From 9384dbf3d21db72cb1ee7fb7c4261312317418ca Mon Sep 17 00:00:00 2001 From: Sabrina Krakau Date: Wed, 26 May 2021 15:08:01 +0200 Subject: [PATCH 1/4] Use --busco_reference by for main CI tests --- conf/test.config | 1 + conf/test_host_rm.config | 1 + conf/test_hybrid.config | 1 + conf/test_hybrid_host_rm.config | 1 + 4 files changed, 4 insertions(+) diff --git a/conf/test.config b/conf/test.config index c751cc30..423c173f 100644 --- a/conf/test.config +++ b/conf/test.config @@ -22,5 +22,6 @@ params { skip_krona = true min_length_unbinned_contigs = 1 max_unbinned_contigs = 2 + busco_reference = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz" gtdb = false } diff --git a/conf/test_host_rm.config b/conf/test_host_rm.config index a2178aa2..a7285387 100644 --- a/conf/test_host_rm.config +++ b/conf/test_host_rm.config @@ -23,5 +23,6 @@ params { skip_krona = true min_length_unbinned_contigs = 1 max_unbinned_contigs = 2 + busco_reference = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz" gtdb = false } diff --git a/conf/test_hybrid.config b/conf/test_hybrid.config index ac91ac5e..85fae6f6 100644 --- a/conf/test_hybrid.config +++ b/conf/test_hybrid.config @@ -19,5 +19,6 @@ params { input = 'https://github.com/nf-core/test-datasets/raw/mag/samplesheets/samplesheet.hybrid.csv' min_length_unbinned_contigs = 1 max_unbinned_contigs = 2 + busco_reference = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz" gtdb = false } diff --git a/conf/test_hybrid_host_rm.config b/conf/test_hybrid_host_rm.config index 09edb1b8..6e343000 100644 --- a/conf/test_hybrid_host_rm.config +++ b/conf/test_hybrid_host_rm.config @@ -20,5 +20,6 @@ params { input = 'https://github.com/nf-core/test-datasets/raw/mag/samplesheets/samplesheet.hybrid_host_rm.csv' min_length_unbinned_contigs = 1 max_unbinned_contigs = 2 + busco_reference = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz" gtdb = false } From 816fd06181a038bd978dcca3922e25b74e0b3738 Mon Sep 17 00:00:00 2001 From: Sabrina Krakau Date: Wed, 26 May 2021 15:09:06 +0200 Subject: [PATCH 2/4] remove centrifuge and kraken2 in test_host_rm test --- conf/test_host_rm.config | 3 --- 1 file changed, 3 deletions(-) diff --git a/conf/test_host_rm.config b/conf/test_host_rm.config index a7285387..474fe288 100644 --- a/conf/test_host_rm.config +++ b/conf/test_host_rm.config @@ -18,9 +18,6 @@ params { // Input data host_fasta = "https://github.com/nf-core/test-datasets/raw/mag/host_reference/genome.hg38.chr21_10000bp_region.fa" input = 'https://github.com/nf-core/test-datasets/raw/mag/samplesheets/samplesheet.host_rm.csv' - centrifuge_db = "https://github.com/nf-core/test-datasets/raw/mag/test_data/minigut_cf.tar.gz" - kraken2_db = "https://github.com/nf-core/test-datasets/raw/mag/test_data/minigut_kraken.tgz" - skip_krona = true min_length_unbinned_contigs = 1 max_unbinned_contigs = 2 busco_reference = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz" From 0a2d85ef7143fd49ccd660d8d917db6a221da16b Mon Sep 17 00:00:00 2001 From: Sabrina Krakau Date: Wed, 26 May 2021 15:18:09 +0200 Subject: [PATCH 3/4] Add test_busco_auto profile --- .github/workflows/ci.yml | 2 +- conf/test_busco_auto.config | 24 ++++++++++++++++++++++++ docs/usage.md | 2 +- nextflow.config | 9 +++++---- 4 files changed, 31 insertions(+), 6 deletions(-) create mode 100644 conf/test_busco_auto.config diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index b67ae0fb..243b2464 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -51,7 +51,7 @@ jobs: strategy: matrix: # Run remaining test profiles with minimum nextflow version - profile: [test_host_rm, test_hybrid, test_hybrid_host_rm] + profile: [test_host_rm, test_hybrid, test_hybrid_host_rm, test_busco_auto] steps: - name: Check out pipeline code uses: actions/checkout@v2 diff --git a/conf/test_busco_auto.config b/conf/test_busco_auto.config new file mode 100644 index 00000000..4bfa282c --- /dev/null +++ b/conf/test_busco_auto.config @@ -0,0 +1,24 @@ +/* + * ------------------------------------------------- + * Nextflow config file for running tests + * ------------------------------------------------- + * Defines bundled input files and everything required + * to run a fast and simple test. Use as follows: + * nextflow run nf-core/mag -profile test_busco_auto, + */ + +params { + config_profile_name = 'Test profile' + config_profile_description = 'Minimal test dataset to check pipeline function' + // Limit resources so that this can run on GitHub Actions + max_cpus = 2 + max_memory = 6.GB + max_time = 48.h + + // Input data + input = 'https://github.com/nf-core/test-datasets/raw/mag/samplesheets/samplesheet.csv' + skip_spades = true + min_length_unbinned_contigs = 1 + max_unbinned_contigs = 2 + gtdb = false +} diff --git a/docs/usage.md b/docs/usage.md index 1d6540ed..bbbd78bd 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -92,7 +92,7 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof * Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter or Charliecloud. * A generic configuration profile to be used with [Conda](https://conda.io/docs/) * Pulls most software from [Bioconda](https://bioconda.github.io/) -* `test`, `test_hybrid`, `test_host_rm`, `test_hybrid_host_rm` +* `test`, `test_hybrid`, `test_host_rm`, `test_hybrid_host_rm`, `test_busco_auto` * Profiles with a complete configuration for automated testing * Includes links to test data so needs no other parameters diff --git a/nextflow.config b/nextflow.config index 0141553e..0daa0c79 100644 --- a/nextflow.config +++ b/nextflow.config @@ -190,11 +190,12 @@ profiles { podman.enabled = false shifter.enabled = false } - test { includeConfig 'conf/test.config' } - test_host_rm { includeConfig 'conf/test_host_rm.config' } - test_hybrid { includeConfig 'conf/test_hybrid.config' } + test { includeConfig 'conf/test.config' } + test_host_rm { includeConfig 'conf/test_host_rm.config' } + test_hybrid { includeConfig 'conf/test_hybrid.config' } test_hybrid_host_rm { includeConfig 'conf/test_hybrid_host_rm.config' } - test_full { includeConfig 'conf/test_full.config' } + test_busco_auto { includeConfig 'conf/test_busco_auto.config' } + test_full { includeConfig 'conf/test_full.config' } } // Export these variables to prevent local Python/R libraries from conflicting with those in the container From 3d5872f98c7d6f84bd962035267a85df65bc55ea Mon Sep 17 00:00:00 2001 From: Sabrina Krakau Date: Wed, 26 May 2021 15:25:52 +0200 Subject: [PATCH 4/4] Update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3c717b6d..6521c859 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -27,6 +27,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#191](https://github.com/nf-core/mag/pull/191) - Update to nf-core 1.14 `TEMPLATE` - [#193](https://github.com/nf-core/mag/pull/193) - Compress CAT output files [#180](https://github.com/nf-core/mag/issues/180) - [#198](https://github.com/nf-core/mag/pull/198) - Requires nextflow version `>= 21.04.0` +- [#200](https://github.com/nf-core/mag/pull/200) - Small changes in GitHub Actions tests ### `Fixed`