Merge branch 'dev' into new_testing_by_file_matrix

.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]') }}
@@ -213,7 +146,7 @@ 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

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"
 }

tests/main.nf.test → tests/tests/default/main.nf.test

@@ -1,11 +1,11 @@
 nextflow_pipeline {
 
     name "Test pipeline"
-    script "../main.nf"
+    script "../../../main.nf"
     tag "rnaseq"
     tag "PIPELINE"
 
-    test("Run with profile test") {
+    test("Default profile test") {
 
         when {
             params {

tests/main.nf.test.snap → 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",

tests/tests/featurecounts/main.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
+        }
+    }
+}

tests/tests/min_mapped_reads/main.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
+        }
+    }
+}

tests/tests/remove_ribo_rna/main.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
+        }
+    }
+}

tests/tests/skip_qc/main.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
+        }
+    }
+}

tests/tests/skip_trimming/main.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
+        }
+    }
+}