From c49f446f65f28751f04fe812a223fa01ce69f1a3 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Thu, 21 Mar 2024 08:08:07 +0000 Subject: [PATCH 01/10] Add direct replacements for existing tests Additions: - Runs simple tests for workflows - Directly replaces existing tests in .github/workflows - No checks for outputs or contents --- tests/{main.nf.test => main.default.nf.test} | 2 +- ...nf.test.snap => main.default.nf.test.snap} | 0 tests/main.featurecounts_group_type.nf.test | 22 +++++++++++++++++++ tests/main.min_mapped_reads_90.nf.test | 22 +++++++++++++++++++ tests/main.remove_ribo_rna.nf.test | 22 +++++++++++++++++++ tests/main.skip_qc.nf.test | 22 +++++++++++++++++++ tests/main.skip_trimming.nf.test | 22 +++++++++++++++++++ 7 files changed, 111 insertions(+), 1 deletion(-) rename tests/{main.nf.test => main.default.nf.test} (94%) rename tests/{main.nf.test.snap => main.default.nf.test.snap} (100%) create mode 100644 tests/main.featurecounts_group_type.nf.test create mode 100644 tests/main.min_mapped_reads_90.nf.test create mode 100644 tests/main.remove_ribo_rna.nf.test create mode 100644 tests/main.skip_qc.nf.test create mode 100644 tests/main.skip_trimming.nf.test diff --git a/tests/main.nf.test b/tests/main.default.nf.test similarity index 94% rename from tests/main.nf.test rename to tests/main.default.nf.test index 3dc8e5df8..f40b97a49 100644 --- a/tests/main.nf.test +++ b/tests/main.default.nf.test @@ -5,7 +5,7 @@ nextflow_pipeline { tag "rnaseq" tag "PIPELINE" - test("Run with profile test") { + test("Default profile test") { when { params { diff --git a/tests/main.nf.test.snap b/tests/main.default.nf.test.snap similarity index 100% rename from tests/main.nf.test.snap rename to tests/main.default.nf.test.snap diff --git a/tests/main.featurecounts_group_type.nf.test b/tests/main.featurecounts_group_type.nf.test new file mode 100644 index 000000000..ed5fa654c --- /dev/null +++ b/tests/main.featurecounts_group_type.nf.test @@ -0,0 +1,22 @@ +nextflow_pipeline { + + name "Test pipeline" + script "../main.nf" + tag "rnaseq" + tag "PIPELINE" + + test("--featurecounts_group_type false") { + + when { + params { + outdir = "$outputDir" + input = 'https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/samplesheet/v3.10/samplesheet_test.csv' + featurecounts_group_type = false + } + } + + then { + assert workflow.success + } + } +} diff --git a/tests/main.min_mapped_reads_90.nf.test b/tests/main.min_mapped_reads_90.nf.test new file mode 100644 index 000000000..8a3a48d88 --- /dev/null +++ b/tests/main.min_mapped_reads_90.nf.test @@ -0,0 +1,22 @@ +nextflow_pipeline { + + name "Test pipeline" + script "../main.nf" + tag "rnaseq" + tag "PIPELINE" + + test("--min_mapped_reads 90") { + + when { + params { + outdir = "$outputDir" + input = 'https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/samplesheet/v3.10/samplesheet_test.csv' + min_mapped_reads = 90 + } + } + + then { + assert workflow.success + } + } +} diff --git a/tests/main.remove_ribo_rna.nf.test b/tests/main.remove_ribo_rna.nf.test new file mode 100644 index 000000000..51f8fbdef --- /dev/null +++ b/tests/main.remove_ribo_rna.nf.test @@ -0,0 +1,22 @@ +nextflow_pipeline { + + name "Test pipeline" + script "../main.nf" + tag "rnaseq" + tag "PIPELINE" + + test("--remove_ribo_rna") { + + when { + params { + outdir = "$outputDir" + input = 'https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/samplesheet/v3.10/samplesheet_test.csv' + remove_ribo_rna = true + } + } + + then { + assert workflow.success + } + } +} diff --git a/tests/main.skip_qc.nf.test b/tests/main.skip_qc.nf.test new file mode 100644 index 000000000..34cc1711b --- /dev/null +++ b/tests/main.skip_qc.nf.test @@ -0,0 +1,22 @@ +nextflow_pipeline { + + name "Test pipeline" + script "../main.nf" + tag "rnaseq" + tag "PIPELINE" + + test("--skip_qc") { + + when { + params { + outdir = "$outputDir" + input = 'https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/samplesheet/v3.10/samplesheet_test.csv' + skip_qc = true + } + } + + then { + assert workflow.success + } + } +} diff --git a/tests/main.skip_trimming.nf.test b/tests/main.skip_trimming.nf.test new file mode 100644 index 000000000..24fa9cbb8 --- /dev/null +++ b/tests/main.skip_trimming.nf.test @@ -0,0 +1,22 @@ +nextflow_pipeline { + + name "Test pipeline" + script "../main.nf" + tag "rnaseq" + tag "PIPELINE" + + test("--skip_trimming") { + + when { + params { + outdir = "$outputDir" + input = 'https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/samplesheet/v3.10/samplesheet_test.csv' + skip_qc = true + } + } + + then { + assert workflow.success + } + } +} From 4d9acbbd0fcd0a1e91cd68ebb3ab331f64a204c1 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Thu, 21 Mar 2024 08:24:47 +0000 Subject: [PATCH 02/10] Reorganised into discrete folders --- tests/{main.default.nf.test => default/main.nf.test} | 0 tests/{main.default.nf.test.snap => default/main.nf.test.snap} | 0 .../main.nf.test} | 0 .../main.nf.test} | 0 .../main.nf.test} | 0 tests/{main.skip_qc.nf.test => skip_qc/main.nf.test} | 0 tests/{main.skip_trimming.nf.test => skip_trimming/main.nf.test} | 0 7 files changed, 0 insertions(+), 0 deletions(-) rename tests/{main.default.nf.test => default/main.nf.test} (100%) rename tests/{main.default.nf.test.snap => default/main.nf.test.snap} (100%) rename tests/{main.featurecounts_group_type.nf.test => featurecounts/main.nf.test} (100%) rename tests/{main.min_mapped_reads_90.nf.test => min_mapped_reads/main.nf.test} (100%) rename tests/{main.remove_ribo_rna.nf.test => remove_ribo_rna/main.nf.test} (100%) rename tests/{main.skip_qc.nf.test => skip_qc/main.nf.test} (100%) rename tests/{main.skip_trimming.nf.test => skip_trimming/main.nf.test} (100%) diff --git a/tests/main.default.nf.test b/tests/default/main.nf.test similarity index 100% rename from tests/main.default.nf.test rename to tests/default/main.nf.test diff --git a/tests/main.default.nf.test.snap b/tests/default/main.nf.test.snap similarity index 100% rename from tests/main.default.nf.test.snap rename to tests/default/main.nf.test.snap diff --git a/tests/main.featurecounts_group_type.nf.test b/tests/featurecounts/main.nf.test similarity index 100% rename from tests/main.featurecounts_group_type.nf.test rename to tests/featurecounts/main.nf.test diff --git a/tests/main.min_mapped_reads_90.nf.test b/tests/min_mapped_reads/main.nf.test similarity index 100% rename from tests/main.min_mapped_reads_90.nf.test rename to tests/min_mapped_reads/main.nf.test diff --git a/tests/main.remove_ribo_rna.nf.test b/tests/remove_ribo_rna/main.nf.test similarity index 100% rename from tests/main.remove_ribo_rna.nf.test rename to tests/remove_ribo_rna/main.nf.test diff --git a/tests/main.skip_qc.nf.test b/tests/skip_qc/main.nf.test similarity index 100% rename from tests/main.skip_qc.nf.test rename to tests/skip_qc/main.nf.test diff --git a/tests/main.skip_trimming.nf.test b/tests/skip_trimming/main.nf.test similarity index 100% rename from tests/main.skip_trimming.nf.test rename to tests/skip_trimming/main.nf.test From 08e89ebbf168fe40dccb3d8fb3e9a5c9433def4a Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Thu, 21 Mar 2024 08:26:56 +0000 Subject: [PATCH 03/10] More all tests into subdirectory for more organisation --- tests/{ => tests}/default/main.nf.test | 0 tests/{ => tests}/default/main.nf.test.snap | 0 tests/{ => tests}/featurecounts/main.nf.test | 0 tests/{ => tests}/min_mapped_reads/main.nf.test | 0 tests/{ => tests}/remove_ribo_rna/main.nf.test | 0 tests/{ => tests}/skip_qc/main.nf.test | 0 tests/{ => tests}/skip_trimming/main.nf.test | 0 7 files changed, 0 insertions(+), 0 deletions(-) rename tests/{ => tests}/default/main.nf.test (100%) rename tests/{ => tests}/default/main.nf.test.snap (100%) rename tests/{ => tests}/featurecounts/main.nf.test (100%) rename tests/{ => tests}/min_mapped_reads/main.nf.test (100%) rename tests/{ => tests}/remove_ribo_rna/main.nf.test (100%) rename tests/{ => tests}/skip_qc/main.nf.test (100%) rename tests/{ => tests}/skip_trimming/main.nf.test (100%) diff --git a/tests/default/main.nf.test b/tests/tests/default/main.nf.test similarity index 100% rename from tests/default/main.nf.test rename to tests/tests/default/main.nf.test diff --git a/tests/default/main.nf.test.snap b/tests/tests/default/main.nf.test.snap similarity index 100% rename from tests/default/main.nf.test.snap rename to tests/tests/default/main.nf.test.snap diff --git a/tests/featurecounts/main.nf.test b/tests/tests/featurecounts/main.nf.test similarity index 100% rename from tests/featurecounts/main.nf.test rename to tests/tests/featurecounts/main.nf.test diff --git a/tests/min_mapped_reads/main.nf.test b/tests/tests/min_mapped_reads/main.nf.test similarity index 100% rename from tests/min_mapped_reads/main.nf.test rename to tests/tests/min_mapped_reads/main.nf.test diff --git a/tests/remove_ribo_rna/main.nf.test b/tests/tests/remove_ribo_rna/main.nf.test similarity index 100% rename from tests/remove_ribo_rna/main.nf.test rename to tests/tests/remove_ribo_rna/main.nf.test diff --git a/tests/skip_qc/main.nf.test b/tests/tests/skip_qc/main.nf.test similarity index 100% rename from tests/skip_qc/main.nf.test rename to tests/tests/skip_qc/main.nf.test diff --git a/tests/skip_trimming/main.nf.test b/tests/tests/skip_trimming/main.nf.test similarity index 100% rename from tests/skip_trimming/main.nf.test rename to tests/tests/skip_trimming/main.nf.test From 967563bdb2dff00f982f692f0a6bd6f54700a033 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Thu, 21 Mar 2024 08:29:33 +0000 Subject: [PATCH 04/10] remove redundant tests --- .github/workflows/ci.yml | 67 ---------------------------------------- 1 file changed, 67 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 92b3345d7..86e2d8739 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -19,73 +19,6 @@ concurrency: group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" cancel-in-progress: true jobs: - star_salmon: - name: Test STAR Salmon with workflow parameters - if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }} - runs-on: ubuntu-latest - strategy: - matrix: - parameters: - - "--skip_qc" - - "--skip_trimming" - - "--min_mapped_reads 90" - - "--with_umi" - - "--with_umi --skip_trimming" - - "--remove_ribo_rna --skip_qualimap" - - "--bam_csi_index" - - "--save_align_intermeds --save_reference" - - "--featurecounts_group_type false" - - "--trimmer fastp" - - steps: - - name: Check out pipeline code - uses: actions/checkout@v4 - - - name: Setup Nextflow - uses: nf-core/setup-nextflow@v1.5 - - - name: Run pipeline with STAR and various parameters - run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_salmon ${{ matrix.parameters }} --outdir ./results - - star_rsem: - name: Test STAR RSEM with workflow parameters - if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }} - runs-on: ubuntu-latest - strategy: - matrix: - parameters: - - "--skip_qc" - steps: - - name: Check out pipeline code - uses: actions/checkout@v4 - - - name: Setup Nextflow - uses: nf-core/setup-nextflow@v1.5 - - - name: Run pipeline with RSEM STAR and various parameters - run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_rsem ${{ matrix.parameters }} --outdir ./results - - hisat2: - name: Test HISAT2 with workflow parameters - if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }} - runs-on: ubuntu-latest - strategy: - matrix: - parameters: - - "--skip_qc" - steps: - - name: Check out pipeline code - uses: actions/checkout@v4 - - - name: Setup Nextflow - uses: nf-core/setup-nextflow@v1.5 - - - name: Run pipeline with HISAT2 and various parameters - run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner hisat2 ${{ matrix.parameters }} --outdir ./results - pseudo: name: Test Pseudoaligners with workflow parameters if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }} From c2861cc76fc15769476176cae31a7aad852e0632 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Thu, 21 Mar 2024 08:36:45 +0000 Subject: [PATCH 05/10] Remove invalid dependencies from GHA confirm-pass --- .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 86e2d8739..a61d32c16 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -177,7 +177,7 @@ jobs: confirm-pass: runs-on: ubuntu-latest - needs: [test, star_salmon, star_rsem, hisat2, pseudo] + needs: [test, pseudo] if: always() steps: - name: All tests ok From c00917c482b89a9ad89cad9849d475de8bcab04e Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Thu, 21 Mar 2024 10:31:17 +0000 Subject: [PATCH 06/10] Correct pipeline test path --- tests/tests/default/main.nf.test | 2 +- tests/tests/featurecounts/main.nf.test | 2 +- tests/tests/min_mapped_reads/main.nf.test | 2 +- tests/tests/remove_ribo_rna/main.nf.test | 2 +- tests/tests/skip_qc/main.nf.test | 2 +- tests/tests/skip_trimming/main.nf.test | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/tests/tests/default/main.nf.test b/tests/tests/default/main.nf.test index f40b97a49..227f54458 100644 --- a/tests/tests/default/main.nf.test +++ b/tests/tests/default/main.nf.test @@ -1,7 +1,7 @@ nextflow_pipeline { name "Test pipeline" - script "../main.nf" + script "../../main.nf" tag "rnaseq" tag "PIPELINE" diff --git a/tests/tests/featurecounts/main.nf.test b/tests/tests/featurecounts/main.nf.test index ed5fa654c..5985a686a 100644 --- a/tests/tests/featurecounts/main.nf.test +++ b/tests/tests/featurecounts/main.nf.test @@ -1,7 +1,7 @@ nextflow_pipeline { name "Test pipeline" - script "../main.nf" + script "../../main.nf" tag "rnaseq" tag "PIPELINE" diff --git a/tests/tests/min_mapped_reads/main.nf.test b/tests/tests/min_mapped_reads/main.nf.test index 8a3a48d88..49b83ad19 100644 --- a/tests/tests/min_mapped_reads/main.nf.test +++ b/tests/tests/min_mapped_reads/main.nf.test @@ -1,7 +1,7 @@ nextflow_pipeline { name "Test pipeline" - script "../main.nf" + script "../../main.nf" tag "rnaseq" tag "PIPELINE" diff --git a/tests/tests/remove_ribo_rna/main.nf.test b/tests/tests/remove_ribo_rna/main.nf.test index 51f8fbdef..2d9ba1fc4 100644 --- a/tests/tests/remove_ribo_rna/main.nf.test +++ b/tests/tests/remove_ribo_rna/main.nf.test @@ -1,7 +1,7 @@ nextflow_pipeline { name "Test pipeline" - script "../main.nf" + script "../../main.nf" tag "rnaseq" tag "PIPELINE" diff --git a/tests/tests/skip_qc/main.nf.test b/tests/tests/skip_qc/main.nf.test index 34cc1711b..84db3c9e8 100644 --- a/tests/tests/skip_qc/main.nf.test +++ b/tests/tests/skip_qc/main.nf.test @@ -1,7 +1,7 @@ nextflow_pipeline { name "Test pipeline" - script "../main.nf" + script "../../main.nf" tag "rnaseq" tag "PIPELINE" diff --git a/tests/tests/skip_trimming/main.nf.test b/tests/tests/skip_trimming/main.nf.test index 24fa9cbb8..b51fdfa6a 100644 --- a/tests/tests/skip_trimming/main.nf.test +++ b/tests/tests/skip_trimming/main.nf.test @@ -1,7 +1,7 @@ nextflow_pipeline { name "Test pipeline" - script "../main.nf" + script "../../main.nf" tag "rnaseq" tag "PIPELINE" From 622d8c6194306643a114ad4b74ad471050a30727 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Thu, 21 Mar 2024 16:00:37 +0000 Subject: [PATCH 07/10] Relative path AGAIN --- tests/tests/default/main.nf.test | 2 +- tests/tests/featurecounts/main.nf.test | 2 +- tests/tests/min_mapped_reads/main.nf.test | 2 +- tests/tests/remove_ribo_rna/main.nf.test | 2 +- tests/tests/skip_qc/main.nf.test | 2 +- tests/tests/skip_trimming/main.nf.test | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/tests/tests/default/main.nf.test b/tests/tests/default/main.nf.test index 227f54458..403e9f5f9 100644 --- a/tests/tests/default/main.nf.test +++ b/tests/tests/default/main.nf.test @@ -1,7 +1,7 @@ nextflow_pipeline { name "Test pipeline" - script "../../main.nf" + script "../../../main.nf" tag "rnaseq" tag "PIPELINE" diff --git a/tests/tests/featurecounts/main.nf.test b/tests/tests/featurecounts/main.nf.test index 5985a686a..bc51fe2e0 100644 --- a/tests/tests/featurecounts/main.nf.test +++ b/tests/tests/featurecounts/main.nf.test @@ -1,7 +1,7 @@ nextflow_pipeline { name "Test pipeline" - script "../../main.nf" + script "../../../main.nf" tag "rnaseq" tag "PIPELINE" diff --git a/tests/tests/min_mapped_reads/main.nf.test b/tests/tests/min_mapped_reads/main.nf.test index 49b83ad19..d0e1dfe36 100644 --- a/tests/tests/min_mapped_reads/main.nf.test +++ b/tests/tests/min_mapped_reads/main.nf.test @@ -1,7 +1,7 @@ nextflow_pipeline { name "Test pipeline" - script "../../main.nf" + script "../../../main.nf" tag "rnaseq" tag "PIPELINE" diff --git a/tests/tests/remove_ribo_rna/main.nf.test b/tests/tests/remove_ribo_rna/main.nf.test index 2d9ba1fc4..a242a8da4 100644 --- a/tests/tests/remove_ribo_rna/main.nf.test +++ b/tests/tests/remove_ribo_rna/main.nf.test @@ -1,7 +1,7 @@ nextflow_pipeline { name "Test pipeline" - script "../../main.nf" + script "../../../main.nf" tag "rnaseq" tag "PIPELINE" diff --git a/tests/tests/skip_qc/main.nf.test b/tests/tests/skip_qc/main.nf.test index 84db3c9e8..788ed432e 100644 --- a/tests/tests/skip_qc/main.nf.test +++ b/tests/tests/skip_qc/main.nf.test @@ -1,7 +1,7 @@ nextflow_pipeline { name "Test pipeline" - script "../../main.nf" + script "../../../main.nf" tag "rnaseq" tag "PIPELINE" diff --git a/tests/tests/skip_trimming/main.nf.test b/tests/tests/skip_trimming/main.nf.test index b51fdfa6a..f23703f35 100644 --- a/tests/tests/skip_trimming/main.nf.test +++ b/tests/tests/skip_trimming/main.nf.test @@ -1,7 +1,7 @@ nextflow_pipeline { name "Test pipeline" - script "../../main.nf" + script "../../../main.nf" tag "rnaseq" tag "PIPELINE" From e01e195c8df12df6eca9f3c4ea5d6e5ba7a6804d Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Tue, 9 Apr 2024 10:18:29 +0100 Subject: [PATCH 08/10] Remove r-base from software versions --- tests/tests/default/main.nf.test.snap | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/tests/default/main.nf.test.snap b/tests/tests/default/main.nf.test.snap index 1170c2912..299628d72 100644 --- a/tests/tests/default/main.nf.test.snap +++ b/tests/tests/default/main.nf.test.snap @@ -1,7 +1,7 @@ { "software_versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.19.2}, SAMTOOLS_IDXSTATS={samtools=1.19.2}, SAMTOOLS_INDEX={samtools=1.19.2}, SAMTOOLS_SORT={samtools=1.19.2}, SAMTOOLS_STATS={samtools=1.19.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={r-base=4.3.2, bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.3}, Workflow={nf-core/rnaseq=v3.15.0dev}}" + "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.19.2}, SAMTOOLS_IDXSTATS={samtools=1.19.2}, SAMTOOLS_INDEX={samtools=1.19.2}, SAMTOOLS_SORT={samtools=1.19.2}, SAMTOOLS_STATS={samtools=1.19.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.3}, Workflow={nf-core/rnaseq=v3.15.0dev}}" ], "meta": { "nf-test": "0.8.4", From 6e6a25425af1327de1842f1bea666dc7401121ec Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Tue, 9 Apr 2024 10:20:30 +0100 Subject: [PATCH 09/10] Move repo tests config to tests/config --- nf-test.config | 2 +- tests/nextflow.config | 41 ----------------------------------------- 2 files changed, 1 insertion(+), 42 deletions(-) delete mode 100644 tests/nextflow.config diff --git a/nf-test.config b/nf-test.config index f126b460a..59b868801 100644 --- a/nf-test.config +++ b/nf-test.config @@ -6,7 +6,7 @@ config { workDir System.getenv("NFT_WORKDIR") ?: ".nf-test" // Location of an optional nextflow.config file specific for executing pipeline tests - configFile "tests/nextflow.config" + configFile "tests/config/nextflow.config" profile "test" } diff --git a/tests/nextflow.config b/tests/nextflow.config deleted file mode 100644 index 6bf8f2929..000000000 --- a/tests/nextflow.config +++ /dev/null @@ -1,41 +0,0 @@ -/* -======================================================================================== - Nextflow config file for running tests -======================================================================================== -*/ - -params { - // Base directory for nf-core/modules test data - modules_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/modules/' - - // Base directory for nf-core/rnaseq test data - pipelines_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/' - - // for hisat2 - hisat2_build_memory = '3.GB' - - validationSchemaIgnoreParams = 'genomes,igenomes_base,modules_testdata_base_path,pipelines_testdata_base_path' - - // TODO: check if we rather do this or disable publishdir for all processes when testing modules/subworkflows - outdir = 'results' -} - -// Impose sensible resource limits for testing -process { - withName: '.*' { - cpus = 2 - memory = 3.GB - time = 2.h - } -} - -// Impose same minimum Nextflow version as the pipeline for testing -manifest { - nextflowVersion = '!>=23.04.0' -} - -// Disable all Nextflow reporting options -timeline { enabled = false } -report { enabled = false } -trace { enabled = false } -dag { enabled = false } From 76473d28d23ebb4320e39d433f9e6ec955f020b9 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Tue, 9 Apr 2024 11:57:33 +0100 Subject: [PATCH 10/10] Add test config --- tests/config/nextflow.config | 41 ++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 tests/config/nextflow.config diff --git a/tests/config/nextflow.config b/tests/config/nextflow.config new file mode 100644 index 000000000..6bf8f2929 --- /dev/null +++ b/tests/config/nextflow.config @@ -0,0 +1,41 @@ +/* +======================================================================================== + Nextflow config file for running tests +======================================================================================== +*/ + +params { + // Base directory for nf-core/modules test data + modules_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/modules/' + + // Base directory for nf-core/rnaseq test data + pipelines_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/' + + // for hisat2 + hisat2_build_memory = '3.GB' + + validationSchemaIgnoreParams = 'genomes,igenomes_base,modules_testdata_base_path,pipelines_testdata_base_path' + + // TODO: check if we rather do this or disable publishdir for all processes when testing modules/subworkflows + outdir = 'results' +} + +// Impose sensible resource limits for testing +process { + withName: '.*' { + cpus = 2 + memory = 3.GB + time = 2.h + } +} + +// Impose same minimum Nextflow version as the pipeline for testing +manifest { + nextflowVersion = '!>=23.04.0' +} + +// Disable all Nextflow reporting options +timeline { enabled = false } +report { enabled = false } +trace { enabled = false } +dag { enabled = false }