Replicates samplesheet test

assets/samplesheet_replicates.csv

@@ -0,0 +1,5 @@
+sample,fastq_1,fastq_2,genome
+SRR389222,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz,,
+SRR389222,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub2.fastq.gz,,
+SRR389222,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub3.fastq.gz,,
+Ecoli_10K_methylated,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz,

conf/test.config

@@ -28,9 +28,5 @@ process {
         memory: '15.GB',
         time: '1.h'
     ]
-
-    withName: PRESEQ_LCEXTRAP {
-        errorStrategy = 'ignore'
-    }
 }
 

conf/test_full.config

@@ -18,9 +18,3 @@ params {
     input  = "${params.pipelines_testdata_base_path}/samplesheet/samplesheet_full.csv"
     genome = 'GRCh38'
 }
-
-process {
-    withName: PRESEQ_LCEXTRAP {
-        errorStrategy = 'ignore'
-    }
-}

tests/bismark_cat_fastq_skip_trimming_skip_deduplication.nf.test

@@ -0,0 +1,42 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf"
+    script "../main.nf"
+    config "./nextflow.config"
+
+    test("Params: bismark | CAT_FASTQ | skip_trimming | skip_deduplication") {
+        when {
+            params {
+                input              = "${projectDir}/assets/samplesheet_replicates.csv"
+                outdir             = "$outputDir"
+                skip_trimming      = true
+                skip_deduplication = true
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // bam_files: All bam files
+            def bam_files  = getAllFilesFromDir(params.outdir, include: ['**/*.bam'])
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"),
+                    // All stable path name
+                    stable_name,
+                    // All files with stable contents
+                    stable_path,
+                    // All bam files
+                    bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] }
+                ).match() }
+            )
+        }
+    }
+
+}

tests/bismark_run_qualimap.nf.test.snap

@@ -556,7 +556,7 @@
                 "genome_mapping_quality_histogram.png:md5,74776b1e7e8c8876af1cf89d9dbb5f31",
                 "genome_reads_content_per_read_position.png:md5,c6920dc357411880132c207c7d0aa68d",
                 "genome_uniq_read_starts_histogram.png:md5,8f7549a63eee3d3f022699aaa5bb858d",
-                "qualimapReport.html:md5,bbc015c0d1f3c41a08c82fb7a6839039",
+                "qualimapReport.html:md5,e2274cb2b25345dc7b76b89fa7730a04",
                 "coverage_across_reference.txt:md5,2bb9eb828acfd71ace8f1e6a2ca124b4",
                 "coverage_histogram.txt:md5,6ee761660a6072e5b6b75b7fe8d2c69e",
                 "duplication_rate_histogram.txt:md5,d5f25ad3572b98880b6904dcf4b3ed25",
@@ -601,7 +601,7 @@
                 "genome_mapping_quality_histogram.png:md5,7ba0db9375d09fd49946b9bca4ba92b4",
                 "genome_reads_content_per_read_position.png:md5,1a6a7717ea948d2518808f72f58ffdef",
                 "genome_uniq_read_starts_histogram.png:md5,395413ab1d0e10af72b116fd8cb12685",
-                "qualimapReport.html:md5,1fe626f663d66a7ce0c6e1e0207d829d",
+                "qualimapReport.html:md5,e841c7cc3bb8beca037a98e55d3d7a12",
                 "coverage_across_reference.txt:md5,081ddc3be3349b0c57d9676c03d84803",
                 "coverage_histogram.txt:md5,47b75803a6925e883e254bb91d6220d2",
                 "duplication_rate_histogram.txt:md5,3d06b34e40d1fdeb55c4ad19dc6ddad1",
@@ -643,7 +643,7 @@
                 "genome_mapping_quality_histogram.png:md5,017451f46bc875ac58e7906bf7979956",
                 "genome_reads_content_per_read_position.png:md5,fd94ec5bfe5ca4adfa6ebdeaebe25157",
                 "genome_uniq_read_starts_histogram.png:md5,2f2555ef88c3bda05315469e684f5b19",
-                "qualimapReport.html:md5,af640b29bd28f80bdc0ab6fe7d9c97f4",
+                "qualimapReport.html:md5,ef10a67a886f948f244a74506ea96071",
                 "coverage_across_reference.txt:md5,a76b3da0ebb2f8bd6c36ec1902cf13f2",
                 "coverage_histogram.txt:md5,ca854c05e9619233b7d95d44051cab80",
                 "duplication_rate_histogram.txt:md5,530bb05c648d610227e121e1e74f41f8",
@@ -685,7 +685,7 @@
                 "genome_mapping_quality_histogram.png:md5,a22ee10fcb9e34a84f607b089855fb92",
                 "genome_reads_content_per_read_position.png:md5,9fa406f353148448f6b9ac11880bc6de",
                 "genome_uniq_read_starts_histogram.png:md5,cf2fe3e30e11e7d6eb2db679cd12dc03",
-                "qualimapReport.html:md5,c8114fbb2a63da68111f0d4cbb8a1973",
+                "qualimapReport.html:md5,c600f4100ccb57a26ac2132c575f8e3e",
                 "coverage_across_reference.txt:md5,fb9c989fc6c15d0a8fd0a58b8d3c20ce",
                 "coverage_histogram.txt:md5,8a3f45461442657433914c6a5ecb1301",
                 "duplication_rate_histogram.txt:md5,ec9a705fd3a300b126d556afa14c326b",
@@ -752,6 +752,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-28T09:47:26.992492832"
+        "timestamp": "2024-11-30T14:38:57.39810446"
     }
-}
+}

workflows/methylseq/main.nf

@@ -36,6 +36,14 @@ workflow METHYLSEQ {
 
     main:
 
+    ch_fastq         = Channel.empty()
+    ch_fastqc_html   = Channel.empty()
+    ch_fastqc_zip    = Channel.empty()
+    ch_reads         = Channel.empty()
+    ch_bam           = Channel.empty()
+    ch_bai           = Channel.empty()
+    ch_qualimap      = Channel.empty()
+    ch_preseq        = Channel.empty()
     ch_multiqc_files = Channel.empty()
 
     //
@@ -64,6 +72,8 @@ workflow METHYLSEQ {
     FASTQC (
         ch_fastq
     )
+    ch_fastqc_html   = FASTQC.out.html
+    ch_fastqc_zip    = FASTQC.out.zip
     ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{ meta, zip -> zip })
     ch_versions      = ch_versions.mix(FASTQC.out.versions.first())
 
@@ -74,10 +84,10 @@ workflow METHYLSEQ {
         TRIMGALORE(
             ch_fastq
         )
-        reads       = TRIMGALORE.out.reads
+        ch_reads    = TRIMGALORE.out.reads
         ch_versions = ch_versions.mix(TRIMGALORE.out.versions.first())
     } else {
-        reads       = ch_fastq
+        ch_reads    = ch_fastq
     }
 
     //
@@ -90,28 +100,30 @@ workflow METHYLSEQ {
         // Run Bismark alignment + downstream processing
         //
         FASTQ_ALIGN_DEDUP_BISMARK (
-            reads,
+            ch_reads,
             ch_fasta,
             ch_bismark_index,
             params.skip_deduplication || params.rrbs,
             params.cytosine_report || params.nomeseq
         )
         ch_versions    = ch_versions.mix(FASTQ_ALIGN_DEDUP_BISMARK.out.versions.unique{ it.baseName })
-        ch_bam         = FASTQ_ALIGN_DEDUP_BISMARK.out.bam
+        ch_bam = FASTQ_ALIGN_DEDUP_BISMARK.out.bam
+        ch_bai = FASTQ_ALIGN_DEDUP_BISMARK.out.bai
         ch_aligner_mqc = FASTQ_ALIGN_DEDUP_BISMARK.out.multiqc
     }
     // Aligner: bwameth
     else if ( params.aligner == 'bwameth' ){
 
         FASTQ_ALIGN_DEDUP_BWAMETH (
-            reads,
+            ch_reads,
             ch_fasta,
             ch_fasta_index.map{ index -> [ [:], index ]},
             ch_bwameth_index,
             params.skip_deduplication || params.rrbs,
         )
         ch_versions    = ch_versions.mix(FASTQ_ALIGN_DEDUP_BWAMETH.out.versions.unique{ it.baseName })
-        ch_bam         = FASTQ_ALIGN_DEDUP_BWAMETH.out.bam
+        ch_bam = FASTQ_ALIGN_DEDUP_BWAMETH.out.bam
+        ch_bai = FASTQ_ALIGN_DEDUP_BWAMETH.out.bai
         ch_aligner_mqc = FASTQ_ALIGN_DEDUP_BWAMETH.out.multiqc
     }
 
@@ -124,6 +136,7 @@ workflow METHYLSEQ {
             ch_bam,
             params.bamqc_regions_file ? Channel.fromPath( params.bamqc_regions_file, checkIfExists: true ).toList() : []
         )
+        ch_qualimap = QUALIMAP_BAMQC.out.results
         ch_versions = ch_versions.mix(QUALIMAP_BAMQC.out.versions.first())
     }
 
@@ -135,6 +148,7 @@ workflow METHYLSEQ {
         PRESEQ_LCEXTRAP (
             ch_bam
         )
+        ch_preseq   = PRESEQ_LCEXTRAP.out.lc_extrap
         ch_versions = ch_versions.mix(PRESEQ_LCEXTRAP.out.versions.first())
     }
 
@@ -199,6 +213,10 @@ workflow METHYLSEQ {
     )
 
     emit:
+    bam            = ch_bam                      // channel: [ path(bam) ]
+    bai            = ch_bai                      // channel: [ path(bai) ]
+    qualimap       = ch_qualimap                 // channel: [ path(qualimap) ]
+    preseq         = ch_preseq                   // channel: [ path(preseq) ]
     multiqc_report = MULTIQC.out.report.toList() // channel: [ path(multiqc_report.html )  ]
     versions       = ch_versions                 // channel: [ path(versions.yml) ]
 }