From 6f3b92567947e6e1f9802017145644e891e768d0 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 9 Apr 2024 17:28:24 +0100
Subject: [PATCH 1/3] Add psueudoaligner pipeline level tests to test suite

---
 .github/workflows/ci.yml               | 22 --------------------
 tests/tests/kallisto/main.nf.test      | 28 ++++++++++++++++++++++++++
 tests/tests/kallisto/main.nf.test.snap | 12 +++++++++++
 tests/tests/salmon/main.nf.test        | 28 ++++++++++++++++++++++++++
 tests/tests/salmon/main.nf.test.snap   | 12 +++++++++++
 5 files changed, 80 insertions(+), 22 deletions(-)
 create mode 100644 tests/tests/kallisto/main.nf.test
 create mode 100644 tests/tests/kallisto/main.nf.test.snap
 create mode 100644 tests/tests/salmon/main.nf.test
 create mode 100644 tests/tests/salmon/main.nf.test.snap

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index a61d32c16..2bcea8bc5 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -19,28 +19,6 @@ concurrency:
   group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
   cancel-in-progress: true
 jobs:
-  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]') }}
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        parameters:
-          - "--pseudo_aligner salmon --skip_qc"
-          - "--pseudo_aligner salmon --skip_alignment --skip_pseudo_alignment"
-          - "--pseudo_aligner kallisto --skip_qc"
-          - "--pseudo_aligner kallisto --skip_alignment --skip_pseudo_alignment"
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v4
-
-      - name: Setup Nextflow
-        uses: nf-core/setup-nextflow@v1.5
-
-      - name: Run pipeline with Salmon or Kallisto and various parameters
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.parameters }} --outdir ./results
-
   nf-test-changes:
     name: Check for changes
     runs-on: ubuntu-latest
diff --git a/tests/tests/kallisto/main.nf.test b/tests/tests/kallisto/main.nf.test
new file mode 100644
index 000000000..e36b4cb9c
--- /dev/null
+++ b/tests/tests/kallisto/main.nf.test
@@ -0,0 +1,28 @@
+nextflow_pipeline {
+
+    name "Test pipeline"
+    script "../../../main.nf"
+    tag "rnaseq"
+    tag "PIPELINE"
+
+    test("Default profile test") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+                input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/samplesheet/v3.10/samplesheet_test.csv'
+                pseudo_aligner = 'kallisto'
+                skip_qc = true
+                skip_alignment = true
+            }
+        }
+
+        then {
+            assert workflow.success
+
+            assertAll(
+                { assert snapshot(UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml")).match("software_versions") }
+            )
+        }
+    }
+}
diff --git a/tests/tests/kallisto/main.nf.test.snap b/tests/tests/kallisto/main.nf.test.snap
new file mode 100644
index 000000000..299628d72
--- /dev/null
+++ b/tests/tests/kallisto/main.nf.test.snap
@@ -0,0 +1,12 @@
+{
+    "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={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",
+            "nextflow": "24.01.0"
+        },
+        "timestamp": "2024-03-04T12:40:26.161319"
+    }
+}
\ No newline at end of file
diff --git a/tests/tests/salmon/main.nf.test b/tests/tests/salmon/main.nf.test
new file mode 100644
index 000000000..72f8fd4e7
--- /dev/null
+++ b/tests/tests/salmon/main.nf.test
@@ -0,0 +1,28 @@
+nextflow_pipeline {
+
+    name "Test pipeline"
+    script "../../../main.nf"
+    tag "rnaseq"
+    tag "PIPELINE"
+
+    test("Default profile test") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+                input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/samplesheet/v3.10/samplesheet_test.csv'
+                pseudo_aligner = 'salmon'
+                skip_qc = true
+                skip_alignment = true
+            }
+        }
+
+        then {
+            assert workflow.success
+
+            assertAll(
+                { assert snapshot(UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml")).match("software_versions") }
+            )
+        }
+    }
+}
diff --git a/tests/tests/salmon/main.nf.test.snap b/tests/tests/salmon/main.nf.test.snap
new file mode 100644
index 000000000..299628d72
--- /dev/null
+++ b/tests/tests/salmon/main.nf.test.snap
@@ -0,0 +1,12 @@
+{
+    "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={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",
+            "nextflow": "24.01.0"
+        },
+        "timestamp": "2024-03-04T12:40:26.161319"
+    }
+}
\ No newline at end of file

From eea41e7e68a750a0bcac37cd8eb37fa6eb6d98af Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 9 Apr 2024 17:30:48 +0100
Subject: [PATCH 2/3] CI fixup

---
 .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 2bcea8bc5..947b1a745 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -155,7 +155,7 @@ jobs:
 
   confirm-pass:
     runs-on: ubuntu-latest
-    needs: [test, pseudo]
+    needs: [test]
     if: always()
     steps:
       - name: All tests ok

From 4299d4714062e7637d008825e9f6e1a0d65c1cba Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Wed, 10 Apr 2024 10:32:14 +0100
Subject: [PATCH 3/3] Correct snaps for pseudoalignment

---
 tests/tests/kallisto/main.nf.test.snap | 6 +++---
 tests/tests/salmon/main.nf.test.snap   | 6 +++---
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/tests/tests/kallisto/main.nf.test.snap b/tests/tests/kallisto/main.nf.test.snap
index 299628d72..2deb6fb8d 100644
--- a/tests/tests/kallisto/main.nf.test.snap
+++ b/tests/tests/kallisto/main.nf.test.snap
@@ -1,12 +1,12 @@
 {
     "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={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}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, CUSTOM_TX2GENE={python=3.9.5}, 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}, KALLISTO_INDEX={kallisto=0.48.0}, KALLISTO_QUANT={kallisto=0.48.0}, SALMON_QUANT={salmon=1.10.1}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UNTAR_SALMON_INDEX={untar=1.3}, Workflow={nf-core/rnaseq=v3.15.0dev}}"
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.01.0"
+            "nextflow": "23.10.1"
         },
-        "timestamp": "2024-03-04T12:40:26.161319"
+        "timestamp": "2024-04-10T10:13:15.867122"
     }
 }
\ No newline at end of file
diff --git a/tests/tests/salmon/main.nf.test.snap b/tests/tests/salmon/main.nf.test.snap
index 299628d72..831b1e14b 100644
--- a/tests/tests/salmon/main.nf.test.snap
+++ b/tests/tests/salmon/main.nf.test.snap
@@ -1,12 +1,12 @@
 {
     "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={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}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, CUSTOM_TX2GENE={python=3.9.5}, 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}, SALMON_QUANT={salmon=1.10.1}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UNTAR_SALMON_INDEX={untar=1.3}, Workflow={nf-core/rnaseq=v3.15.0dev}}"
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.01.0"
+            "nextflow": "23.10.1"
         },
-        "timestamp": "2024-03-04T12:40:26.161319"
+        "timestamp": "2024-04-10T10:31:20.108379"
     }
 }
\ No newline at end of file