88c", + "CpG_OB_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz:md5,54def6bf13e27f38adbbd3dd06297596", + "CpG_OB_SRR389222.merged_bismark_bt2.txt.gz:md5,b8b2de10044869b6c1097afc21c878a0", + "CpG_OT_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz:md5,9712eef973883f44dcc0a307af28ba70", + "CpG_OT_SRR389222.merged_bismark_bt2.txt.gz:md5,9e517e44422a8bb22de1281ff2cd34d1" ], "Ecoli_10K_methylated_R1_bismark_bt2_pe_splitting_report.txt:md5,fa089f6146df9667862970b6ddc998b0", "SRR389222.merged_bismark_bt2_splitting_report.txt:md5,0ece57f8fc3aa659d2f0b7a09cf48398", @@ -171,38 +171,38 @@ "genome_results.txt:md5,b6ba7868b12971aaad0d4a04e25acd0b", "genome_results.txt:md5,f0d293867800a75becf2583c23729083" ], - "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" } }