Update bclconvert

modules/nf-core/bclconvert/main.nf

@@ -8,14 +8,14 @@ process BCLCONVERT {
     tuple val(meta), path(samplesheet), path(run_dir)
 
     output:
-    tuple val(meta), path("output/**_S[1-9]*_R?_00?.fastq.gz")           , emit: fastq
-    tuple val(meta), path("output/**_S[1-9]*_I?_00?.fastq.gz")           , optional:true, emit: fastq_idx
-    tuple val(meta), path("output/**Undetermined_S0*_R?_00?.fastq.gz")   , optional:true, emit: undetermined
-    tuple val(meta), path("output/**Undetermined_S0*_I?_00?.fastq.gz")   , optional:true, emit: undetermined_idx
-    tuple val(meta), path("output/Reports")                              , emit: reports
-    tuple val(meta), path("output/Logs")                                 , emit: logs
-    tuple val(meta), path("**/InterOp/*.bin", includeInputs: true), emit: interop
-    path("versions.yml")                                          , emit: versions
+    tuple val(meta), path("output/**_S[1-9]*_R?_00?.fastq.gz")         , emit: fastq
+    tuple val(meta), path("output/**_S[1-9]*_I?_00?.fastq.gz")         , emit: fastq_idx,        optional:true
+    tuple val(meta), path("output/**Undetermined_S0*_R?_00?.fastq.gz") , emit: undetermined,     optional:true
+    tuple val(meta), path("output/**Undetermined_S0*_I?_00?.fastq.gz") , emit: undetermined_idx, optional:true
+    tuple val(meta), path("output/Reports")                            , emit: reports
+    tuple val(meta), path("output/Logs")                               , emit: logs
+    tuple val(meta), path("**/InterOp/*.bin", includeInputs: true)     , emit: interop
+    path("versions.yml")                                               , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -25,9 +25,9 @@ process BCLCONVERT {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         error "BCLCONVERT module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-    def args = task.ext.args ?: ''
-    def args2 = task.ext.args2 ?: ''
-    def args3 = task.ext.args3 ?: ''
+    def args      = task.ext.args  ?: ''
+    def args2     = task.ext.args2 ?: ''
+    def args3     = task.ext.args3 ?: ''
     def input_tar = run_dir.toString().endsWith(".tar.gz") ? true : false
     def input_dir = input_tar ? run_dir.toString() - '.tar.gz' : run_dir
     """
@@ -37,27 +37,27 @@ process BCLCONVERT {
 
     if ${input_tar}; then
         ## Ensures --strip-components only applied when top level of tar contents is a directory
-        ## If just files or multiple directories, place all in $input_dir
+        ## If just files or multiple directories, place all in ${input_dir}
 
         if [[ \$(tar -taf ${run_dir} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then
             tar \\
-                -C $input_dir --strip-components 1 \\
+                -C ${input_dir} --strip-components 1 \\
                 -xavf \\
-                $args2 \\
-                $run_dir \\
-                $args3
+                ${args2} \\
+                ${run_dir} \\
+                ${args3}
         else
             tar \\
-                -C $input_dir \\
+                -C ${input_dir} \\
                 -xavf \\
-                $args2 \\
-                $run_dir \\
-                $args3
+                ${args2} \\
+                ${run_dir} \\
+                ${args3}
         fi
     fi
 
     bcl-convert \\
-        $args \\
+        ${args} \\
         --output-directory output \\
         --bcl-input-directory ${input_dir} \\
         --sample-sheet ${samplesheet}
@@ -67,4 +67,41 @@ process BCLCONVERT {
         bclconvert: \$(bcl-convert -V 2>&1 | head -n 1 | sed 's/^.*Version //')
     END_VERSIONS
     """
+
+    stub:
+    """
+    mkdir -p output/Reports
+    mkdir -p output/Logs
+    echo "" | gzip > output/Sample1_S1_L001_R1_001.fastq.gz
+    echo "" | gzip > output/Undetermined_S0_L001_R1_001.fastq.gz
+    touch output/Reports/Adapter_Cycle_Metrics.csv
+    touch output/Reports/Adapter_Metrics.csv
+    touch output/Reports/Demultiplex_Stats.csv
+    touch output/Reports/Demultiplex_Tile_Stats.csv
+    touch output/Reports/fastq_list.csv
+    touch output/Reports/Index_Hopping_Counts.csv
+    touch output/Reports/IndexMetricsOut.bin
+    touch output/Reports/Quality_Metrics.csv
+    touch output/Reports/Quality_Tile_Metrics.csv
+    touch output/Reports/RunInfo.xml
+    touch output/Reports/SampleSheet.csv
+    touch output/Reports/Top_Unknown_Barcodes.csv
+    touch output/Logs/Errors.log
+    touch output/Logs/FastqComplete.log
+    touch output/Logs/Info.log
+    touch output/Logs/Warnings.log
+    mkdir -p flowcell/InterOp
+    touch flowcell/InterOp/ControlMetricsOut.bin
+    touch flowcell/InterOp/CorrectedIntMetricsOut.bin
+    touch flowcell/InterOp/ErrorMetricsOut.bin
+    touch flowcell/InterOp/ExtractionMetricsOut.bin
+    touch flowcell/InterOp/IndexMetricsOut.bin
+    touch flowcell/InterOp/QMetricsOut.bin
+    touch flowcell/InterOp/TileMetricsOut.bin
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bclconvert: \$(bcl-convert -V 2>&1 | head -n 1 | sed 's/^.*Version //')
+    END_VERSIONS
+    """
 }

modules/nf-core/bclconvert/tests/main.nf.test

@@ -4,11 +4,12 @@ nextflow_process {
     script "../main.nf"
     process "BCLCONVERT"
     config "./nextflow.config"
+
     tag "bclconvert"
     tag "modules"
     tag "modules_nfcore"
 
-    test("homo sapiens illumina [bcl]") {
+    test("homo_sapiens illumina [bcl]") {
         when {
             process {
                 //TODO use new test dataset when available, see https://github.com/nf-core/test-datasets/issues/996
@@ -26,15 +27,43 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    process.out.reports,
-                    process.out.versions,
                     process.out.fastq,
-                    file(process.out.logs.get(0).get(1)).list().sort(),
-                    process.out.interop.get(0).get(1).findAll { file(it).name != "IndexMetricsOut.bin" },
-                    ).match()
-                },
-                { assert process.out.undetermined.get(0).get(1) ==~ ".*/Undetermined_S0_L001_R1_001.fastq.gz"},
-                { assert file(process.out.interop.get(0).get(1).find { file(it).name == "IndexMetricsOut.bin" }).exists() }
+                    process.out.fastq_idx,
+                    process.out.undetermined.collect { meta, fastq -> file(fastq).name },
+                    process.out.undetermined_idx,
+                    process.out.reports,
+                    process.out.logs.collect { meta, logs -> file(logs).list().sort() },
+                    process.out.interop.collect { meta, interop ->
+                                                interop.findAll { interopfile ->
+                                                file(interopfile).name != "IndexMetricsOut.bin" } },
+                    process.out.versions
+                ).match() },
+                { assert process.out.interop.collect { meta, interop ->
+                                                        interop.find { interopfile -> file(interopfile).name == "IndexMetricsOut.bin" } } }
+            )
+        }
+    }
+
+    test("homo_sapiens illumina [bcl] - stub") {
+        options "-stub"
+
+        when {
+            process {
+                //TODO use new test dataset when available, see https://github.com/nf-core/test-datasets/issues/996
+                """
+                input[0] = [
+                    [ id: 'test', lane:1 ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bcl/flowcell_samplesheet.csv', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bcl/flowcell.tar.gz', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
             )
         }
     }