Merge pull request #152

Refactor tests
nf-core · Aug 5, 2024 · 98d646b · 98d646b
2 parents 6592199 + 04d4162
commit 98d646b
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Showing 24 changed files with 648 additions and 550 deletions.
diff --git a/assets/small_samplesheet.csv b/assets/small_samplesheet.csv
@@ -0,0 +1,4 @@
+sample,fastq_1,fastq_2
+cd4_REP1,https://raw.githubusercontent.com/nf-core/test-datasets/nascent/testdata/SRX882903_T1.fastq.gz,
+cd4_REP2,https://raw.githubusercontent.com/nf-core/test-datasets/nascent/testdata/SRX882903_T2.fastq.gz,
+jurkat,https://raw.githubusercontent.com/nf-core/test-datasets/nascent/testdata/SRX882904_T1.fastq.gz,
diff --git a/nf-test.config b/nf-test.config
@@ -3,5 +3,8 @@ config {
     testsDir "."
     workDir System.getenv("NFT_WORKDIR") ?: ".nf-test"
     configFile "tests/nextflow.config"
+    plugins {
+        load "nft-bam@0.3.0"
+    }
 
 }
diff --git a/tests/lib/UTILS.groovy b/tests/lib/UTILS.groovy
@@ -0,0 +1,11 @@
+// Function to remove Nextflow version from pipeline_software_mqc_versions.yml
+
+class UTILS {
+    public static String removeNextflowVersion(pipeline_software_mqc_versions) {
+        def softwareVersions = path(pipeline_software_mqc_versions).yaml
+        if (softwareVersions.containsKey("Workflow")) {
+            softwareVersions.Workflow.remove("Nextflow")
+        }
+        return softwareVersions
+    }
+}
diff --git a/tests/nextflow.config b/tests/nextflow.config
@@ -30,7 +30,7 @@ dag      { enabled = false }
 // HACK Hard code all the params for now
 params {
     // Input data
-    input = "${projectDir}/assets/samplesheet.csv"
+    input = "${projectDir}/assets/small_samplesheet.csv"
 
     // Genome references
     fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/nascent/reference/GRCh38_chr21.fa'

diff --git a/workflows/tests/aligner/bowtie2.nf.test b/workflows/tests/aligner/bowtie2.nf.test
@@ -0,0 +1,48 @@
+nextflow_pipeline {
+
+    name "Bowtie2"
+    script "../../../main.nf"
+    tag "aligner"
+    tag "bowtie2"
+
+    test("Should run with defaults") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+                aligner = "bowtie2"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml")).match("software_versions") },
+                { assert snapshot(
+                    workflow.trace.tasks().size(),
+                    path("$outputDir/bbmap").list(),
+                    // BUG https://github.com/nf-core/nascent/issues/102
+                    // path("$outputDir/bedtools").list(),
+                    // FIXME gtf2bed isn't deterministic
+                    // path("$outputDir/bwa/featurecounts/gene").list(),
+                    // FIXME cd4 isn't deterministic
+                    // path("$outputDir/bwa/featurecounts/predicted").list(),
+                    // path("$outputDir/deeptools").list(),
+                    // path("$outputDir/fastp/*.json").list(),
+                    // FIXME gtf2bed isn't deterministic
+                    // path("$outputDir/gtf2bed").list(),
+                    path("$outputDir/homer/cd4.bed"),
+                    path("$outputDir/homer/jurkat.bed"),
+                    // FIXME https://github.com/nf-core/nascent/issues/148
+                    // path("$outputDir/preseq").list(),
+                    // path("$outputDir/rseqc").list(),
+                    // FIXME Bowtie2 isn't deterministic
+                    bam("$outputDir/samtools/cd4_REP1.sorted.bam").getHeaderMD5(),
+                    bam("$outputDir/samtools/cd4_REP2.sorted.bam").getHeaderMD5(),
+                    bam("$outputDir/samtools/jurkat.sorted.bam").getHeaderMD5(),
+                ).match("output_files")
+                }
+            )
+        }
+    }
+}
diff --git a/workflows/tests/aligner/bowtie2.nf.test.snap b/workflows/tests/aligner/bowtie2.nf.test.snap
@@ -0,0 +1,35 @@
+{
+    "output_files": {
+        "content": [
+            75,
+            [
+                "cd4_REP1.coverage.hist.txt:md5,ffd8c0a94869dd782779fc871a9b781a",
+                "cd4_REP1.coverage.stats.txt:md5,bebdef1adcce4296878f8699a0f5cb32",
+                "cd4_REP2.coverage.hist.txt:md5,6e0ca13df7b06ff6a81fb21596df4ca4",
+                "cd4_REP2.coverage.stats.txt:md5,ffb701c2be33360a96ce85b1330b13f8",
+                "jurkat.coverage.hist.txt:md5,656e30e8c4bd12e45a036c62c18730c1",
+                "jurkat.coverage.stats.txt:md5,627f0ec96ea9bdbd7f41b09b64c389d6"
+            ],
+            "cd4.bed:md5,c311e32ebdca7f3e978a271407de7241",
+            "jurkat.bed:md5,5e170e72c4e2b27a7bb0a6de7b735c1c",
+            "7945f971cd63ad99ff2d9cc81e19ea39",
+            "43982cec9077e7030428267841cf04ef",
+            "8813c6dd42cabd94042f4f9e4aee3560"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-03T22:17:27.92555495"
+    },
+    "software_versions": {
+        "content": [
+            "{BBMAP_PILEUP={bbmap=39.01, samtools=1.16.1, pigz=2.6}, BEDTOOLS_GENOMECOV_MINUS={bedtools=2.31.1}, BEDTOOLS_GENOMECOV_PLUS={bedtools=2.31.1}, BEDTOOLS_INTERSECT={bedtools=2.31.1}, BEDTOOLS_INTERSECT_FILTER={bedtools=2.31.1}, BOWTIE2_ALIGN={bowtie2=2.5.2, samtools=1.18, pigz=2.6}, DEEPTOOLS_BAMCOVERAGE_MINUS={deeptools=3.5.1}, DEEPTOOLS_BAMCOVERAGE_PLUS={deeptools=3.5.1}, FASTP={fastp=0.23.4}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, HOMER_MAKETAGDIRECTORY={homer=4.11, samtools=1.11}, PRESEQ_CCURVE={preseq=3.1.1}, PRESEQ_LCEXTRAP={preseq=3.1.1}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SUBREAD_FEATURECOUNTS_GENE={subread=2.0.1}, Workflow={nf-core/nascent=v2.3.0dev}}"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-03T21:20:15.261777672"
+    }
+}
diff --git a/workflows/tests/aligner/bwa.nf.test b/workflows/tests/aligner/bwa.nf.test
@@ -0,0 +1,97 @@
+nextflow_pipeline {
+
+    name "BWA"
+    script "../../../main.nf"
+    tag "aligner"
+    tag "bwa"
+
+    test("Should run with defaults") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+                aligner = "bwa"
+                input = "${projectDir}/assets/samplesheet.csv"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml")).match("software_versions") },
+                { assert snapshot(
+                    workflow.trace.tasks().size(),
+                    path("$outputDir/bbmap").list(),
+                    // BUG https://github.com/nf-core/nascent/issues/102
+                    // path("$outputDir/bedtools").list(),
+                    // FIXME gtf2bed isn't deterministic
+                    // path("$outputDir/bwa/featurecounts/gene").list(),
+                    // FIXME cd4 isn't deterministic
+                    // path("$outputDir/bwa/featurecounts/predicted").list(),
+                    // path("$outputDir/deeptools").list(),
+                    // path("$outputDir/fastp/*.json").list(),
+                    // FIXME gtf2bed isn't deterministic
+                    // path("$outputDir/gtf2bed").list(),
+                    path("$outputDir/homer/cd4.bed"),
+                    path("$outputDir/homer/jurkat.bed"),
+                    // FIXME https://github.com/nf-core/nascent/issues/148
+                    // path("$outputDir/preseq").list(),
+                    // path("$outputDir/rseqc").list(),
+                    bam("$outputDir/samtools/cd4_REP1.sorted.bam").getSamLinesMD5(),
+                    bam("$outputDir/samtools/cd4_REP2.sorted.bam").getSamLinesMD5(),
+                    bam("$outputDir/samtools/cd4_REP3.sorted.bam").getSamLinesMD5(),
+                    bam("$outputDir/samtools/cd4_REP4.sorted.bam").getSamLinesMD5(),
+                    bam("$outputDir/samtools/jurkat_REP1.sorted.bam").getSamLinesMD5(),
+                    bam("$outputDir/samtools/jurkat_REP2.sorted.bam").getSamLinesMD5(),
+                ).match("output_files")
+                }
+            )
+        }
+    }
+
+    def igenomes_base = 's3://ngi-igenomes/igenomes'
+
+    // https://github.com/nf-core/nascent/issues/106
+    test("Should work with BWA Index") {
+        // FIXME PINTS Fails because it doesn't find anything.
+        config '../skip_pints.config'
+        when {
+            params {
+                outdir = "$outputDir"
+                aligner = "bwa"
+                // TODO Update these to human
+                bwa_index = "${igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0/"
+                fasta = "${igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa"
+                gtf = "${igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.gtf"
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert snapshot(
+                workflow.trace.tasks().size(),
+            ).match()
+        }
+    }
+
+    // https://github.com/nf-core/nascent/issues/119
+    test("Should work with gzipped references") {
+        config '../skip_gzip.config'
+        when {
+            params {
+                outdir = "$outputDir"
+                aligner = "bwa"
+                fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/genome.fasta.gz'
+                gtf = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/genes.gtf.gz'
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert snapshot(
+                workflow.trace.tasks().size(),
+            ).match()
+        }
+
+    }
+}
diff --git a/workflows/tests/aligner/bwa.nf.test.snap b/workflows/tests/aligner/bwa.nf.test.snap
@@ -0,0 +1,64 @@
+{
+    "output_files": {
+        "content": [
+            134,
+            [
+                "cd4_REP1.coverage.hist.txt:md5,7cbb473be8d3b32ff2e52fdf4e5d10d2",
+                "cd4_REP1.coverage.stats.txt:md5,f1471b61ac17dba283d80e08450c7e55",
+                "cd4_REP2.coverage.hist.txt:md5,8d5258a0882494bc4e3f1aa6aa5ed685",
+                "cd4_REP2.coverage.stats.txt:md5,3cdb4473211f9da44166ffa6aaa5b602",
+                "cd4_REP3.coverage.hist.txt:md5,4a8397c1ea08f35ca7046e3c2c014a08",
+                "cd4_REP3.coverage.stats.txt:md5,b88592b469d504a93f2389255ac15f38",
+                "cd4_REP4.coverage.hist.txt:md5,d2cbf89e1f753d99bcd03b4e472270dd",
+                "cd4_REP4.coverage.stats.txt:md5,4c2b5fe6793aab8560cc87c176ac06ab",
+                "jurkat_REP1.coverage.hist.txt:md5,71a893d9d1d55fd47399f6d47b628d6e",
+                "jurkat_REP1.coverage.stats.txt:md5,381c69a30099d82066a959deab1a2569",
+                "jurkat_REP2.coverage.hist.txt:md5,d124bdadaf2dc5cdd9e3db5a1ab4c588",
+                "jurkat_REP2.coverage.stats.txt:md5,b1940346719e4070091f2eef6e508f49"
+            ],
+            "cd4.bed:md5,ab94918610a560772fdbec591200295f",
+            "jurkat.bed:md5,41908723fa423a78476feb2e7627a3a4",
+            "c529a16c839e85e119b98354f109352d",
+            "9e63b682af88fa902cf92b5c485845b1",
+            "2aa200bbbce374ec7dedb9b46ce4aae1",
+            "122274730dd5386e1b26c174df886a8b",
+            "c2adf5327ff6d4edda2fdad00c7cb9bf",
+            "63fea3b1e2e08e5f6fdf3f7ba0aa7818"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-03T08:58:17.037588077"
+    },
+    "Should work with gzipped references": {
+        "content": [
+            53
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-03T07:39:38.160960801"
+    },
+    "software_versions": {
+        "content": [
+            "{BBMAP_PILEUP={bbmap=39.01, samtools=1.16.1, pigz=2.6}, BEDTOOLS_GENOMECOV_MINUS={bedtools=2.31.1}, BEDTOOLS_GENOMECOV_PLUS={bedtools=2.31.1}, BEDTOOLS_INTERSECT={bedtools=2.31.1}, BEDTOOLS_INTERSECT_FILTER={bedtools=2.31.1}, BWA_MEM={bwa=0.7.18-r1243-dirty, samtools=1.2}, DEEPTOOLS_BAMCOVERAGE_MINUS={deeptools=3.5.1}, DEEPTOOLS_BAMCOVERAGE_PLUS={deeptools=3.5.1}, FASTP={fastp=0.23.4}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, HOMER_MAKETAGDIRECTORY={homer=4.11, samtools=1.11}, PINTS_CALLER={python=3.10.6, pints=1.1.8}, PRESEQ_CCURVE={preseq=3.1.1}, PRESEQ_LCEXTRAP={preseq=3.1.1}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SUBREAD_FEATURECOUNTS_GENE={subread=2.0.1}, Workflow={nf-core/nascent=v2.3.0dev}}"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-03T07:37:00.256122533"
+    },
+    "Should work with BWA Index": {
+        "content": [
+            59
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-03T07:38:19.100788775"
+    }
+}
diff --git a/workflows/tests/aligner/bwamem2.nf.test b/workflows/tests/aligner/bwamem2.nf.test
@@ -0,0 +1,45 @@
+nextflow_pipeline {
+
+    name "bwamem2"
+    script "../../../main.nf"
+
+    test("Should run with defaults") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+                aligner = "bwamem2"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml")).match("software_versions") },
+                { assert snapshot(
+                    workflow.trace.tasks().size(),
+                    path("$outputDir/bbmap").list(),
+                    // BUG https://github.com/nf-core/nascent/issues/102
+                    // path("$outputDir/bedtools").list(),
+                    // FIXME gtf2bed isn't deterministic
+                    // path("$outputDir/bwa/featurecounts/gene").list(),
+                    // FIXME cd4 isn't deterministic
+                    // path("$outputDir/bwa/featurecounts/predicted").list(),
+                    // path("$outputDir/deeptools").list(),
+                    // path("$outputDir/fastp/*.json").list(),
+                    // FIXME gtf2bed isn't deterministic
+                    // path("$outputDir/gtf2bed").list(),
+                    path("$outputDir/homer/cd4.bed"),
+                    path("$outputDir/homer/jurkat.bed"),
+                    // FIXME https://github.com/nf-core/nascent/issues/148
+                    // path("$outputDir/preseq").list(),
+                    // path("$outputDir/rseqc").list(),
+                    bam("$outputDir/samtools/cd4_REP1.sorted.bam").getSamLinesMD5(),
+                    bam("$outputDir/samtools/cd4_REP2.sorted.bam").getSamLinesMD5(),
+                    bam("$outputDir/samtools/jurkat.sorted.bam").getSamLinesMD5(),
+                ).match("output_files")
+                }
+            )
+        }
+    }
+}
diff --git a/workflows/tests/aligner/bwamem2.nf.test.snap b/workflows/tests/aligner/bwamem2.nf.test.snap
@@ -0,0 +1,35 @@
+{
+    "output_files": {
+        "content": [
+            77,
+            [
+                "cd4_REP1.coverage.hist.txt:md5,7cbb473be8d3b32ff2e52fdf4e5d10d2",
+                "cd4_REP1.coverage.stats.txt:md5,f1471b61ac17dba283d80e08450c7e55",
+                "cd4_REP2.coverage.hist.txt:md5,8d5258a0882494bc4e3f1aa6aa5ed685",
+                "cd4_REP2.coverage.stats.txt:md5,3cdb4473211f9da44166ffa6aaa5b602",
+                "jurkat.coverage.hist.txt:md5,71a893d9d1d55fd47399f6d47b628d6e",
+                "jurkat.coverage.stats.txt:md5,381c69a30099d82066a959deab1a2569"
+            ],
+            "cd4.bed:md5,b55e5290d78941f36c3d1ecfef8e0062",
+            "jurkat.bed:md5,383cfaf10535dbe5d7f47607e345f4cb",
+            "c529a16c839e85e119b98354f109352d",
+            "9e63b682af88fa902cf92b5c485845b1",
+            "c2adf5327ff6d4edda2fdad00c7cb9bf"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-03T10:28:23.205786296"
+    },
+    "software_versions": {
+        "content": [
+            "{BBMAP_PILEUP={bbmap=39.01, samtools=1.16.1, pigz=2.6}, BEDTOOLS_GENOMECOV_MINUS={bedtools=2.31.1}, BEDTOOLS_GENOMECOV_PLUS={bedtools=2.31.1}, BEDTOOLS_INTERSECT={bedtools=2.31.1}, BEDTOOLS_INTERSECT_FILTER={bedtools=2.31.1}, BWAMEM2_MEM={bwamem2=2.2.1, samtools=1.19.2}, DEEPTOOLS_BAMCOVERAGE_MINUS={deeptools=3.5.1}, DEEPTOOLS_BAMCOVERAGE_PLUS={deeptools=3.5.1}, FASTP={fastp=0.23.4}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, HOMER_MAKETAGDIRECTORY={homer=4.11, samtools=1.11}, PINTS_CALLER={python=3.10.6, pints=1.1.8}, PRESEQ_CCURVE={preseq=3.1.1}, PRESEQ_LCEXTRAP={preseq=3.1.1}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SUBREAD_FEATURECOUNTS_GENE={subread=2.0.1}, Workflow={nf-core/nascent=v2.3.0dev}}"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-01T19:59:55.332896924"
+    }
+}