Fix version commands: round 3 (#754)

* Fix version commands: round 3

* Fix seqkit/split2 modules

modules/bbmap/align/main.nf

@@ -57,6 +57,8 @@ process BBMAP_ALIGN {
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
         ${getSoftwareName(task.process)}: \$(bbversion.sh)
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+        pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
     END_VERSIONS
     """
 }

modules/bowtie/align/main.nf

@@ -58,6 +58,7 @@ process BOWTIE_ALIGN {
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
         ${getSoftwareName(task.process)}: \$(echo \$(bowtie --version 2>&1) | sed 's/^.*bowtie-align-s version //; s/ .*\$//')
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """
 }

modules/bowtie2/align/main.nf

@@ -48,6 +48,8 @@ process BOWTIE2_ALIGN {
         cat <<-END_VERSIONS > versions.yml
         ${getProcessName(task.process)}:
             ${getSoftwareName(task.process)}: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
+            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+            pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
         END_VERSIONS
         """
     } else {
@@ -70,9 +72,12 @@ process BOWTIE2_ALIGN {
         if [ -f ${prefix}.unmapped.fastq.2.gz ]; then
             mv ${prefix}.unmapped.fastq.2.gz ${prefix}.unmapped_2.fastq.gz
         fi
+
         cat <<-END_VERSIONS > versions.yml
         ${getProcessName(task.process)}:
             ${getSoftwareName(task.process)}: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
+            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+            pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
         END_VERSIONS
         """
     }

modules/bwa/mem/main.nf

@@ -45,6 +45,7 @@ process BWA_MEM {
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
         ${getSoftwareName(task.process)}: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//')
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """
 }

modules/bwa/sampe/main.nf

@@ -44,6 +44,7 @@ process BWA_SAMPE {
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
         ${getSoftwareName(task.process)}: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//')
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """
 }

modules/bwa/samse/main.nf

@@ -44,6 +44,7 @@ process BWA_SAMSE {
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
         ${getSoftwareName(task.process)}: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//')
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """
 }

modules/bwamem2/mem/main.nf

@@ -46,6 +46,7 @@ process BWAMEM2_MEM {
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
         ${getSoftwareName(task.process)}: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //')
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """
 }

modules/chromap/index/main.nf

@@ -24,14 +24,16 @@ process CHROMAP_INDEX {
     path fasta
 
     output:
-    path "*.index"      , emit: index
+    path "*.index"     , emit: index
-    path "versions.yml" , emit: version
+    path "versions.yml", emit: version
 
     script:
     def software = getSoftwareName(task.process)
     def prefix   = fasta.baseName
     """
-    chromap -i $options.args \\
+    chromap \\
+        -i \\
+        $options.args \\
         -t $task.cpus \\
         -r $fasta \\
         -o ${prefix}.index
@@ -39,6 +41,7 @@ process CHROMAP_INDEX {
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
         ${getSoftwareName(task.process)}: \$(echo "$VERSION")
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """
 }

modules/hisat2/align/main.nf

@@ -62,6 +62,7 @@ process HISAT2_ALIGN {
         cat <<-END_VERSIONS > versions.yml
         ${getProcessName(task.process)}:
             ${getSoftwareName(task.process)}: \$(echo $VERSION)
+            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
         END_VERSIONS
         """
     } else {
@@ -93,6 +94,7 @@ process HISAT2_ALIGN {
         cat <<-END_VERSIONS > versions.yml
         ${getProcessName(task.process)}:
             ${getSoftwareName(task.process)}: \$(echo $VERSION)
+            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
         END_VERSIONS
         """
     }

modules/kraken2/kraken2/main.nf

@@ -51,6 +51,7 @@ process KRAKEN2_KRAKEN2 {
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
         ${getSoftwareName(task.process)}: \$(echo \$(kraken2 --version 2>&1) | sed 's/^.*Kraken version //; s/ .*\$//')
+        pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
     END_VERSIONS
     """
 }

modules/rapidnj/main.nf

@@ -4,6 +4,8 @@ include { initOptions; saveFiles; getSoftwareName; getProcessName } from './func
 params.options = [:]
 options        = initOptions(params.options)
 
+def VERSION = '2.3.2' // No version information printed
+
 process RAPIDNJ {
     label 'process_medium'
     publishDir "${params.outdir}",
@@ -21,9 +23,9 @@ process RAPIDNJ {
     path alignment
 
     output:
-    path "*.sth"        , emit: stockholm_alignment
+    path "*.sth"       , emit: stockholm_alignment
-    path "*.tre"        , emit: phylogeny
+    path "*.tre"       , emit: phylogeny
-    path "versions.yml" , emit: version
+    path "versions.yml", emit: version
 
     script:
     def software = getSoftwareName(task.process)
@@ -38,10 +40,10 @@ process RAPIDNJ {
         -c $task.cpus \\
         -x rapidnj_phylogeny.tre
 
-    # Doesn't appear to be a way of getting the version number
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(echo 2.3.2)
+        ${getSoftwareName(task.process)}: \$(echo $VERSION)
+        biopython: \$(python -c "import Bio; print(Bio.__version__)")
     END_VERSIONS
     """
 }

modules/rsem/calculateexpression/main.nf

@@ -34,8 +34,8 @@ process RSEM_CALCULATEEXPRESSION {
     tuple val(meta), path("${prefix}.transcript.bam"), optional:true, emit: bam_transcript
 
     script:
-    def software   = getSoftwareName(task.process)
+    def software = getSoftwareName(task.process)
-    prefix         = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    prefix       = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
 
     def strandedness = ''
     if (meta.strandedness == 'forward') {
@@ -59,6 +59,7 @@ process RSEM_CALCULATEEXPRESSION {
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
         ${getSoftwareName(task.process)}: \$(rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g")
+        star: \$(STAR --version | sed -e "s/STAR_//g")
     END_VERSIONS
     """
 }

modules/rsem/preparereference/main.nf

@@ -53,6 +53,7 @@ process RSEM_PREPAREREFERENCE {
         cat <<-END_VERSIONS > versions.yml
         ${getProcessName(task.process)}:
             ${getSoftwareName(task.process)}: \$(rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g")
+            star: \$(STAR --version | sed -e "s/STAR_//g")
         END_VERSIONS
         """
     } else {
@@ -67,6 +68,7 @@ process RSEM_PREPAREREFERENCE {
         cat <<-END_VERSIONS > versions.yml
         ${getProcessName(task.process)}:
             ${getSoftwareName(task.process)}: \$(rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g")
+            star: \$(STAR --version | sed -e "s/STAR_//g")
         END_VERSIONS
         """
     }

modules/samtools/faidx/main.nf

@@ -22,8 +22,8 @@ process SAMTOOLS_FAIDX {
     path fasta
 
     output:
-    path "*.fai"        , emit: fai
+    path "*.fai"       , emit: fai
-    path "versions.yml" , emit: version
+    path "versions.yml", emit: version
 
     script:
     def software = getSoftwareName(task.process)

modules/seacr/callpeak/main.nf

@@ -40,6 +40,8 @@ process SEACR_CALLPEAK {
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
         ${getSoftwareName(task.process)}: \$(echo $VERSION)
+        bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
+        r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/seqkit/split2/main.nf

@@ -7,13 +7,11 @@ options        = initOptions(params.options)
 process SEQKIT_SPLIT2 {
     tag "$meta.id"
     label 'process_medium'
-
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? 'bioconda::seqkit=0.16.1' : null)
-
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
         container "https://depot.galaxyproject.org/singularity/seqkit:0.16.1--h9ee0642_0"
     } else {
@@ -24,42 +22,40 @@ process SEQKIT_SPLIT2 {
     tuple val(meta), path(reads)
 
     output:
-    tuple val(meta), path("*.split/*.gz"), emit: reads
+    tuple val(meta), path("*${prefix}/*.gz"), emit: reads
-    path("versions.yml")                       , emit: version
+    path "versions.yml"                     , emit: version
-
 
     script:
     def software = getSoftwareName(task.process)
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    prefix       = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-
     if(meta.single_end){
-    """
+        """
-    seqkit \
+        seqkit \\
-        split2 \
+            split2 \\
-        $options.args \
+            $options.args \\
-        --threads $task.cpus \
+            --threads $task.cpus \\
-        -1 ${reads} \
+            -1 $reads \\
-        --out-dir ${prefix}.split
+            --out-dir $prefix
 
-    cat <<-END_VERSIONS > versions.yml
+        cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+        ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(seqkit --version 2>&1 | sed 's/^.*seqkit //; s/Using.*\$//')
+            ${getSoftwareName(task.process)}: \$(echo \$(seqkit 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
-    END_VERSIONS
+        END_VERSIONS
-    """
+        """
     } else {
-    """
+        """
-    seqkit \
+        seqkit \\
-        split2 \
+            split2 \\
-        $options.args \
+            $options.args \\
-        --threads $task.cpus \
+            --threads $task.cpus \\
-        -1 ${reads[0]} \
+            -1 ${reads[0]} \\
-        -2 ${reads[1]} \
+            -2 ${reads[1]} \\
-        --out-dir ${prefix}.split
+            --out-dir $prefix
 
-    cat <<-END_VERSIONS > versions.yml
+        cat <<-END_VERSIONS > versions.yml
-    ${getProcessName(task.process)}:
+        ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(seqkit --version 2>&1 | sed 's/^.*seqkit //; s/Using.*\$//')
+            ${getSoftwareName(task.process)}: \$(echo \$(seqkit 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
-    END_VERSIONS
+        END_VERSIONS
-    """
+        """
     }
 }

modules/seqtk/sample/main.nf

@@ -40,7 +40,7 @@ process SEQTK_SAMPLE {
 
         cat <<-END_VERSIONS > versions.yml
         ${getProcessName(task.process)}:
-            ${getSoftwareName(task.process)}: \$(seqtk 2>&1 | sed 's/^.*Version: //; s/ .*\$//')
+            ${getSoftwareName(task.process)}: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
         END_VERSIONS
         """
     } else {
@@ -64,7 +64,7 @@ process SEQTK_SAMPLE {
 
         cat <<-END_VERSIONS > versions.yml
         ${getProcessName(task.process)}:
-            ${getSoftwareName(task.process)}: \$(seqtk 2>&1 | sed 's/^.*Version: //; s/ .*\$//')
+            ${getSoftwareName(task.process)}: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
         END_VERSIONS
         """
     }

modules/seqtk/subseq/main.nf

@@ -43,7 +43,7 @@ process SEQTK_SUBSEQ {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(seqtk 2>&1 | sed 's/^.*Version: //; s/ .*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/sequenzautils/bam2seqz/main.nf

@@ -24,8 +24,8 @@ process SEQUENZAUTILS_BAM2SEQZ {
     path wigfile
 
     output:
-    tuple val(meta), path("*.seqz.gz"), emit: seqz
+    tuple val(meta), path("*.gz"), emit: seqz
-    path "versions.yml"           , emit: version
+    path "versions.yml"          , emit: version
 
     script:
     def software = getSoftwareName(task.process)
@@ -38,11 +38,11 @@ process SEQUENZAUTILS_BAM2SEQZ {
         -t $tumourbam \\
         --fasta $fasta \\
         -gc $wigfile \\
-        -o ${prefix}.seqz.gz
+        -o ${prefix}.gz
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(sequenzautils --version 2>&1 | sed 's/^.*sequenzautils //; s/Using.*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(sequenza-utils 2>&1) | sed 's/^.*is version //; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/sequenzautils/gcwiggle/main.nf

@@ -23,7 +23,7 @@ process SEQUENZAUTILS_GCWIGGLE {
 
     output:
     tuple val(meta), path("*.wig.gz"), emit: wig
-    path "versions.yml"           , emit: version
+    path "versions.yml"              , emit: version
 
     script:
     def software = getSoftwareName(task.process)
@@ -37,7 +37,7 @@ process SEQUENZAUTILS_GCWIGGLE {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(sequenzautils --version 2>&1 | sed 's/^.*sequenzautils //; s/Using.*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(sequenza-utils 2>&1) | sed 's/^.*is version //; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/shovill/main.nf

@@ -44,7 +44,7 @@ process SHOVILL {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(shovill --version 2>&1 | sed 's/^.*shovill //' )
+        ${getSoftwareName(task.process)}: \$(echo \$(shovill --version 2>&1) | sed 's/^.*shovill //')
     END_VERSIONS
     """
 }

modules/star/genomegenerate/main.nf

@@ -46,6 +46,8 @@ process STAR_GENOMEGENERATE {
         cat <<-END_VERSIONS > versions.yml
         ${getProcessName(task.process)}:
             ${getSoftwareName(task.process)}: \$(STAR --version | sed -e "s/STAR_//g")
+            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+            gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
         END_VERSIONS
         """
     } else {
@@ -67,6 +69,8 @@ process STAR_GENOMEGENERATE {
         cat <<-END_VERSIONS > versions.yml
         ${getProcessName(task.process)}:
             ${getSoftwareName(task.process)}: \$(STAR --version | sed -e "s/STAR_//g")
+            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+            gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
         END_VERSIONS
         """
     }

modules/tiddit/sv/main.nf

@@ -35,14 +35,15 @@ process TIDDIT_SV {
     def reference = fasta == "dummy_file.txt" ? "--ref $fasta" : ""
     """
     tiddit \\
-        --sv $options.args \\
+        --sv \\
+        $options.args \\
         --bam $bam \\
         $reference \\
         -o $prefix
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(tiddit -h 2>&1 | sed 's/^.*Version: //; s/(.*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(tiddit 2>&1) | sed 's/^.*TIDDIT-//; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/ucsc/bedgraphtobigwig/main.nf

@@ -32,7 +32,11 @@ process UCSC_BEDGRAPHTOBIGWIG {
     def software = getSoftwareName(task.process)
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     """
-    bedGraphToBigWig $bedgraph $sizes ${prefix}.bigWig
+    bedGraphToBigWig \\
+        $bedgraph \\
+        $sizes \\
+        ${prefix}.bigWig
+
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
         ${getSoftwareName(task.process)}: \$(echo $VERSION)

modules/ucsc/bigwigaverageoverbed/main.nf

@@ -4,6 +4,8 @@ include { initOptions; saveFiles; getSoftwareName; getProcessName } from './func
 params.options = [:]
 options        = initOptions(params.options)
 
+def VERSION = '377'
+
 process UCSC_BIGWIGAVERAGEOVERBED {
     tag "$meta.id"
     label 'process_medium'
@@ -23,19 +25,23 @@ process UCSC_BIGWIGAVERAGEOVERBED {
     path bigwig
 
     output:
-    tuple val(meta), path("*.tab")           , emit: tab
+    tuple val(meta), path("*.tab"), emit: tab
-    path "versions.yml"                      , emit: version
+    path "versions.yml"           , emit: version
 
     script:
     def software = getSoftwareName(task.process)
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     """
     # there is a bug that bigWigAverageOverBed can not handle ensembl seqlevels style.
-    bigWigAverageOverBed ${options.args} $bigwig $bed ${bed.getSimpleName()}.tab
+    bigWigAverageOverBed \\
+        $options.args \\
+        $bigwig \\
+        $bed \\
+        ${prefix}.tab
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(bigWigAverageOverBed 2>&1 | sed 's/bigWigAverageOverBed v//; s/ - Compute.*\$//')
+        ${getSoftwareName(task.process)}: \$(echo $VERSION)
     END_VERSIONS
     """
 }

modules/unicycler/main.nf

@@ -44,7 +44,7 @@ process UNICYCLER {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(unicycler --version 2>&1 | sed 's/^.*Unicycler v//; s/ .*\$//')
+        ${getSoftwareName(task.process)}: \$(echo \$(unicycler --version 2>&1) | sed 's/^.*Unicycler v//; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/yara/index/main.nf

@@ -22,21 +22,25 @@ process YARA_INDEX {
     path fasta
 
     output:
-    path "yara", emit: index
+    path "yara"        , emit: index
-    path "versions.yml"           , emit: version
+    path "versions.yml", emit: version
 
     script:
     def software = getSoftwareName(task.process)
 
     """
     mkdir yara
-    yara_indexer $fasta -o "yara"
+
+    yara_indexer \\
+        $fasta \\
+        -o "yara"
+
     mv *.{lf,rid,sa,txt}.* yara
     cp $fasta yara/yara.fasta
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$(yara_indexer --help  2>&1 | grep -e "yara_indexer version:" | sed 's/yara_indexer version: //g')
+        ${getSoftwareName(task.process)}: \$(echo \$(yara_indexer --version 2>&1) | sed 's/^.*yara_indexer version: //; s/ .*\$//')
     END_VERSIONS
     """
 }

modules/yara/mapper/main.nf

@@ -24,31 +24,44 @@ process YARA_MAPPER {
 
     output:
     tuple val(meta), path("*.mapped.bam"), emit: bam
-    path "versions.yml"           , emit: version
+    path "versions.yml"                  , emit: version
 
     script:
     def software = getSoftwareName(task.process)
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    if (meta.single_end) {
+        """
+        yara_mapper \\
+            $options.args \\
+            -t $task.cpus \\
+            -f bam \\
+            ${index}/yara \\
+            $reads | samtools view -@ $task.cpus -hb -F4 > ${prefix}.mapped.bam
 
-    if(meta.single_end) {
+        cat <<-END_VERSIONS > versions.yml
-    """
+        ${getProcessName(task.process)}:
-    yara_mapper $options.args -t ${task.cpus} -f bam ${index}/yara $reads | samtools view -@ ${task.cpus} -hb -F4 > ${prefix}.mapped.bam
+            ${getSoftwareName(task.process)}: \$(echo \$(yara_mapper --version 2>&1) | sed 's/^.*yara_mapper version: //; s/ .*\$//')
-
+            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    cat <<-END_VERSIONS > versions.yml
+        END_VERSIONS
-    ${getProcessName(task.process)}:
+        """
-        ${getSoftwareName(task.process)}: \$(yara_mapper --help  2>&1)
-    END_VERSIONS
-    """
     } else {
-    """
+        """
-    yara_mapper $options.args -t ${task.cpus} -f bam ${index}/yara ${reads[0]} ${reads[1]} > output.bam
+        yara_mapper \\
-    samtools view -@ ${task.cpus} -hF 4 -f 0x40 -b output.bam > ${prefix}_1.mapped.bam
+            $options.args \\
-    samtools view -@ ${task.cpus} -hF 4 -f 0x80 -b output.bam > ${prefix}_2.mapped.bam
+            -t ${task.cpus} \\
-    cat <<-END_VERSIONS > versions.yml
+            -f bam \\
-    ${getProcessName(task.process)}:
+            ${index}/yara \\
-        ${getSoftwareName(task.process)}: \$(yara_mapper --version  2>&1 | grep -e "yara_mapper version:" | sed 's/yara_mapper version: //g')
+            ${reads[0]} \\
-    END_VERSIONS
+            ${reads[1]} > output.bam
-    """
-    }
 
+        samtools view -@ $task.cpus -hF 4 -f 0x40 -b output.bam > ${prefix}_1.mapped.bam
+        samtools view -@ $task.cpus -hF 4 -f 0x80 -b output.bam > ${prefix}_2.mapped.bam
+
+        cat <<-END_VERSIONS > versions.yml
+        ${getProcessName(task.process)}:
+            ${getSoftwareName(task.process)}: \$(echo \$(yara_mapper --version 2>&1) | sed 's/^.*yara_mapper version: //; s/ .*\$//')
+            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+        END_VERSIONS
+        """
+    }
 }

tests/modules/seacr/callpeak/main.nf

@@ -5,10 +5,11 @@ nextflow.enable.dsl = 2
 include { SEACR_CALLPEAK } from '../../../../modules/seacr/callpeak/main.nf' addParams( options: [ args:'norm stringent' ] )
 
 workflow test_seacr_callpeak {
-    input = [ [ id:'test_1'],
+    input = [
-              file("${launchDir}/tests/data/generic/bedgraph/K27me3_1_to_chr20.bedgraph", checkIfExists: true),
+        [ id:'test_1'],
-              file("${launchDir}/tests/data/generic/bedgraph/IgG_1_to_chr20.bedgraph", checkIfExists: true) 
+        file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/bedgraph/K27me3_1_to_chr20.bedgraph", checkIfExists: true),
-            ]
+        file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/bedgraph/IgG_1_to_chr20.bedgraph", checkIfExists: true)
+    ]
 
     SEACR_CALLPEAK ( input )
 }

tests/modules/seqkit/split2/test.yml

@@ -4,9 +4,9 @@
     - seqkit
     - seqkit/split2
   files:
-    - path: output/seqkit/test.split/test_1.part_001.fastq.gz
+    - path: output/seqkit/test/test_1.part_001.fastq.gz
       md5sum: 6f7d58ba35c254c0817fe9a7c69862e4
-    - path: output/seqkit/test.split/test_1.part_002.fastq.gz
+    - path: output/seqkit/test/test_1.part_002.fastq.gz
       md5sum: cf38c51506e45380fe25abdd1bd5ccc6
 
 - name: seqkit split2 single-end size
@@ -15,9 +15,9 @@
     - seqkit
     - seqkit/split2
   files:
-    - path: output/seqkit/test.split/test_1.part_001.fastq.gz
+    - path: output/seqkit/test/test_1.part_001.fastq.gz
       md5sum: bf835e685d597fc1ab5e5ac7dd689619
-    - path: output/seqkit/test.split/test_1.part_002.fastq.gz
+    - path: output/seqkit/test/test_1.part_002.fastq.gz
       md5sum: 703d95ff4fbb5b7fb4da8a164ba9aa54
 
 - name: seqkit split2 single-end part
@@ -26,11 +26,11 @@
     - seqkit
     - seqkit/split2
   files:
-    - path: output/seqkit/test.split/test_1.part_001.fastq.gz
+    - path: output/seqkit/test/test_1.part_001.fastq.gz
       md5sum: fa25951435471238d5567fd2cae31f55
-    - path: output/seqkit/test.split/test_1.part_002.fastq.gz
+    - path: output/seqkit/test/test_1.part_002.fastq.gz
       md5sum: 1dcf631aaaa5e7e0bd6c9668fbc6e04a
-    - path: output/seqkit/test.split/test_1.part_003.fastq.gz
+    - path: output/seqkit/test/test_1.part_003.fastq.gz
       md5sum: 8bc86ba83a611c54f592f4eae19b680f
 
 - name: seqkit split2 paired-end length
@@ -39,13 +39,13 @@
     - seqkit
     - seqkit/split2
   files:
-    - path: output/seqkit/test.split/test_1.part_001.fastq.gz
+    - path: output/seqkit/test/test_1.part_001.fastq.gz
       md5sum: 6f7d58ba35c254c0817fe9a7c69862e4
-    - path: output/seqkit/test.split/test_1.part_002.fastq.gz
+    - path: output/seqkit/test/test_1.part_002.fastq.gz
       md5sum: cf38c51506e45380fe25abdd1bd5ccc6
-    - path: output/seqkit/test.split/test_2.part_001.fastq.gz
+    - path: output/seqkit/test/test_2.part_001.fastq.gz
       md5sum: 6b094b1ba7c439fe44c1bb5e99a02ba4
-    - path: output/seqkit/test.split/test_2.part_002.fastq.gz
+    - path: output/seqkit/test/test_2.part_002.fastq.gz
       md5sum: 927097c6ac7522199a9e016333181a8e
 
 - name: seqkit split2 paired-end size
@@ -54,13 +54,13 @@
     - seqkit
     - seqkit/split2
   files:
-    - path: output/seqkit/test.split/test_1.part_001.fastq.gz
+    - path: output/seqkit/test/test_1.part_001.fastq.gz
       md5sum: bf835e685d597fc1ab5e5ac7dd689619
-    - path: output/seqkit/test.split/test_1.part_002.fastq.gz
+    - path: output/seqkit/test/test_1.part_002.fastq.gz
       md5sum: 703d95ff4fbb5b7fb4da8a164ba9aa54
-    - path: output/seqkit/test.split/test_2.part_001.fastq.gz
+    - path: output/seqkit/test/test_2.part_001.fastq.gz
       md5sum: 09d0dd83b5b1b9b95d316eeed79ea5ba
-    - path: output/seqkit/test.split/test_2.part_002.fastq.gz
+    - path: output/seqkit/test/test_2.part_002.fastq.gz
       md5sum: 8796c3f327b1094244bfcdb36d536526
 
 - name: seqkit split2 paired-end part
@@ -69,15 +69,15 @@
     - seqkit
     - seqkit/split2
   files:
-    - path: output/seqkit/test.split/test_1.part_001.fastq.gz
+    - path: output/seqkit/test/test_1.part_001.fastq.gz
       md5sum: fa25951435471238d5567fd2cae31f55
-    - path: output/seqkit/test.split/test_1.part_002.fastq.gz
+    - path: output/seqkit/test/test_1.part_002.fastq.gz
       md5sum: 1dcf631aaaa5e7e0bd6c9668fbc6e04a
-    - path: output/seqkit/test.split/test_1.part_003.fastq.gz
+    - path: output/seqkit/test/test_1.part_003.fastq.gz
       md5sum: 8bc86ba83a611c54f592f4eae19b680f
-    - path: output/seqkit/test.split/test_2.part_001.fastq.gz
+    - path: output/seqkit/test/test_2.part_001.fastq.gz
       md5sum: f0055c99cd193fd97466b3cde9dd1b8f
-    - path: output/seqkit/test.split/test_2.part_002.fastq.gz
+    - path: output/seqkit/test/test_2.part_002.fastq.gz
       md5sum: 8a90df768201785f7a7cd5dbb41e846a
-    - path: output/seqkit/test.split/test_2.part_003.fastq.gz
+    - path: output/seqkit/test/test_2.part_003.fastq.gz
       md5sum: 890b90083e8e1606bd13ba34149cedd7

tests/modules/sequenzautils/bam2seqz/test.yml

@@ -4,5 +4,5 @@
     - sequenzautils
     - sequenzautils/bam2seqz
   files:
-    - path: output/sequenzautils/test.seqz.gz
+    - path: output/sequenzautils/test.gz
       md5sum: 12b41979a498ac10c0aff162b12e6a6e

tests/modules/ucsc/bigwigaverageoverbed/main.nf

@@ -5,9 +5,10 @@ nextflow.enable.dsl = 2
 include { UCSC_BIGWIGAVERAGEOVERBED } from '../../../../modules/ucsc/bigwigaverageoverbed/main.nf' addParams( options: [:] )
 
 workflow test_ucsc_bigwigaverageoverbed {
-    input = [ [ id: 'test' ], // meta map
+    input = [
-              [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true ) ]
+        [ id: 'test' ], // meta map
-            ]
+        [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true ) ]
+    ]
     bigwig = file(params.test_data['sarscov2']['illumina']['test_bigwig'], checkIfExists: true)
 
     UCSC_BIGWIGAVERAGEOVERBED ( input, bigwig )

tests/modules/yara/index/main.nf

@@ -2,11 +2,11 @@
 
 nextflow.enable.dsl = 2
 
-include { YARA_INDEX } from '../../../../modules/yara/index/main.nf' addParams( options: [:] )
+include { YARA_INDEX } from '../../../../modules/yara/index/main.nf' addParams( options: [publish_dir:'yara'] )
 
 workflow test_yara_index {
 
-    def input = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
+    input = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 
     YARA_INDEX ( input )
 }

tests/modules/yara/index/test.yml

@@ -4,27 +4,27 @@
     - yara/index
     - yara
   files:
-    - path: output/index/yara/yara.rid.limits
+    - path: output/yara/yara/yara.rid.limits
       md5sum: 8b814661f30a0c9e350bfbcb454930ce
-    - path: output/index/yara/yara.sa.len
+    - path: output/yara/yara/yara.sa.len
       md5sum: 45677f66c28c79c02250ceb8b58645e8
-    - path: output/index/yara/yara.sa.ind
+    - path: output/yara/yara/yara.sa.ind
       md5sum: 464314583efb5f07260b0efecc29a1ce
-    - path: output/index/yara/yara.lf.drp
+    - path: output/yara/yara/yara.lf.drp
       md5sum: 3ef99a87a4e44513f46d42f4261f7842
-    - path: output/index/yara/yara.txt.size
+    - path: output/yara/yara/yara.txt.size
       md5sum: 063987b3c3f747be7d2b8043c9d91000
-    - path: output/index/yara/yara.rid.concat
+    - path: output/yara/yara/yara.rid.concat
       md5sum: 1e4e4c88ddeaf907a12f02f0d88367c5
-    - path: output/index/yara/yara.txt.concat
+    - path: output/yara/yara/yara.txt.concat
       md5sum: 6074d1933c9e7e5ab05fa0def5ce28c0
-    - path: output/index/yara/yara.lf.drs
+    - path: output/yara/yara/yara.lf.drs
       md5sum: 55a54008ad1ba589aa210d2629c1df41
-    - path: output/index/yara/yara.txt.limits
+    - path: output/yara/yara/yara.txt.limits
       md5sum: 4480a068db603e4c9a27bc4fa9ceaf14
-    - path: output/index/yara/yara.sa.val
+    - path: output/yara/yara/yara.sa.val
       md5sum: ce57cc82e2d3ae7b9824210f54168ce9
-    - path: output/index/yara/yara.lf.pst
+    - path: output/yara/yara/yara.lf.pst
       md5sum: e8daba34298e99e42942435286f9b3f0
-    - path: output/index/yara/yara.lf.drv
+    - path: output/yara/yara/yara.lf.drv
       md5sum: cf6408307fe9fd7f99c33f521bf95550