update bclconvert module, as used in nf-core/demultiplex (#1569)

* update bclconvert module, as used in nf-core/demultiplex

* reconfigure test with new test data

* update test

* formatting

* update outputs, update meta

* update module and test

* update test config, test.yml

* fix linting

* emit logs and reports as dir

* fix typo, recreate test.yml

* fix linting

Co-authored-by: CMGG ICT Team <ict@cmgg.be>

modules/bclconvert/main.nf

@@ -1,5 +1,5 @@
 process BCLCONVERT {
-    tag '$samplesheet'
+    tag "$meta.id"
     label 'process_high'
 
     if (params.enable_conda) {
@@ -8,15 +8,17 @@ process BCLCONVERT {
     container "nfcore/bclconvert:3.9.3"
 
     input:
-    path samplesheet
+    tuple val(meta), path(samplesheet), path(run_dir)
-    path run_dir
 
     output:
-    path "*.fastq.gz"               ,emit: fastq
+    tuple val(meta), path("**[!Undetermined]_S*_L00?_R?_00?.fastq.gz")  ,emit: fastq
-    path "Reports/*.{csv,xml,bin}"  ,emit: reports
+    tuple val(meta), path("**_S*_L00?_I?_00?.fastq.gz")                 ,optional:true ,emit: fastq_idx
-    path "Logs/*.{log,txt}"         ,emit: logs
+    tuple val(meta), path("Undetermined_S0_L00?_R?_00?.fastq.gz")       ,emit: undetermined
-    path "InterOp/*.bin"            ,emit: interop
+    tuple val(meta), path("Undetermined_S0_L00?_I?_00?.fastq.gz")       ,optional:true, emit: undetermined_idx
-    path "versions.yml"             ,emit: versions
+    tuple val(meta), path("Reports")                                    ,emit: reports
+    tuple val(meta), path("Logs")                                       ,emit: logs
+    tuple val(meta), path("**.bin")                                     ,emit: interop
+    path("versions.yml")                                                ,emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -25,54 +27,13 @@ process BCLCONVERT {
     def args = task.ext.args ?: ''
 
     """
-    bcl-convert \
+    bcl-convert \\
         $args \\
         --output-directory . \\
         --bcl-input-directory ${run_dir} \\
         --sample-sheet ${samplesheet} \\
         --bcl-num-parallel-tiles ${task.cpus}
 
-    mkdir InterOp
-    cp ${run_dir}/InterOp/*.bin InterOp/
-    mv Reports/*.bin InterOp/
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        bclconvert: \$(bcl-convert -V 2>&1 | head -n 1 | sed 's/^.*Version //')
-    END_VERSIONS
-    """
-
-    stub:
-    """
-    echo "sample1_S1_L001_R1_001" > sample1_S1_L001_R1_001.fastq.gz
-    echo "sample1_S1_L001_R2_001" > sample1_S1_L001_R2_001.fastq.gz
-    echo "sample1_S1_L002_R1_001" > sample1_S1_L002_R1_001.fastq.gz
-    echo "sample1_S1_L002_R2_001" > sample1_S1_L002_R2_001.fastq.gz
-    echo "sample2_S2_L001_R1_001" > sample2_S2_L001_R1_001.fastq.gz
-    echo "sample2_S2_L001_R2_001" > sample2_S2_L001_R2_001.fastq.gz
-    echo "sample2_S2_L002_R1_001" > sample2_S2_L002_R1_001.fastq.gz
-    echo "sample2_S2_L002_R2_001" > sample2_S2_L002_R2_001.fastq.gz
-
-    mkdir Reports
-    echo "Adapter_Metrics" >  Reports/Adapter_Metrics.csv
-    echo "Demultiplex_Stats" >  Reports/Demultiplex_Stats.csv
-    echo "fastq_list" >  Reports/fastq_list.csv
-    echo "Index_Hopping_Counts" >  Reports/Index_Hopping_Counts.csv
-    echo "IndexMetricsOut" >  Reports/IndexMetricsOut.bin
-    echo "Quality_Metrics" >  Reports/Quality_Metrics.csv
-    echo "RunInfo" >  Reports/RunInfo.xml
-    echo "SampleSheet" >  Reports/SampleSheet.csv
-    echo "Top_Unknown_Barcodes" >  Reports/Top_Unknown_Barcodes.csv
-
-    mkdir Logs
-    echo "Errors" > Logs/Errors.log
-    echo "FastqComplete" > Logs/FastqComplete.txt
-    echo "Info" > Logs/Info.log
-    echo "Warnings" > Logs/Warnings.log
-
-    mkdir InterOp/
-    echo "InterOp" > InterOp/InterOp.bin
-
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         bclconvert: \$(bcl-convert -V 2>&1 | head -n 1 | sed 's/^.*Version //')

modules/bclconvert/meta.yml

@@ -12,6 +12,10 @@ tools:
       licence: "ILLUMINA"
 
 input:
+  - meta:
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
   - samplesheet:
       type: file
       description: "Input samplesheet"
@@ -27,8 +31,20 @@ output:
       pattern: "versions.yml"
   - fastq:
       type: file
-      description: Demultiplexed FASTQ files
+      description: Demultiplexed sample FASTQ files
-      pattern: "*.{fastq.gz}"
+      pattern: "**_S*_L00?_R?_00?.fastq.gz"
+  - fastq_idx:
+      type: file
+      description: Optional demultiplexed index FASTQ files
+      pattern: "**_S*_L00?_I?_00?.fastq.gz"
+  - undetermined:
+      type: file
+      description: Undetermined sample FASTQ files
+      pattern: "Undetermined_S0_L00?_R?_00?.fastq.gz"
+  - undetermined_idx:
+      type: file
+      description: Optional undetermined index FASTQ files
+      pattern: "Undetermined_S0_L00?_I?_00?.fastq.gz"
   - reports:
       type: file
       description: Demultiplexing Reports
@@ -40,6 +56,6 @@ output:
   - interop:
       type: file
       description: Interop files
-      pattern: "Interop/*.{bin}"
+      pattern: "*.{bin}"
 authors:
   - "@matthdsm"

tests/config/test_data.config

@@ -336,6 +336,8 @@ params {
                 test_pytor                                    = "${test_data_dir}/genomics/homo_sapiens/illumina/pytor/test.pytor"
 
                 test_flowcell                                 = "${test_data_dir}/genomics/homo_sapiens/illumina/bcl/flowcell.tar.gz"
+                test_flowcell_samplesheet                     = "${test_data_dir}/genomics/homo_sapiens/illumina/bcl/flowcell_samplesheet.csv"
+
             }
             'pacbio' {
                 primers                         = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/primers.fasta"

tests/modules/bclconvert/main.nf

@@ -3,20 +3,21 @@
 nextflow.enable.dsl = 2
 
 include { BCLCONVERT } from '../../../modules/bclconvert/main.nf'
-
+include { UNTAR      } from '../../../modules/untar/main.nf'
-process STUB_BCLCONVERT_INPUT {
-    output:
-    path "SampleSheet.csv"          ,emit: samplesheet
-    path "DDMMYY_SERIAL_FLOWCELL"   ,emit: run_dir
-
-    stub:
-    """
-    mkdir DDMMYY_SERIAL_FLOWCELL
-    echo "SampleSheet" > SampleSheet.csv
-    """
-}
 
 workflow test_bclconvert {
-    STUB_BCLCONVERT_INPUT ()
+    ch_flowcell = Channel.value([
-    BCLCONVERT (STUB_BCLCONVERT_INPUT.out.samplesheet, STUB_BCLCONVERT_INPUT.out.run_dir)
+            [id:'test', lane:1 ], // meta map
+            file(params.test_data['homo_sapiens']['illumina']['test_flowcell_samplesheet'], checkIfExists: true),
+            file(params.test_data['homo_sapiens']['illumina']['test_flowcell'], checkIfExists: true)])
+
+    ch_flowcell
+    .multiMap { meta, ss, run ->
+        samplesheet: [meta, ss]
+        tar: [meta, run]
+    }.set{ ch_fc_split }
+
+    ch_flowcell_untar = ch_fc_split.samplesheet.join( UNTAR ( ch_fc_split.tar ).untar )
+
+    BCLCONVERT (ch_flowcell_untar)
 }

tests/modules/bclconvert/nextflow.config

@@ -1,5 +1,14 @@
 process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-    
+    withName: BCLCONVERT {
+        ext.args = {[
+            meta.lane ? "--bcl-only-lane ${meta.lane}" : "",
+            "--force",
+            "--first-tile-only true"
+        ].join(" ").trim()}
+    }
+    withName: UNTAR {
+        publishDir = [ enabled: false ]
+    }
 }

tests/modules/bclconvert/test.yml

@@ -1,52 +1,44 @@
 - name: bclconvert test_bclconvert
-  command: nextflow run tests/modules/bclconvert -entry test_bclconvert -c tests/config/nextflow.config -stub-run
+  command: nextflow run ./tests/modules/bclconvert -entry test_bclconvert -c ./tests/config/nextflow.config  -c ./tests/modules/bclconvert/nextflow.config
   tags:
     - bclconvert
   files:
-    - path: output/bclconvert/InterOp/InterOp.bin
-      md5sum: d3dea0bb4ab1c8754af324f40b001481
     - path: output/bclconvert/Logs/Errors.log
-      md5sum: 334645f09074b2597a692e395b716a9c
     - path: output/bclconvert/Logs/FastqComplete.txt
-      md5sum: a4c4c6ce2d0de67d3b7ac7d1fcb512e4
     - path: output/bclconvert/Logs/Info.log
-      md5sum: d238822d379f2277cac950ca986cb660
     - path: output/bclconvert/Logs/Warnings.log
-      md5sum: aeefd2d631817e170f88f25ecaaf4664
     - path: output/bclconvert/Reports/Adapter_Metrics.csv
-      md5sum: af62e9c7b44940cfd8ea11064a1f42ae
+      md5sum: 989240b8840b2169ac1061f952c90f6c
     - path: output/bclconvert/Reports/Demultiplex_Stats.csv
-      md5sum: d11313931fcaabb5ce159462ad3dd1da
+      md5sum: bb2ed9c6b46e03fbc060efd2c75398b0
     - path: output/bclconvert/Reports/IndexMetricsOut.bin
-      md5sum: 6bcee11c8145e3b1059ceaa91d2f5be7
+      md5sum: 9e688c58a5487b8eaf69c9e1005ad0bf
     - path: output/bclconvert/Reports/Index_Hopping_Counts.csv
-      md5sum: 697e40e0c0d48b4bd25f138ef60b0bde
+      md5sum: 1059369e375fd8f8423c0f6c934be978
     - path: output/bclconvert/Reports/Quality_Metrics.csv
-      md5sum: 3902fd38f6b01f1ce0f0e8724238f8f2
+      md5sum: 6614accb1bb414fe312b17b81f5521f7
     - path: output/bclconvert/Reports/RunInfo.xml
-      md5sum: 5bef7c7e76360231b0c4afdfc915fd44
+      md5sum: 03038959f4dd181c86bc97ae71fe270a
     - path: output/bclconvert/Reports/SampleSheet.csv
-      md5sum: c579e7d2c9c917c4cfb875a0373c0936
+      md5sum: dc0dffd39541dd6cc5b4801d768a8d2b
     - path: output/bclconvert/Reports/Top_Unknown_Barcodes.csv
-      md5sum: 39a5e7f6d21c12d6051afdc8261b6330
+      md5sum: 2e2faba761137f228e56bd3428453ccc
     - path: output/bclconvert/Reports/fastq_list.csv
-      md5sum: 32c51ab10e013fd547928de57361ffcb
+      md5sum: 05bc84f51840f5754cfb8381b36f2cb0
-    - path: output/bclconvert/sample1_S1_L001_R1_001.fastq.gz
+    - path: output/bclconvert/Sample1_S1_L001_R1_001.fastq.gz
-      md5sum: 9b831a39755935333f86f167527a094d
+      md5sum: 883037281293a2ec4995d34257f19866
-    - path: output/bclconvert/sample1_S1_L001_R2_001.fastq.gz
+    - path: output/bclconvert/Undetermined_S0_L001_R1_001.fastq.gz
-      md5sum: 082f4f767b7619f409ca7e752ef482bf
+      md5sum: a4745abc5e7fdb89cc6df3069f3c6e69
-    - path: output/bclconvert/sample1_S1_L002_R1_001.fastq.gz
+    - path: output/bclconvert/flowcell/InterOp/ControlMetricsOut.bin
-      md5sum: 837764c89db93dfb53cd663c4f26f3d7
+      md5sum: 6d77b38d0793a6e1ce1e85706e488953
-    - path: output/bclconvert/sample1_S1_L002_R2_001.fastq.gz
+    - path: output/bclconvert/flowcell/InterOp/CorrectedIntMetricsOut.bin
-      md5sum: 1a42cf6ba0bb8fc7770f278e6d1ab676
+      md5sum: 2bbf84d3be72734addaa2fe794711434
-    - path: output/bclconvert/sample2_S2_L001_R1_001.fastq.gz
+    - path: output/bclconvert/flowcell/InterOp/ErrorMetricsOut.bin
-      md5sum: 475bc426b7cc48d0551d40e31457dc78
+      md5sum: 38c88def138e9bb832539911affdb286
-    - path: output/bclconvert/sample2_S2_L001_R2_001.fastq.gz
+    - path: output/bclconvert/flowcell/InterOp/ExtractionMetricsOut.bin
-      md5sum: f670ccd7d9352e0e67fe1c1232429d94
+      md5sum: 7497c3178837eea8f09350b5cd252e99
-    - path: output/bclconvert/sample2_S2_L002_R1_001.fastq.gz
+    - path: output/bclconvert/flowcell/InterOp/IndexMetricsOut.bin
-      md5sum: ebd5ff6fa5603e7d704b5a10598de58c
+    - path: output/bclconvert/flowcell/InterOp/QMetricsOut.bin
-    - path: output/bclconvert/sample2_S2_L002_R2_001.fastq.gz
+      md5sum: 7e9f198d53ebdfbb699a5f94cf1ed51c
-      md5sum: 2f83b460f52620d2548c7ef8845b31d7
+    - path: output/bclconvert/flowcell/InterOp/TileMetricsOut.bin
-    - path: output/stub/SampleSheet.csv
+      md5sum: 83891751ec1c91a425a524b476b6ca3c
-      md5sum: c579e7d2c9c917c4cfb875a0373c0936
-    - path: output/bclconvert/versions.yml