feat: add stub blocks to 41 modules (#4570)

modules/nf-core/deepvariant/main.nf

@@ -36,5 +36,16 @@ The processing stages used by the subworkflow are implemented as module subcomma
 """
     prefix = task.ext.prefix ?: "${meta.id}"
     assert false: deprecation_message
+    stub:
+    """
+    echo | gzip > ${prefix}.g.vcf.gz
+    touch ${prefix}.vcf.gz.tbi
+    echo | gzip > ${prefix}.vcf.gz
+    touch ${prefix}.g.vcf.gz.tbi
+    cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            deepvariant: \$(echo "stub")
+        END_VERSIONS
+    """
 
 }

modules/nf-core/ectyper/main.nf

@@ -42,4 +42,15 @@ process ECTYPER {
         ectyper: \$(echo \$(ectyper --version 2>&1)  | sed 's/.*ectyper //; s/ .*\$//')
     END_VERSIONS
     """
+    stub:
+    """
+    touch ectyper_stub.tsv
+    touch ectyper_stub.log
+    touch ectyper_stub.txt
+    cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            ectyper: \$(echo \$(ectyper --version 2>&1)  | sed 's/.*ectyper //; s/ .*\$//')
+        END_VERSIONS
+    """
+
 }

modules/nf-core/emmtyper/main.nf

@@ -31,4 +31,13 @@ process EMMTYPER {
         emmtyper: \$( echo \$(emmtyper --version 2>&1) | sed 's/^.*emmtyper v//' )
     END_VERSIONS
     """
+    stub:
+    """
+    touch emmtyper_stub.tsv
+    cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            emmtyper: \$( echo \$(emmtyper --version 2>&1) | sed 's/^.*emmtyper v//' )
+        END_VERSIONS
+    """
+
 }

modules/nf-core/fastqscan/main.nf

@@ -30,4 +30,13 @@ process FASTQSCAN {
         fastqscan: \$( echo \$(fastq-scan -v 2>&1) | sed 's/^.*fastq-scan //' )
     END_VERSIONS
     """
+    stub:
+    """
+    touch fastqscan_stub.json
+    cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            fastqscan: \$( echo \$(fastq-scan -v 2>&1) | sed 's/^.*fastq-scan //' )
+        END_VERSIONS
+    """
+
 }

modules/nf-core/fasttree/main.nf

@@ -30,4 +30,13 @@ process FASTTREE {
         fasttree: \$(fasttree -help 2>&1 | head -1  | sed 's/^FastTree \\([0-9\\.]*\\) .*\$/\\1/')
     END_VERSIONS
     """
+    stub:
+    """
+    touch fasttree_stub.tre
+    cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            fasttree: \$(fasttree -help 2>&1 | head -1  | sed 's/^FastTree \\([0-9\\.]*\\) .*\$/\\1/')
+        END_VERSIONS
+    """
+
 }

modules/nf-core/ffq/main.nf

@@ -33,4 +33,13 @@ process FFQ {
         ffq: \$(echo \$(ffq --help 2>&1) | sed 's/^.*ffq //; s/: A command.*\$//' )
     END_VERSIONS
     """
+    stub:
+    """
+    touch ffq_stub.json
+    cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            ffq: \$(echo \$(ffq --help 2>&1) | sed 's/^.*ffq //; s/: A command.*\$//' )
+        END_VERSIONS
+    """
+
 }

modules/nf-core/filtlong/main.nf

@@ -31,4 +31,14 @@ process FILTLONG {
         2>| >(tee ${prefix}.log >&2) \\
         | gzip -n > ${prefix}.fastq.gz
     """
+    stub:
+    """
+    echo | gzip > filtlong_stub.fastq.gz
+    touch filtlong_stub.log
+    cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            filtlong: \$(echo "stub")
+        END_VERSIONS
+    """
+
 }

modules/nf-core/genrich/main.nf

@@ -51,4 +51,17 @@ process GENRICH {
         genrich: \$(echo \$(Genrich --version 2>&1) | sed 's/^Genrich, version //; s/ .*\$//')
     END_VERSIONS
     """
+    stub:
+    """
+    touch genrich_stub.pvalues.bedGraph
+    touch genrich_stub.duplicates.txt
+    touch genrich_stub.pileup.bedGraph
+    touch genrich_stub.intervals.bed
+    touch genrich_stub.narrowPeak
+    cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            genrich: \$(echo \$(Genrich --version 2>&1) | sed 's/^Genrich, version //; s/ .*\$//')
+        END_VERSIONS
+    """
+
 }

modules/nf-core/islandpath/main.nf

@@ -34,4 +34,14 @@ process ISLANDPATH {
         islandpath: $VERSION
     END_VERSIONS
     """
+    stub:
+    """
+    touch islandpath_stub.gff
+    touch Dimob.log
+    cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            islandpath: $VERSION
+        END_VERSIONS
+    """
+
 }

modules/nf-core/kofamscan/main.nf

@@ -39,4 +39,14 @@ process KOFAMSCAN {
         kofamscan: \$(echo \$(exec_annotation --version 2>&1) | sed 's/^.*exec_annotation //;')
     END_VERSIONS
     """
+    stub:
+    """
+    touch kofamscan_stub.tsv
+    touch kofamscan_stub.txt
+    cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            kofamscan: \$(echo \$(exec_annotation --version 2>&1) | sed 's/^.*exec_annotation //;')
+        END_VERSIONS
+    """
+
 }

modules/nf-core/maltextract/main.nf

@@ -36,4 +36,13 @@ process MALTEXTRACT {
         maltextract: \$(MaltExtract --help | head -n 2 | tail -n 1 | sed 's/MaltExtract version//')
     END_VERSIONS
     """
+    stub:
+    """
+    touch results
+    cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            maltextract: \$(MaltExtract --help | head -n 2 | tail -n 1 | sed 's/MaltExtract version//')
+        END_VERSIONS
+    """
+
 }

modules/nf-core/medaka/main.nf

@@ -37,4 +37,13 @@ process MEDAKA {
         medaka: \$( medaka --version 2>&1 | sed 's/medaka //g' )
     END_VERSIONS
     """
+    stub:
+    """
+    echo | gzip > medaka_stub.fa.gz
+    cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            medaka: \$( medaka --version 2>&1 | sed 's/medaka //g' )
+        END_VERSIONS
+    """
+
 }

modules/nf-core/mlst/main.nf

@@ -32,5 +32,13 @@ process MLST {
         mlst: \$( echo \$(mlst --version 2>&1) | sed 's/mlst //' )
     END_VERSIONS
     """
+    stub:
+    """
+    touch mlst_stub.tsv
+    cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            mlst: \$( echo \$(mlst --version 2>&1) | sed 's/mlst //' )
+        END_VERSIONS
+    """
 
 }

modules/nf-core/mygene/main.nf

@@ -20,4 +20,14 @@ process MYGENE {
 
     script:
     template "mygene.py"
+    stub:
+    """
+    touch mygene_stub.gmt
+    touch mygene_stub.tsv
+    cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            mygene: \$(echo "stub")
+        END_VERSIONS
+    """
+
 }

modules/nf-core/ncbigenomedownload/main.nf

@@ -47,4 +47,25 @@ process NCBIGENOMEDOWNLOAD {
         $groups
 
     """
+    stub:
+    """
+    echo | gzip > ncbigenomedownload_stub_genomic.fna.gz
+    echo | gzip > ncbigenomedownload_stub_cds_from_genomic.fna.gz
+    echo | gzip > ncbigenomedownload_stub_protein.faa.gz
+    echo | gzip > ncbigenomedownload_stub_rna_from_genomic.fna.gz
+    touch ncbigenomedownload_stub_assembly_report.txt
+    echo | gzip > ncbigenomedownload_stub_rna.fna.gz
+    echo | gzip > ncbigenomedownload_stub_wgsmaster.gbff.gz
+    echo | gzip > ncbigenomedownload_stub_feature_table.txt.gz
+    echo | gzip > ncbigenomedownload_stub_protein.gpff.gz
+    echo | gzip > ncbigenomedownload_stub_genomic.gff.gz
+    touch ncbigenomedownload_stub_assembly_stats.txt
+    echo | gzip > ncbigenomedownload_stub_rm.out.gz
+    echo | gzip > ncbigenomedownload_stub_genomic.gbff.gz
+    cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            ncbigenomedownload: \$(echo "stub")
+        END_VERSIONS
+    """
+
 }

modules/nf-core/optitype/main.nf

@@ -47,4 +47,14 @@ process OPTITYPE {
         optitype: \$(cat \$(which OptiTypePipeline.py) | grep -e "Version:" | sed -e "s/Version: //g")
     END_VERSIONS
     """
+    stub:
+    """
+    touch ${prefix}/optitype_stub.pdf
+    touch ${prefix}/optitype_stub.tsv
+    cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            optitype: \$(cat \$(which OptiTypePipeline.py) | grep -e "Version:" | sed -e "s/Version: //g")
+        END_VERSIONS
+    """
+
 }

modules/nf-core/pairix/main.nf

@@ -29,4 +29,13 @@ process PAIRIX {
         pairix: \$(echo \$(pairix --help 2>&1) | sed 's/^.*Version: //; s/Usage.*\$//')
     END_VERSIONS
     """
+    stub:
+    """
+    touch pairix_stub.px2
+    cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            pairix: \$(echo \$(pairix --help 2>&1) | sed 's/^.*Version: //; s/Usage.*\$//')
+        END_VERSIONS
+    """
+
 }

modules/nf-core/plasmidid/main.nf

@@ -42,4 +42,20 @@ process PLASMIDID {
         plasmidid: \$(echo \$(plasmidID --version 2>&1))
     END_VERSIONS
     """
+    stub:
+    """
+    touch ${prefix}/data/
+    touch ${prefix}/database/
+    touch ${prefix}/plasmidid_stubfinal_results.tab
+    touch ${prefix}/images/
+    touch ${prefix}/logs/
+    touch ${prefix}/fasta_files/
+    touch ${prefix}/plasmidid_stubfinal_results.html
+    touch ${prefix}/kmer/
+    cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            plasmidid: \$(echo \$(plasmidID --version 2>&1))
+        END_VERSIONS
+    """
+
 }

modules/nf-core/prinseqplusplus/main.nf

@@ -58,4 +58,16 @@ process PRINSEQPLUSPLUS {
         END_VERSIONS
         """
     }
+    stub:
+    """
+    echo | gzip > prinseqplusplus_stub_bad_outprinseqplusplus_stub.fastq.gz
+    echo | gzip > prinseqplusplus_stub_good_outprinseqplusplus_stub.fastq.gz
+    echo | gzip > prinseqplusplus_stub_single_outprinseqplusplus_stub.fastq.gz
+    touch prinseqplusplus_stub.log
+    cat <<-END_VERSIONS > versions.yml
+            "${task.process}":
+                prinseqplusplus: \$(echo \$(prinseq++ --version | cut -f 2 -d ' ' ))
+            END_VERSIONS
+    """
+
 }

modules/nf-core/pycoqc/main.nf

@@ -33,4 +33,14 @@ process PYCOQC {
         pycoqc: \$(pycoQC --version 2>&1 | sed 's/^.*pycoQC v//; s/ .*\$//')
     END_VERSIONS
     """
+    stub:
+    """
+    touch pycoqc_stub.html
+    touch pycoqc_stub.json
+    cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            pycoqc: \$(pycoQC --version 2>&1 | sed 's/^.*pycoQC v//; s/ .*\$//')
+        END_VERSIONS
+    """
+
 }

modules/nf-core/racon/main.nf

@@ -35,4 +35,13 @@ process RACON {
         racon: \$( racon --version 2>&1 | sed 's/^.*v//' )
     END_VERSIONS
     """
+    stub:
+    """
+    echo | gzip > racon_stub_assembly_consensus.fasta.gz
+    cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            racon: \$( racon --version 2>&1 | sed 's/^.*v//' )
+        END_VERSIONS
+    """
+
 }

modules/nf-core/rapidnj/main.nf

@@ -38,4 +38,15 @@ process RAPIDNJ {
         biopython: \$(python -c "import Bio; print(Bio.__version__)")
     END_VERSIONS
     """
+    stub:
+    """
+    touch rapidnj_stub.tre
+    touch rapidnj_stub.sth
+    cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            rapidnj: $VERSION
+            biopython: \$(python -c "import Bio; print(Bio.__version__)")
+        END_VERSIONS
+    """
+
 }

modules/nf-core/rasusa/main.nf

@@ -30,4 +30,13 @@ process RASUSA {
         --input $reads \\
         $output
     """
+    stub:
+    """
+    echo | gzip > rasusa_stub.fastq.gz
+    cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            rasusa: \$(echo "stub")
+        END_VERSIONS
+    """
+
 }

modules/nf-core/raven/main.nf

@@ -33,4 +33,14 @@ process RAVEN {
     # compress assembly graph
     gzip -c ${prefix}.gfa > ${prefix}.gfa.gz
     """
+    stub:
+    """
+    echo | gzip > raven_stub.gfa.gz
+    echo | gzip > raven_stub.fasta.gz
+    cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            raven: \$(echo "stub")
+        END_VERSIONS
+    """
+
 }

modules/nf-core/salsa2/main.nf

@@ -49,4 +49,15 @@ process SALSA2 {
         SALSA2: $VERSION
     END_VERSIONS
     """
+    stub:
+    """
+    touch salsa2_stub_scaffolds_FINAL.fasta
+    touch salsa2_stub/salsa2_stubscaffolds_FINAL.original-coordinates.agp
+    touch salsa2_stub_scaffolds_FINAL.agp
+    cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            SALSA2: $VERSION
+        END_VERSIONS
+    """
+
 }