Merge branch 'nf-core:master' into master

modules/adapterremoval/main.nf

@@ -12,14 +12,13 @@ process ADAPTERREMOVAL {
     path(adapterlist)
 
     output:
-    tuple val(meta), path("${prefix}.truncated.gz")            , optional: true, emit: singles_truncated
+    tuple val(meta), path("${prefix}.truncated.fastq.gz")            , optional: true, emit: singles_truncated
-    tuple val(meta), path("${prefix}.discarded.gz")            , optional: true, emit: discarded
+    tuple val(meta), path("${prefix}.discarded.fastq.gz")            , optional: true, emit: discarded
-    tuple val(meta), path("${prefix}.pair1.truncated.gz")      , optional: true, emit: pair1_truncated
+    tuple val(meta), path("${prefix}.pair{1,2}.truncated.fastq.gz")  , optional: true, emit: paired_truncated
-    tuple val(meta), path("${prefix}.pair2.truncated.gz")      , optional: true, emit: pair2_truncated
+    tuple val(meta), path("${prefix}.collapsed.fastq.gz")            , optional: true, emit: collapsed
-    tuple val(meta), path("${prefix}.collapsed.gz")            , optional: true, emit: collapsed
+    tuple val(meta), path("${prefix}.collapsed.truncated.fastq.gz")  , optional: true, emit: collapsed_truncated
-    tuple val(meta), path("${prefix}.collapsed.truncated.gz")  , optional: true, emit: collapsed_truncated
+    tuple val(meta), path("${prefix}.paired.fastq.gz")               , optional: true, emit: paired_interleaved
-    tuple val(meta), path("${prefix}.paired.gz")               , optional: true, emit: paired_interleaved
+    tuple val(meta), path('*.settings')                              , emit: settings
-    tuple val(meta), path('*.log')                             , emit: log
     path "versions.yml"                                              , emit: versions
 
     when:
@@ -38,10 +37,19 @@ process ADAPTERREMOVAL {
             $adapterlist \\
             --basename ${prefix} \\
             --threads ${task.cpus} \\
-            --settings ${prefix}.log \\
             --seed 42 \\
             --gzip
 
+        ensure_fastq() {
+            if [ -f "\${1}" ]; then
+                mv "\${1}" "\${1::-3}.fastq.gz"
+            fi
+
+        }
+
+        ensure_fastq '${prefix}.truncated.gz'
+        ensure_fastq '${prefix}.discarded.gz'
+
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
             adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
@@ -56,10 +64,24 @@ process ADAPTERREMOVAL {
             $adapterlist \\
             --basename ${prefix} \\
             --threads $task.cpus \\
-            --settings ${prefix}.log \\
             --seed 42 \\
             --gzip
 
+        ensure_fastq() {
+            if [ -f "\${1}" ]; then
+                mv "\${1}" "\${1::-3}.fastq.gz"
+            fi
+
+        }
+
+        ensure_fastq '${prefix}.truncated.gz'
+        ensure_fastq '${prefix}.discarded.gz'
+        ensure_fastq '${prefix}.pair1.truncated.gz'
+        ensure_fastq '${prefix}.pair2.truncated.gz'
+        ensure_fastq '${prefix}.collapsed.gz'
+        ensure_fastq '${prefix}.collapsed.truncated.gz'
+        ensure_fastq '${prefix}.paired.gz'
+
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
             adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")

modules/adapterremoval/meta.yml

@@ -43,43 +43,43 @@ output:
         Adapter trimmed FastQ files of either single-end reads, or singleton
         'orphaned' reads from merging of paired-end data (i.e., one of the pair
         was lost due to filtering thresholds).
-      pattern: "*.truncated.gz"
+      pattern: "*.truncated.fastq.gz"
   - discarded:
       type: file
       description: |
         Adapter trimmed FastQ files of reads that did not pass filtering
         thresholds.
-      pattern: "*.discarded.gz"
+      pattern: "*.discarded.fastq.gz"
   - pair1_truncated:
       type: file
       description: |
         Adapter trimmed R1 FastQ files of paired-end reads that did not merge
         with their respective R2 pair due to long templates. The respective pair
         is stored in 'pair2_truncated'.
-      pattern: "*.pair1.truncated.gz"
+      pattern: "*.pair1.truncated.fastq.gz"
   - pair2_truncated:
       type: file
       description: |
         Adapter trimmed R2 FastQ files of paired-end reads that did not merge
         with their respective R1 pair due to long templates. The respective pair
         is stored in 'pair1_truncated'.
-      pattern: "*.pair2.truncated.gz"
+      pattern: "*.pair2.truncated.fastq.gz"
   - collapsed:
       type: file
       description: |
         Collapsed FastQ of paired-end reads that successfully merged with their
         respective R1 pair but were not trimmed.
-      pattern: "*.collapsed.gz"
+      pattern: "*.collapsed.fastq.gz"
   - collapsed_truncated:
       type: file
       description: |
         Collapsed FastQ of paired-end reads that successfully merged with their
         respective R1 pair and were trimmed of adapter due to sufficient overlap.
-      pattern: "*.collapsed.truncated.gz"
+      pattern: "*.collapsed.truncated.fastq.gz"
   - log:
       type: file
       description: AdapterRemoval log file
-      pattern: "*.log"
+      pattern: "*.settings"
   - versions:
       type: file
       description: File containing software versions

modules/biobambam/bammarkduplicates2/main.nf

@@ -2,10 +2,8 @@ process BIOBAMBAM_BAMMARKDUPLICATES2 {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::biobambam=2.0.182" : null)
+    conda (params.enable_conda ? "bioconda::biobambam=2.0.183" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/biobambam:2.0.183--h9f5acd7_1' : 'quay.io/biocontainers/biobambam:2.0.183--h9f5acd7_1'}"
-        'https://depot.galaxyproject.org/singularity/biobambam:2.0.182--h7d875b9_0':
-        'quay.io/biocontainers/biobambam:2.0.182--h7d875b9_0' }"
 
     input:
     tuple val(meta), path(bam)

modules/biobambam/bamsormadup/main.nf

@@ -0,0 +1,46 @@
+process BIOBAMBAM_BAMSORMADUP {
+    tag "$meta.id"
+    label "process_medium"
+
+    conda (params.enable_conda ? "bioconda::biobambam=2.0.183" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/biobambam:2.0.183--h9f5acd7_1' : 'quay.io/biocontainers/biobambam:2.0.183--h9f5acd7_1'}"
+
+    input:
+    tuple val(meta), path(bams)
+    path(fasta)
+
+    output:
+    tuple val(meta), path("*.{bam,cram}")       ,emit: bam
+    tuple val(meta), path("*.bam.bai")          ,optional:true, emit: bam_index
+    tuple val(meta), path("*.metrics.txt")      ,emit: metrics
+    path "versions.yml"                         ,emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def suffix = args.contains("outputformat=cram") ? "cram" : "bam"
+    def input_string = bams.join(" I=")
+
+    if (args.contains("outputformat=cram") && reference == null) error "Reference required for CRAM output."
+
+    """
+    bamcat \\
+        I=${input_string} \\
+        level=0 \\
+    | bamsormadup \\
+        $args \\
+        M=${prefix}.metrics.txt \\
+        tmpfile=$prefix \\
+        threads=$task.cpus \\
+        > ${prefix}.${suffix}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bamcat: \$(echo \$(bamsormadup --version 2>&1) | sed 's/^This is biobambam2 version //; s/..biobambam2 is .*\$//' )
+        bamsormadup: \$(echo \$(bamsormadup --version 2>&1) | sed 's/^This is biobambam2 version //; s/..biobambam2 is .*\$//' )
+    END_VERSIONS
+    """
+}

modules/biobambam/bamsormadup/meta.yml

@@ -0,0 +1,52 @@
+name: biobambam_bamsormadup
+description: Parallel sorting and duplicate marking
+keywords:
+  - markduplicates
+  - sort
+  - bam
+  - cram
+tools:
+  - biobambam:
+      description: |
+        biobambam is a set of tools for early stage alignment file processing.
+      homepage: https://gitlab.com/german.tischler/biobambam2
+      documentation: https://gitlab.com/german.tischler/biobambam2/-/blob/master/README.md
+      doi: 10.1186/1751-0473-9-13
+      licence: ["GPL v3"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bams:
+      type: file
+      description: List containing 1 or more bam files
+  - fasta:
+      type: file
+      description: Reference genome in FASTA format (optional)
+      pattern: "*.{fa,fasta}"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: BAM/CRAM file with duplicate reads marked/removed
+      pattern: "*.{bam,cram}"
+  - bam_index:
+      type: file
+      description: BAM index file
+      pattern: "*.{bai}"
+  - metrics:
+      type: file
+      description: Duplicate metrics file generated by biobambam
+      pattern: "*.{metrics.txt}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@matthdsm"

modules/centrifuge/centrifuge/main.nf

@@ -1,4 +1,4 @@
-process CENTRIFUGE {
+process CENTRIFUGE_CENTRIFUGE {
     tag "$meta.id"
     label 'process_high'
 
@@ -17,7 +17,6 @@ process CENTRIFUGE {
     output:
     tuple val(meta), path('*report.txt')                 , emit: report
     tuple val(meta), path('*results.txt')                , emit: results
-    tuple val(meta), path('*kreport.txt')                , emit: kreport
     tuple val(meta), path('*.sam')                       , optional: true, emit: sam
     tuple val(meta), path('*.mapped.fastq{,.1,.2}.gz')   , optional: true, emit: fastq_mapped
     tuple val(meta), path('*.unmapped.fastq{,.1,.2}.gz') , optional: true, emit: fastq_unmapped
@@ -30,7 +29,6 @@ process CENTRIFUGE {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def paired = meta.single_end ? "-U ${reads}" :  "-1 ${reads[0]} -2 ${reads[1]}"
-    def db_name = db.toString().replace(".tar.gz","")
     def unaligned = ''
     def aligned = ''
     if (meta.single_end) {
@@ -42,9 +40,10 @@ process CENTRIFUGE {
     }
     def sam_output = sam_format ? "--out-fmt 'sam'" : ''
     """
-    tar -xf $db
+    ## we add "-no-name ._" to ensure silly Mac OSX metafiles files aren't included
+    db_name=`find -L ${db} -name "*.1.cf" -not -name "._*"  | sed 's/.1.cf//'`
     centrifuge \\
-        -x $db_name \\
+        -x \$db_name \\
         -p $task.cpus \\
         $paired \\
         --report-file ${prefix}.report.txt \\
@@ -53,7 +52,6 @@ process CENTRIFUGE {
         $aligned \\
         $sam_output \\
         $args
-    centrifuge-kreport -x $db_name ${prefix}.results.txt > ${prefix}.kreport.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/centrifuge/centrifuge/meta.yml

@@ -1,4 +1,4 @@
-name: centrifuge
+name: centrifuge_centrifuge
 description: Classifies metagenomic sequence data
 keywords:
   - classify
@@ -25,8 +25,7 @@ input:
         respectively.
   - db:
       type: directory
-      description: Centrifuge database in .tar.gz format
+      description: Path to directory containing centrifuge database files
-      pattern: "*.tar.gz"
   - save_unaligned:
       type: value
       description: If true unmapped fastq files are saved
@@ -49,12 +48,6 @@ output:
       description: |
         File containing classification results
       pattern: "*.{results.txt}"
-  - kreport:
-      type: file
-      description: |
-        File containing kraken-style report from centrifuge
-        out files.
-      pattern: "*.{kreport.txt}"
   - fastq_unmapped:
       type: file
       description: Unmapped fastq files

modules/cnvpytor/histogram/main.nf

@@ -32,7 +32,7 @@ process CNVPYTOR_HISTOGRAM {
 
     stub:
     """
-    touch test.pytor
+    touch ${pytor.baseName}.pytor
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/cnvpytor/partition/main.nf

@@ -32,7 +32,7 @@ process CNVPYTOR_PARTITION {
 
     stub:
     """
-    touch test.pytor
+    touch ${pytor.baseName}.pytor
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/controlfreec/assesssignificance/main.nf

@@ -21,7 +21,7 @@ process CONTROLFREEC_ASSESSSIGNIFICANCE {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    cat /usr/local/bin/assess_significance.R | R --slave --args ${cnvs} ${ratio}
+    cat \$(which assess_significance.R) | R --slave --args ${cnvs} ${ratio}
 
     mv *.p.value.txt ${prefix}.p.value.txt
 
@@ -30,4 +30,15 @@ process CONTROLFREEC_ASSESSSIGNIFICANCE {
         controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC  //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" )
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.p.value.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC  //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" )
+    END_VERSIONS
+    """
 }

modules/controlfreec/freec/main.nf

@@ -21,7 +21,7 @@ process CONTROLFREEC_FREEC {
 
     output:
     tuple val(meta), path("*_ratio.BedGraph")   , emit: bedgraph, optional: true
-    tuple val(meta), path("*_control.cpn")      , emit: control_cpn
+    tuple val(meta), path("*_control.cpn")      , emit: control_cpn, optional: true
     tuple val(meta), path("*_sample.cpn")       , emit: sample_cpn
     tuple val(meta), path("GC_profile.*.cpn")   , emit: gcprofile_cpn, optional:true
     tuple val(meta), path("*_BAF.txt")          , emit: BAF
@@ -155,4 +155,22 @@ process CONTROLFREEC_FREEC {
         controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC  //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" )
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_ratio.BedGraph
+    touch ${prefix}_sample.cpn
+    touch GC_profile.${prefix}.cpn
+    touch ${prefix}_BAF.txt
+    touch ${prefix}_CNVs
+    touch ${prefix}_info.txt
+    touch ${prefix}_ratio.txt
+    touch config.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC  //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" )
+    END_VERSIONS
+    """
 }

modules/controlfreec/freec2bed/main.nf

@@ -28,4 +28,15 @@ process CONTROLFREEC_FREEC2BED {
         controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC  //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" )
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.bed
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC  //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" )
+    END_VERSIONS
+    """
 }

modules/controlfreec/freec2circos/main.nf

@@ -28,4 +28,15 @@ process CONTROLFREEC_FREEC2CIRCOS {
         controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC  //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" )
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.circos.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC  //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" )
+    END_VERSIONS
+    """
 }

modules/controlfreec/makegraph/main.nf

@@ -25,12 +25,24 @@ process CONTROLFREEC_MAKEGRAPH {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def baf = baf ?: ""
     """
-    cat /usr/local/bin/makeGraph.R | R --slave --args ${args} ${ratio} ${baf}
+    cat \$(which makeGraph.R) | R --slave --args ${args} ${ratio} ${baf}
 
     mv *_BAF.txt.png ${prefix}_BAF.png
     mv *_ratio.txt.log2.png ${prefix}_ratio.log2.png
     mv *_ratio.txt.png ${prefix}_ratio.png
 
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC  //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" )
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_BAF.png
+    touch ${prefix}_ratio.log2.png
+    touch ${prefix}_ratio.png
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/dastool/dastool/main.nf

@@ -14,8 +14,8 @@ process DASTOOL_DASTOOL {
 
     output:
     tuple val(meta), path("*.log")                                      , emit: log
-    tuple val(meta), path("*_summary.tsv")                              , emit: summary
+    tuple val(meta), path("*_summary.tsv")              , optional: true, emit: summary
-    tuple val(meta), path("*_DASTool_contig2bin.tsv")                   , emit: contig2bin
+    tuple val(meta), path("*_DASTool_contig2bin.tsv")   , optional: true, emit: contig2bin
     tuple val(meta), path("*.eval")                     , optional: true, emit: eval
     tuple val(meta), path("*_DASTool_bins/*.fa")        , optional: true, emit: bins
     tuple val(meta), path("*.pdf")                      , optional: true, emit: pdfs

modules/dshbio/exportsegments/main.nf

@@ -2,10 +2,10 @@ process DSHBIO_EXPORTSEGMENTS {
     tag "${meta.id}"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::dsh-bio=2.0.7" : null)
+    conda (params.enable_conda ? "bioconda::dsh-bio=2.0.8" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.7--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.8--hdfd78af_0' :
-        'quay.io/biocontainers/dsh-bio:2.0.7--hdfd78af_0' }"
+        'quay.io/biocontainers/dsh-bio:2.0.8--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(gfa)

modules/dshbio/filterbed/main.nf

@@ -2,10 +2,10 @@ process DSHBIO_FILTERBED {
     tag "${meta.id}"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::dsh-bio=2.0.7" : null)
+    conda (params.enable_conda ? "bioconda::dsh-bio=2.0.8" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.7--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.8--hdfd78af_0' :
-        'quay.io/biocontainers/dsh-bio:2.0.7--hdfd78af_0' }"
+        'quay.io/biocontainers/dsh-bio:2.0.8--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bed)

modules/dshbio/filtergff3/main.nf

@@ -2,10 +2,10 @@ process DSHBIO_FILTERGFF3 {
     tag "${meta.id}"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::dsh-bio=2.0.7" : null)
+    conda (params.enable_conda ? "bioconda::dsh-bio=2.0.8" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.7--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.8--hdfd78af_0' :
-        'quay.io/biocontainers/dsh-bio:2.0.7--hdfd78af_0' }"
+        'quay.io/biocontainers/dsh-bio:2.0.8--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(gff3)

modules/dshbio/splitbed/main.nf

@@ -2,10 +2,10 @@ process DSHBIO_SPLITBED {
     tag "${meta.id}"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::dsh-bio=2.0.7" : null)
+    conda (params.enable_conda ? "bioconda::dsh-bio=2.0.8" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.7--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.8--hdfd78af_0' :
-        'quay.io/biocontainers/dsh-bio:2.0.7--hdfd78af_0' }"
+        'quay.io/biocontainers/dsh-bio:2.0.8--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bed)

modules/dshbio/splitgff3/main.nf

@@ -2,10 +2,10 @@ process DSHBIO_SPLITGFF3 {
     tag "${meta.id}"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::dsh-bio=2.0.7" : null)
+    conda (params.enable_conda ? "bioconda::dsh-bio=2.0.8" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.7--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.8--hdfd78af_0' :
-        'quay.io/biocontainers/dsh-bio:2.0.7--hdfd78af_0' }"
+        'quay.io/biocontainers/dsh-bio:2.0.8--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(gff3)

modules/picard/crosscheckfingerprints/main.nf

@@ -0,0 +1,51 @@
+process PICARD_CROSSCHECKFINGERPRINTS {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(input1)
+    path input2
+    path haplotype_map
+
+    output:
+    tuple val(meta), path("*.crosscheck_metrics.txt"), emit: crosscheck_metrics
+    path "versions.yml"                              , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    def input1_string = input1.join(" --INPUT ")
+    def input2_string = input2 ? "--SECOND_INPUT " + input2.join(" --SECOND_INPUT ") : ""
+
+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[Picard CrosscheckFingerprints] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
+    """
+    picard \\
+        -Xmx${avail_mem}g \\
+        CrosscheckFingerprints \\
+        $args \\
+        --NUM_THREADS ${task.cpus} \\
+        --INPUT $input1_string \\
+        $input2_string \\
+        --HAPLOTYPE_MAP ${haplotype_map} \\
+        --OUTPUT ${prefix}.crosscheck_metrics.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        picard: \$( picard CrosscheckFingerprints --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d: )
+    END_VERSIONS
+    """
+}

modules/picard/crosscheckfingerprints/meta.yml

@@ -0,0 +1,53 @@
+name: "picard_crosscheckfingerprints"
+description: Checks that all data in the set of input files appear to come from the same individual
+keywords:
+  - alignment
+  - metrics
+  - statistics
+  - fingerprint
+  - bam
+tools:
+  - picard:
+      description: |
+        A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)
+        data and formats such as SAM/BAM/CRAM and VCF.
+      homepage: https://broadinstitute.github.io/picard/
+      documentation: https://broadinstitute.github.io/picard/
+      tool_dev_url: https://github.com/broadinstitute/picard/
+      licence: ["MIT"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - input1:
+      type: file
+      description: List containing 1 or more bam/vcf files or a file containing filepaths
+      pattern: "*.{bam,vcf,vcf.gz,txt,fofn}"
+  - input2:
+      type: file
+      description: Optional list containing 1 or more bam/vcf files or a file containing filepaths
+      pattern: "*.{bam,vcf,vcf.gz,txt,fofn}"
+  - haplotype_map:
+      type: file
+      description: Haplotype map file
+      pattern: "*.{txt,vcf,vcf.gz}"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - crosscheck_metrics:
+      type: file
+      description: Metrics created by crosscheckfingerprints
+      pattern: "*.{crosscheck_metrics.txt}"
+
+authors:
+  - "@matthdsm"

modules/picard/liftovervcf/main.nf

@@ -0,0 +1,49 @@
+process PICARD_LIFTOVERVCF {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(input_vcf)
+    path dict
+    path chain
+    path fasta
+
+    output:
+    tuple val(meta), path("*lifted.vcf.gz")  , emit: vcf_lifted
+    tuple val(meta), path("*unlifted.vcf.gz"), emit: vcf_unlifted
+    path "versions.yml"                      , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def avail_mem = 1
+    if (!task.memory) {
+        log.info '[Picard LiftoverVcf] Available memory not known - defaulting to 1GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
+    """
+    picard \\
+        -Xmx${avail_mem}g \\
+        LiftoverVcf \\
+        $args \\
+        I=$input_vcf \\
+        O=${prefix}.lifted.vcf.gz \\
+        CHAIN=$chain \\
+        REJECT=${prefix}.unlifted.vcf.gz \\
+        R=$fasta
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        picard: \$(picard LiftoverVcf --version 2>&1 | grep -o 'Version.*' | cut -f2- -d:)
+    END_VERSIONS
+    """
+}

modules/picard/liftovervcf/meta.yml

@@ -0,0 +1,55 @@
+name: picard_liftovervcf
+description: convert between genome builds
+keywords:
+  - liftOver
+  - picard
+tools:
+  - picard:
+      description: Move annotations from one assembly to another
+      homepage: https://gatk.broadinstitute.org/hc/en-us/articles/360037060932-LiftoverVcf-Picard
+      documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037060932-LiftoverVcf-Picard
+      tool_dev_url: https://github.com/broadinstitute/picard
+      doi: ""
+      licence: ["MIT"]
+
+input:
+  - meta:
+      type: map
+      description: Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - input_vcf:
+      type: file
+      description: VCF file
+      pattern: "*.{vcf,vcf.gz}"
+  - chain:
+      type: file
+      description: The liftover chain file
+  - fasta:
+      type: file
+      description: fasta file
+      pattern: "*.fasta"
+  - dict:
+      type: file
+      description: dictionary for fasta file
+      pattern: "*.{dict}"
+
+output:
+  - meta:
+      type: map
+      description: Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - vcf_lifted:
+      type: file
+      description: VCF file containing successfully lifted variants
+      pattern: "*.{lifted.vcf.gz}"
+  - vcf_unlifted:
+      type: file
+      description: VCF file containing unsuccessfully lifted variants
+      pattern: "*.{unlifted.vcf.gz}"
+
+authors:
+  - "@lucpen"

modules/prinseqplusplus/main.nf

@@ -0,0 +1,61 @@
+process PRINSEQPLUSPLUS {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::prinseq-plus-plus=1.2.3" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/prinseq-plus-plus:1.2.3--hc90279e_1':
+        'quay.io/biocontainers/prinseq-plus-plus:1.2.3--hc90279e_1' }"
+
+    input:
+    tuple val(meta), path(reads)
+
+    output:
+    tuple val(meta), path("*_good_out*.fastq.gz")                  , emit: good_reads
+    tuple val(meta), path("*_single_out*.fastq.gz"), optional: true, emit: single_reads
+    tuple val(meta), path("*_bad_out*.fastq.gz")   , optional: true, emit: bad_reads
+    tuple val(meta), path("*.log")                                 , emit: log
+    path "versions.yml"                                            , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    if (meta.single_end) {
+        """
+        prinseq++ \\
+            -threads $task.cpus \\
+            -fastq ${reads} \\
+            -out_name ${prefix} \\
+            -out_gz \\
+            -VERBOSE 1 \\
+            $args \\
+            | tee ${prefix}.log
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            prinseqplusplus: \$(echo \$(prinseq++ --version | cut -f 2 -d ' ' ))
+        END_VERSIONS
+        """
+    } else {
+        """
+        prinseq++ \\
+            -threads $task.cpus \\
+            -fastq ${reads[0]} \\
+            -fastq2 ${reads[1]} \\
+            -out_name ${prefix} \\
+            -out_gz \\
+            -VERBOSE 1 \\
+            $args \\
+            | tee ${prefix}.log
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            prinseqplusplus: \$(echo \$(prinseq++ --version | cut -f 2 -d ' ' ))
+        END_VERSIONS
+        """
+    }
+}

modules/prinseqplusplus/meta.yml

@@ -0,0 +1,60 @@
+name: "prinseqplusplus"
+description: PRINSEQ++ is a C++ implementation of the prinseq-lite.pl program. It can be used to filter, reformat or trim genomic and metagenomic sequence data
+keywords:
+  - fastq
+  - fasta
+  - filter
+  - trim
+tools:
+  - "prinseqplusplus":
+      description: "PRINSEQ++ - Multi-threaded C++ sequence cleaning"
+      homepage: "https://github.com/Adrian-Cantu/PRINSEQ-plus-plus"
+      documentation: "https://github.com/Adrian-Cantu/PRINSEQ-plus-plus"
+      tool_dev_url: "https://github.com/Adrian-Cantu/PRINSEQ-plus-plus"
+      doi: "10.7287/peerj.preprints.27553v1"
+      licence: "['GPL v2']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - reads:
+      type: file
+      description: |
+        List of input FastQ files of size 1 and 2 for single-end and paired-end
+        data, respectively.
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - good_reads:
+      type: file
+      description: Reads passing filter(s) in gzipped FASTQ format
+      pattern: "*_good_out_{R1,R2}.fastq.gz"
+  - single_reads:
+      type: file
+      description: |
+        Single reads without the pair passing filter(s) in gzipped FASTQ format
+      pattern: "*_single_out_{R1,R2}.fastq.gz"
+  - bad_reads:
+      type: file
+      description: |
+        Reads without not passing filter(s) in gzipped FASTQ format
+      pattern: "*_bad_out_{R1,R2}.fastq.gz"
+  - log:
+      type: file
+      description: |
+        Verbose level 2 STDOUT information in a log file
+      pattern: "*.log"
+
+authors:
+  - "@jfy133"

modules/snapaligner/index/main.nf

@@ -0,0 +1,59 @@
+process SNAPALIGNER_INDEX {
+    tag '$fasta'
+    label 'process_high'
+
+    conda (params.enable_conda ? "bioconda::snap-aligner=2.0.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/snap-aligner:2.0.1--hd03093a_1':
+        'quay.io/biocontainers/snap-aligner:2.0.1--hd03093a_1' }"
+
+    input:
+    path fasta
+    path altcontigfile
+    path nonaltcontigfile
+    path altliftoverfile
+
+    output:
+    path "snap/*"            ,emit: index
+    path "versions.yml"      ,emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def altcontigfile_arg = altcontigfile ? '-altContigFile ' + altcontigfile : ''
+    def nonaltcontigfile_arg = nonaltcontigfile ? '-nonAltContigFile ' + nonaltcontigfile : ''
+    def altliftoverfile_arg = altliftoverfile ? '-altLiftoverFile ' + altliftoverfile : ''
+    """
+    mkdir snap
+
+    snap-aligner \\
+        index \\
+        $fasta \\
+        snap \\
+        -t${task.cpus} \\
+        $altcontigfile_arg \\
+        $nonaltcontigfile_arg \\
+        $altliftoverfile_arg \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        snapaligner: \$(snap-aligner 2>&1| head -n 1 | sed 's/^.*version //')
+    END_VERSIONS
+    """
+    stub:
+    """
+    mkdir snap
+    echo "Genome" > snap/Genome
+    echo "GenomeIndex" > snap/GenomeIndex
+    echo "GenomeIndexHash" > snap/GenomeIndexHash
+    echo "OverflowTable" > snap/OverflowTable
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        snapaligner: \$(snap-aligner 2>&1| head -n 1 | sed 's/^.*version //;s/\.\$//')
+    END_VERSIONS
+    """
+}

modules/snapaligner/index/meta.yml

@@ -0,0 +1,39 @@
+name: "snapaligner_index"
+description: Create a SNAP index for reference genome
+keywords:
+  - index
+  - fasta
+  - genome
+  - reference
+tools:
+  - "snapaligner":
+      description: "Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data"
+      homepage: "http://snap.cs.berkeley.edu"
+      documentation: "https://1drv.ms/b/s!AhuEg_0yZD86hcpblUt-muHKYsG8fA?e=R8ogug"
+      tool_dev_url: "https://github.com/amplab/snap"
+      doi: "10.1101/2021.11.23.469039"
+      licence: "['Apache v2']"
+input:
+  - fasta:
+      type: file
+      description: Input genome fasta file
+  - altcontigfile:
+      type: file
+      description: Optional file with a list of alt contig names, one per line.
+  - nonaltcontigfile:
+      type: file
+      description: Optional file that contains a list of contigs (one per line) that will not be marked ALT regardless of size.
+  - altliftoverfile:
+      type: file
+      description: Optional file containing ALT-to-REF mappings (SAM format). e.g., hs38DH.fa.alt from bwa-kit.
+output:
+  - index:
+      type: file
+      description: SNAP genome index files
+      pattern: "{Genome,GenomeIndex,GenomeIndexHash,OverflowTable}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@matthdsm"

modules/stadeniolib/scramble/main.nf

@@ -0,0 +1,61 @@
+process STADENIOLIB_SCRAMBLE {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::staden_io_lib=1.14.14" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/staden_io_lib:1.14.14--h0d9da7e_3' :
+        'quay.io/biocontainers/staden_io_lib:1.14.14--h0d9da7e_3' }"
+
+    input:
+    tuple val(meta), path(reads)
+    path(fasta)
+    path(fai)
+    path(gzi)
+
+    output:
+    tuple val(meta), path("*.cram") ,emit: cram
+    path "*.gzi"                    ,emit: gzi, optional: true
+    path "versions.yml"             ,emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    def inputformat = reads.getExtension
+    def outputformat = "cram"
+    if ("-O sam" in args) {
+        outputformat = "sam"
+    } else if ("-O bam" in args) {
+        outputformat = "bam"
+    }
+
+    def reference = if fasta && fai : "--r ${fasta}" else ""
+    if (outputformat == "cram" && !reference) {
+        error "Cannot convert to CRAM without a reference"
+    }
+
+    def gz_index = if gzi : "--g ${gzi}" else ""
+    if (outputformat == "cram" || outputformat == "sam") {
+        gz_index = ""
+        warning "Cannot use gzip index for CRAM or SAM output"
+    }
+
+    """
+    scramble \
+        $args \
+        -I ${inputformat} \
+        $reference \
+        -t $task.cpus \
+        ${reads} \
+        ${prefix}.${outputformat}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        stadeniolib: \$(echo \$(scramble -h | head -n 1 |sed 's/^.*version //'))
+    END_VERSIONS
+    """
+}

modules/stadeniolib/scramble/meta.yml

@@ -0,0 +1,58 @@
+name: "stadeniolib_scramble"
+description: Advanced sequence file format conversions
+keywords:
+  - sam
+  - bam
+  - cram
+  - compression
+tools:
+  - "scramble":
+      description: "Staden Package 'io_lib' (sometimes referred to as libstaden-read by distributions). This contains code for reading and writing a variety of Bioinformatics / DNA Sequence formats."
+      homepage: "https://github.com/jkbonfield/io_lib"
+      documentation: "https://github.com/jkbonfield/io_lib/blob/master/README.md"
+      tool_dev_url: "https://github.com/jkbonfield/io_lib"
+      licence: "['BSD']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - reads:
+      type: file
+      description: BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+  - fasta:
+      type: file
+      description: Reference genome in FASTA format
+      pattern: "*.{fa,fasta}"
+  - fai:
+      type: file
+      description: FASTA index file from samtools faidx
+      pattern: "*.{fai}"
+  - gzi:
+      type: file
+      description: Optional gzip index file for BAM inputs
+      pattern: "*.gzi"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - reads:
+      type: file
+      description: Converted reads
+      pattern: "*.{sam, bam, cram}"
+  - gzi:
+      type: Optional file
+      description: gzip index file for BAM outputs
+      pattern: ".{bam.gzi}"
+authors:
+  - "@matthdsm"

modules/untar/main.nf

@@ -2,10 +2,10 @@ process UNTAR {
     tag "$archive"
     label 'process_low'
 
-    conda (params.enable_conda ? "conda-forge::tar=1.32" : null)
+    conda (params.enable_conda ? "conda-forge::tar=1.34" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
+        'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv2/biocontainers_v1.2.0_cv2.img' :
-        'biocontainers/biocontainers:v1.2.0_cv1' }"
+        'biocontainers/biocontainers:v1.2.0_cv2' }"
 
     input:
     tuple val(meta), path(archive)

subworkflows/nf-core/homer/groseq/main.nf

@@ -0,0 +1,50 @@
+/*
+ * Identify transcripts with homer
+ */
+
+include { HOMER_MAKETAGDIRECTORY      } from '../../../../modules/homer/maketagdirectory/main'
+include { HOMER_MAKEUCSCFILE          } from '../../../../modules/homer/makeucscfile/main'
+include { HOMER_FINDPEAKS             } from '../../../../modules/homer/findpeaks/main'
+include { HOMER_POS2BED               } from '../../../../modules/homer/pos2bed/main'
+
+workflow HOMER_GROSEQ {
+    take:
+    bam   // channel: [ val(meta), [ reads ] ]
+    fasta //    file: /path/to/bwa/index/
+
+    main:
+
+    ch_versions = Channel.empty()
+
+    /*
+    * Create a Tag Directory From The GRO-Seq experiment
+    */
+    HOMER_MAKETAGDIRECTORY ( bam, fasta )
+    ch_versions = ch_versions.mix(HOMER_MAKETAGDIRECTORY.out.versions.first())
+
+    /*
+    * Creating UCSC Visualization Files
+    */
+    HOMER_MAKEUCSCFILE ( HOMER_MAKETAGDIRECTORY.out.tagdir )
+    ch_versions = ch_versions.mix(HOMER_MAKEUCSCFILE.out.versions.first())
+
+    /*
+    * Find transcripts directly from GRO-Seq
+    */
+    HOMER_FINDPEAKS ( HOMER_MAKETAGDIRECTORY.out.tagdir )
+    ch_versions = ch_versions.mix(HOMER_FINDPEAKS.out.versions.first())
+
+    /*
+    * Convert peak file to bed file
+    */
+    HOMER_POS2BED ( HOMER_FINDPEAKS.out.txt )
+    ch_versions = ch_versions.mix(HOMER_POS2BED.out.versions.first())
+
+    emit:
+    tagdir             = HOMER_MAKETAGDIRECTORY.out.tagdir // channel: [ val(meta), [ tagdir ] ]
+    bed_graph          = HOMER_MAKEUCSCFILE.out.bedGraph   // channel: [ val(meta), [ tag_dir/*ucsc.bedGraph.gz ] ]
+    peaks              = HOMER_FINDPEAKS.out.txt           // channel: [ val(meta), [ *peaks.txt ] ]
+    bed                = HOMER_POS2BED.out.bed             // channel: [ val(meta), [ *peaks.txt ] ]
+
+    versions = ch_versions                                 // channel: [ versions.yml ]
+}

subworkflows/nf-core/homer/groseq/meta.yml

@@ -0,0 +1,48 @@
+name: homer_groseq
+description: Perform variant calling on a set of normal samples using mutect2 panel of normals mode. Group them into a genomicsdbworkspace using genomicsdbimport, then use this to create a panel of normals using createsomaticpanelofnormals.
+keywords:
+  - homer
+  - groseq
+  - nascent
+modules:
+  - homer/maketagdirectory
+  - homer/makeucscfile
+  - homer/findpeaks
+  - homer/pos2bed
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test' ]
+  - input:
+      type: list
+      description: list of BAM files, also able to take SAM and BED as input
+      pattern: "[ *.{bam/sam/bed} ]"
+  - fasta:
+      type: file
+      description: The reference fasta file
+      pattern: "*.fasta"
+output:
+  - tagdir:
+      type: directory
+      description: The "Tag Directory"
+      pattern: "*_tagdir"
+  - bedGraph:
+      type: file
+      description: The UCSC bed graph
+      pattern: "*.bedGraph.gz"
+  - peaks:
+      type: file
+      description: The found peaks
+      pattern: "*.peaks.txt"
+  - bed:
+      type: file
+      description: A BED file of the found peaks
+      pattern: "*.bed"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@Emiller88"

tests/config/pytest_modules.yml

@@ -214,6 +214,10 @@ biobambam/bammarkduplicates2:
   - modules/biobambam/bammarkduplicates2/**
   - tests/modules/biobambam/bammarkduplicates2/**
 
+biobambam/bamsormadup:
+  - modules/biobambam/bamsormadup/**
+  - tests/modules/biobambam/bamsormadup/**
+
 biscuit/align:
   - modules/biscuit/index/**
   - modules/biscuit/align/**
@@ -391,9 +395,9 @@ cellranger/mkref:
   - modules/cellranger/gtf/**
   - tests/modules/cellranger/gtf/**
 
-centrifuge:
+centrifuge/centrifuge:
-  - modules/centrifuge/**
+  - modules/centrifuge/centrifuge/**
-  - tests/modules/centrifuge/**
+  - tests/modules/centrifuge/centrifuge/**
 
 checkm/lineagewf:
   - modules/checkm/lineagewf/**
@@ -1339,6 +1343,10 @@ picard/createsequencedictionary:
   - modules/picard/createsequencedictionary/**
   - tests/modules/picard/createsequencedictionary/**
 
+picard/crosscheckfingerprints:
+  - modules/picard/crosscheckfingerprints/**
+  - tests/modules/picard/crosscheckfingerprints/**
+
 picard/filtersamreads:
   - modules/picard/filtersamreads/**
   - tests/modules/picard/filtersamreads/**
@@ -1347,6 +1355,10 @@ picard/fixmateinformation:
   - modules/picard/fixmateinformation/**
   - tests/modules/picard/fixmateinformation/**
 
+picard/liftovervcf:
+  - modules/picard/liftovervcf/**
+  - tests/modules/picard/liftovervcf/**
+
 picard/markduplicates:
   - modules/picard/markduplicates/**
   - tests/modules/picard/markduplicates/**
@@ -1407,6 +1419,10 @@ preseq/lcextrap:
   - modules/preseq/lcextrap/**
   - tests/modules/preseq/lcextrap/**
 
+prinseqplusplus:
+  - modules/prinseqplusplus/**
+  - tests/modules/prinseqplusplus/**
+
 prodigal:
   - modules/prodigal/**
   - tests/modules/prodigal/**
@@ -1651,6 +1667,10 @@ sistr:
   - modules/sistr/**
   - tests/modules/sistr/**
 
+snapaligner/index:
+  - modules/snapaligner/index/**
+  - tests/modules/snapaligner/index/**
+
 snpdists:
   - modules/snpdists/**
   - tests/modules/snpdists/**
@@ -1691,6 +1711,10 @@ ssuissero:
   - modules/ssuissero/**
   - tests/modules/ssuissero/**
 
+stadeniolib/scramble:
+  - modules/stadeniolib/scramble/**
+  - tests/modules/stadeniolib/scramble/**
+
 staphopiasccmec:
   - modules/staphopiasccmec/**
   - tests/modules/staphopiasccmec/**

tests/config/test_data.config

@@ -161,6 +161,7 @@ params {
                 gnomad_r2_1_1_21_vcf_gz_tbi                    = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi"
                 mills_and_1000g_indels_21_vcf_gz               = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz"
                 mills_and_1000g_indels_21_vcf_gz_tbi           = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi"
+                haplotype_map                                  = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/haplotype_map.txt"
 
                 index_salmon                                   = "${test_data_dir}/genomics/homo_sapiens/genome/index/salmon"
                 repeat_expansions                              = "${test_data_dir}/genomics/homo_sapiens/genome/loci/repeat_expansions.json"

tests/modules/adapterremoval/test.yml

@@ -3,10 +3,10 @@
   tags:
     - adapterremoval
   files:
-    - path: output/adapterremoval/test.discarded.gz
+    - path: output/adapterremoval/test.discarded.fastq.gz
-    - path: output/adapterremoval/test.log
+    - path: output/adapterremoval/test.settings
       md5sum: 2fd3d5d703b63ba33a83021fccf25f77
-    - path: output/adapterremoval/test.truncated.gz
+    - path: output/adapterremoval/test.truncated.fastq.gz
       md5sum: 62139afee94defad5b83bdd0b8475a1f
     - path: output/adapterremoval/versions.yml
       md5sum: ac5b46719719b7ee62739530b80869fc
@@ -16,12 +16,12 @@
   tags:
     - adapterremoval
   files:
-    - path: output/adapterremoval/test.discarded.gz
+    - path: output/adapterremoval/test.discarded.fastq.gz
-    - path: output/adapterremoval/test.log
+    - path: output/adapterremoval/test.settings
       md5sum: b8a451d3981b327f3fdb44f40ba2d6d1
-    - path: output/adapterremoval/test.pair1.truncated.gz
+    - path: output/adapterremoval/test.pair1.truncated.fastq.gz
       md5sum: 294a6277f0139bd597e57c6fa31f39c7
-    - path: output/adapterremoval/test.pair2.truncated.gz
+    - path: output/adapterremoval/test.pair2.truncated.fastq.gz
       md5sum: de7b38e2c881bced8671acb1ab452d78
     - path: output/adapterremoval/versions.yml
       md5sum: fa621c887897da5a379c719399c17db7
@@ -31,15 +31,15 @@
   tags:
     - adapterremoval
   files:
-    - path: output/adapterremoval/test.collapsed.gz
+    - path: output/adapterremoval/test.collapsed.fastq.gz
       md5sum: ff956de3532599a56c3efe5369f0953f
-    - path: output/adapterremoval/test.collapsed.truncated.gz
+    - path: output/adapterremoval/test.collapsed.truncated.fastq.gz
-    - path: output/adapterremoval/test.discarded.gz
+    - path: output/adapterremoval/test.discarded.fastq.gz
-    - path: output/adapterremoval/test.log
+    - path: output/adapterremoval/test.settings
       md5sum: 7f0b2328152226e46101a535cce718b3
-    - path: output/adapterremoval/test.pair1.truncated.gz
+    - path: output/adapterremoval/test.pair1.truncated.fastq.gz
       md5sum: 683be19bc1c83008944b6b719bfa34e1
-    - path: output/adapterremoval/test.pair2.truncated.gz
+    - path: output/adapterremoval/test.pair2.truncated.fastq.gz
       md5sum: e6548fe061f3ef86368b26da930174d0
     - path: output/adapterremoval/versions.yml
       md5sum: 78f589bb313c8da0147ca8ce77d7f3bf

tests/modules/biobambam/bammarkduplicates2/test.yml

@@ -5,8 +5,8 @@
     - biobambam
   files:
     - path: output/biobambam/test.bam
-      md5sum: 1cf7f957eb20b4ace9f10d0cf0a0649a
+      md5sum: 603edff09029096ddf2bb8a3f12d7aa7
     - path: output/biobambam/test.metrics.txt
       md5sum: 30d6e7d90bb5df46329d4bc0144ce927
     - path: output/biobambam/versions.yml
-      md5sum: 0d6f3137ed4515333d73c779f2c24445
+      md5sum: dfdf2b084655d124acac0bfb4eda86cc

tests/modules/biobambam/bamsormadup/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BIOBAMBAM_BAMSORMADUP } from '../../../../modules/biobambam/bamsormadup/main.nf'
+
+workflow test_biobambam_bamsormadup {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)],
+    ]
+
+    BIOBAMBAM_BAMSORMADUP ( input, [] )
+}

tests/modules/biobambam/bamsormadup/nextflow.config

@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}

tests/modules/biobambam/bamsormadup/test.yml

@@ -0,0 +1,11 @@
+- name: biobambam bamsormadup test_biobambam_bamsormadup
+  command: nextflow run tests/modules/biobambam/bamsormadup -entry test_biobambam_bamsormadup -c tests/config/nextflow.config
+  tags:
+    - biobambam/bamsormadup
+    - biobambam
+  files:
+    - path: output/biobambam/test.bam
+      md5sum: 243a77fb0642fd46bb16a4d3432d19dc
+    - path: output/biobambam/test.metrics.txt
+      md5sum: 1721879bea1f3888ecd33b35e6ee0e72
+    - path: output/biobambam/versions.yml

tests/modules/centrifuge/centrifuge/main.nf

@@ -0,0 +1,37 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UNTAR                 } from '../../../../modules/untar/main.nf'
+include { CENTRIFUGE_CENTRIFUGE } from '../../../../modules/centrifuge/centrifuge/main.nf'
+
+workflow test_centrifuge_centrifuge_single_end {
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+            ]
+    db    =  [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/minigut_cf.tar.gz', checkIfExists: true) ]
+    save_unaligned = true
+    save_aligned = false
+    sam_format = false
+
+    UNTAR ( db )
+    CENTRIFUGE_CENTRIFUGE ( input, UNTAR.out.untar.map{ it[1] }, save_unaligned, save_aligned, sam_format )
+
+}
+
+workflow test_centrifuge_centrifuge_paired_end {
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ]
+     db    =  [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/minigut_cf.tar.gz', checkIfExists: true) ]
+     //db_name = "minigut_cf"
+     save_unaligned = true
+     save_aligned = false
+     sam_format = false
+
+    UNTAR ( db )
+    CENTRIFUGE_CENTRIFUGE ( input, UNTAR.out.untar.map{ it[1] }, save_unaligned, save_aligned, sam_format )
+
+
+}

tests/modules/centrifuge/centrifuge/test.yml

@@ -1,20 +1,20 @@
-- name: centrifuge test_centrifuge_single_end
+- name: centrifuge centrifuge test_centrifuge_centrifuge_single_end
-  command: nextflow run tests/modules/centrifuge -entry test_centrifuge_single_end -c tests/config/nextflow.config
+  command: nextflow run tests/modules/centrifuge/centrifuge -entry test_centrifuge_centrifuge_single_end -c tests/config/nextflow.config
   tags:
     - centrifuge
+    - centrifuge/centrifuge
   files:
-    - path: output/centrifuge/test.kreport.txt
     - path: output/centrifuge/test.report.txt
     - path: output/centrifuge/test.results.txt
     - path: output/centrifuge/test.unmapped.fastq.gz
     - path: output/centrifuge/versions.yml
 
-- name: centrifuge test_centrifuge_paired_end
+- name: centrifuge centrifuge test_centrifuge_centrifuge_paired_end
-  command: nextflow run tests/modules/centrifuge -entry test_centrifuge_paired_end -c tests/config/nextflow.config
+  command: nextflow run tests/modules/centrifuge/centrifuge -entry test_centrifuge_centrifuge_paired_end -c tests/config/nextflow.config
   tags:
     - centrifuge
+    - centrifuge/centrifuge
   files:
-    - path: output/centrifuge/test.kreport.txt
     - path: output/centrifuge/test.report.txt
     - path: output/centrifuge/test.results.txt
     - path: output/centrifuge/test.unmapped.fastq.1.gz

tests/modules/centrifuge/main.nf

@@ -1,33 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { CENTRIFUGE } from '../../../modules/centrifuge/main.nf'
-
-workflow test_centrifuge_single_end {
-    input = [ [ id:'test', single_end:true ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-            ]
-    db   =  file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/minigut_cf.tar.gz", checkIfExists: true)
-    save_unaligned = true
-    save_aligned = false
-    sam_format = false
-
-    CENTRIFUGE ( input, db, save_unaligned, save_aligned, sam_format )
-
-}
-
-workflow test_centrifuge_paired_end {
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-            ]
-     db   =  file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/minigut_cf.tar.gz", checkIfExists: true)
-     save_unaligned = true
-     save_aligned = false
-     sam_format = false
-
-    CENTRIFUGE ( input, db, save_unaligned, save_aligned, sam_format )
-
-
-}

tests/modules/controlfreec/assesssignificance/main.nf

@@ -40,3 +40,38 @@ workflow test_controlfreec_assesssignificance {
     sig_in = CONTROLFREEC_FREEC.out.CNV.join(CONTROLFREEC_FREEC.out.ratio)
     CONTROLFREEC_ASSESSSIGNIFICANCE ( sig_in )
 }
+
+workflow test_controlfreec_assesssignificance_single {
+
+    input = [
+        [ id:'test', single_end:false, sex:'XX' ], // meta map
+        [],
+        file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
+        [],[],[],[]
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+
+    dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
+    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
+
+    chrfiles = [ [], file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true) ]
+    target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+
+    UNTAR(chrfiles)
+    CONTROLFREEC_FREEC (input,
+                        fasta,
+                        fai,
+                        [],
+                        dbsnp,
+                        dbsnp_tbi,
+                        UNTAR.out.untar.map{ it[1] },
+                        [],
+                        target_bed,
+                        []
+                        )
+
+    sig_in = CONTROLFREEC_FREEC.out.CNV.join(CONTROLFREEC_FREEC.out.ratio)
+    CONTROLFREEC_ASSESSSIGNIFICANCE ( sig_in )
+}

tests/modules/controlfreec/assesssignificance/test.yml

@@ -7,4 +7,12 @@
     - path: output/controlfreec/test.p.value.txt
       md5sum: 44e23b916535fbc1a3f47b57fad292df
     - path: output/controlfreec/versions.yml
-      md5sum: 0aa42fed10d61e4570fe1e0e83ffe932
+
+- name: controlfreec assesssignificance test_controlfreec_assesssignificance_single
+  command: nextflow run tests/modules/controlfreec/assesssignificance -entry test_controlfreec_assesssignificance_single -c tests/config/nextflow.config -stub-run
+  tags:
+    - controlfreec/assesssignificance
+    - controlfreec
+  files:
+    - path: output/controlfreec/test.p.value.txt
+    - path: output/controlfreec/versions.yml

tests/modules/controlfreec/freec/main.nf

@@ -36,3 +36,36 @@ workflow test_controlfreec_freec {
                         []
                         )
 }
+
+workflow test_controlfreec_freec_single {
+
+    input = [
+        [ id:'test2', single_end:false, sex:'XX' ], // meta map
+        [],
+        file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
+        [],[],[],[]
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+
+    dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
+    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
+
+    chrfiles = [ [], file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true) ]
+    target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+
+    UNTAR(chrfiles)
+    CONTROLFREEC_FREEC (input,
+                        fasta,
+                        fai,
+                        [],
+                        dbsnp,
+                        dbsnp_tbi,
+                        UNTAR.out.untar.map{ it[1] },
+                        [],
+                        target_bed,
+                        []
+                        )
+}
+

tests/modules/controlfreec/freec/test.yml

@@ -20,4 +20,18 @@
     - path: output/controlfreec/test2.mpileup.gz_sample.cpn
       md5sum: c80dad58a77b1d7ba6d273999f4b4b4b
     - path: output/controlfreec/versions.yml
-      md5sum: 3ab250a2ab3be22628124c7c65324651
+
+- name: controlfreec test_controlfreec_freec_single
+  command: nextflow run tests/modules/controlfreec/freec -entry test_controlfreec_freec_single -c tests/config/nextflow.config -stub-run
+  tags:
+    - controlfreec
+    - controlfreec/freec
+  files:
+    - path: output/controlfreec/config.txt
+    - path: output/controlfreec/test2_BAF.txt
+    - path: output/controlfreec/test2_CNVs
+    - path: output/controlfreec/test2_info.txt
+    - path: output/controlfreec/test2_ratio.BedGraph
+    - path: output/controlfreec/test2_ratio.txt
+    - path: output/controlfreec/test2_sample.cpn
+    - path: output/controlfreec/versions.yml

tests/modules/controlfreec/freec2bed/main.nf

@@ -39,3 +39,37 @@ workflow test_controlfreec_freec2bed {
 
     CONTROLFREEC_FREEC2BED ( CONTROLFREEC_FREEC.out.ratio )
 }
+
+workflow test_controlfreec_freec2bed_single {
+
+      input = [
+        [ id:'test', single_end:false, sex:'XX' ], // meta map
+        [],
+        file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
+        [],[],[],[]
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+
+    dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
+    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
+
+    chrfiles = [ [], file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true) ]
+    target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+
+    UNTAR(chrfiles)
+    CONTROLFREEC_FREEC (input,
+                        fasta,
+                        fai,
+                        [],
+                        dbsnp,
+                        dbsnp_tbi,
+                        UNTAR.out.untar.map{ it[1] },
+                        [],
+                        target_bed,
+                        []
+                        )
+
+    CONTROLFREEC_FREEC2BED ( CONTROLFREEC_FREEC.out.ratio )
+}

tests/modules/controlfreec/freec2bed/test.yml

@@ -6,3 +6,11 @@
   files:
     - path: output/controlfreec/test.bed
       md5sum: abe10b7ce94ba903503e697394c17297
+
+- name: controlfreec freec2bed test_controlfreec_freec2bed_single
+  command: nextflow run tests/modules/controlfreec/freec2bed -entry test_controlfreec_freec2bed_single -c tests/config/nextflow.config -stub-run
+  tags:
+    - controlfreec/freec2bed
+    - controlfreec
+  files:
+    - path: output/controlfreec/test.bed

tests/modules/controlfreec/freec2circos/main.nf

@@ -39,3 +39,37 @@ workflow test_controlfreec_freec2circos {
 
     CONTROLFREEC_FREEC2CIRCOS ( CONTROLFREEC_FREEC.out.ratio )
 }
+
+workflow test_controlfreec_freec2circos_single {
+
+    input = [
+        [ id:'test', single_end:false, sex:'XX' ], // meta map
+        [],
+        file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
+        [],[],[],[]
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+
+    dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
+    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
+
+    chrfiles = [ [], file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true) ]
+    target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+
+    UNTAR(chrfiles)
+    CONTROLFREEC_FREEC (input,
+                        fasta,
+                        fai,
+                        [],
+                        dbsnp,
+                        dbsnp_tbi,
+                        UNTAR.out.untar.map{ it[1] },
+                        [],
+                        target_bed,
+                        []
+                        )
+
+    CONTROLFREEC_FREEC2CIRCOS ( CONTROLFREEC_FREEC.out.ratio )
+}

tests/modules/controlfreec/freec2circos/test.yml

@@ -6,3 +6,11 @@
   files:
     - path: output/controlfreec/test.circos.txt
       md5sum: 19cf35f2c36b46f717dc8342b8a5a645
+
+- name: controlfreec freec2circos test_controlfreec_freec2circos_single
+  command: nextflow run tests/modules/controlfreec/freec2circos -entry test_controlfreec_freec2circos_single -c tests/config/nextflow.config -stub-run
+  tags:
+    - controlfreec
+    - controlfreec/freec2circos
+  files:
+    - path: output/controlfreec/test.circos.txt

tests/modules/controlfreec/makegraph/main.nf

@@ -40,3 +40,38 @@ workflow test_controlfreec_makegraph {
     makegraph_in = CONTROLFREEC_FREEC.out.ratio.join(CONTROLFREEC_FREEC.out.BAF)
     CONTROLFREEC_MAKEGRAPH ( makegraph_in )
 }
+
+workflow test_controlfreec_makegraph_single {
+
+    input = [
+        [ id:'test', single_end:false, sex:'XX' ], // meta map
+        [],
+        file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
+        [],[],[],[]
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+
+    dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
+    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
+
+    chrfiles = [ [], file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true) ]
+    target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+
+    UNTAR(chrfiles)
+    CONTROLFREEC_FREEC (input,
+                        fasta,
+                        fai,
+                        [],
+                        dbsnp,
+                        dbsnp_tbi,
+                        UNTAR.out.untar.map{ it[1] },
+                        [],
+                        target_bed,
+                        []
+                        )
+
+    makegraph_in = CONTROLFREEC_FREEC.out.ratio.join(CONTROLFREEC_FREEC.out.BAF)
+    CONTROLFREEC_MAKEGRAPH ( makegraph_in )
+}

tests/modules/controlfreec/makegraph/test.yml

@@ -10,3 +10,13 @@
       md5sum: b3c7916b1b4951a0cc3da20d8e9e0262
     - path: output/controlfreec/test_ratio.png
       md5sum: 1435b29536b3b1555b4c423f8f4fb000
+
+- name: controlfreec makegraph test_controlfreec_makegraph_single
+  command: nextflow run tests/modules/controlfreec/makegraph -entry test_controlfreec_makegraph_single -c tests/config/nextflow.config -stub-run
+  tags:
+    - controlfreec
+    - controlfreec/makegraph
+  files:
+    - path: output/controlfreec/test_BAF.png
+    - path: output/controlfreec/test_ratio.log2.png
+    - path: output/controlfreec/test_ratio.png

tests/modules/picard/crosscheckfingerprints/main.nf

@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PICARD_CROSSCHECKFINGERPRINTS } from '../../../../modules/picard/crosscheckfingerprints/main.nf'
+
+workflow test_picard_crosscheckfingerprints {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)],
+    ]
+    PICARD_CROSSCHECKFINGERPRINTS ( input,[], file(params.test_data['homo_sapiens']['genome']['haplotype_map'], checkIfExists: true))
+}

tests/modules/picard/crosscheckfingerprints/nextflow.config

@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    withName: PICARD_CROSSCHECKFINGERPRINTS {ext.args = "--EXIT_CODE_WHEN_MISMATCH 0"}
+}

tests/modules/picard/crosscheckfingerprints/test.yml

@@ -0,0 +1,8 @@
+- name: "picard crosscheckfingerprints"
+  command: nextflow run ./tests/modules/picard/crosscheckfingerprints -entry test_picard_crosscheckfingerprints -c ./tests/config/nextflow.config -c ./tests/modules/picard/crosscheckfingerprints/nextflow.config
+  tags:
+    - "picard"
+    - "picard/crosscheckfingerprints"
+  files:
+    - path: "output/picard/test.crosscheck_metrics.txt"
+    - path: output/picard/versions.yml

tests/modules/picard/liftovervcf/main.nf

@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PICARD_LIFTOVERVCF } from '../../../../modules/picard/liftovervcf/main.nf'
+
+workflow test_picard_liftovervcf {
+
+    input_vcf = [ [ id:'test' ],
+        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true)
+            ]
+    dict =  file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+    chain =  file(params.test_data['homo_sapiens']['genome']['genome_chain_gz'], checkIfExists: true)
+    fasta  = [ file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
+
+    PICARD_LIFTOVERVCF ( input_vcf, dict, chain, fasta )
+}

tests/modules/picard/liftovervcf/nextflow.config

@@ -0,0 +1,5 @@
+process {
+    ext.args = "WARN_ON_MISSING_CONTIG=true"
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}

tests/modules/picard/liftovervcf/test.yml

@@ -0,0 +1,11 @@
+- name: picard liftovervcf test_picard_liftovervcf
+  command: nextflow run tests/modules/picard/liftovervcf -entry test_picard_liftovervcf -c tests/config/nextflow.config
+  tags:
+    - picard/liftovervcf
+    - picard
+  files:
+    - path: output/picard/test.lifted.vcf.gz
+      contains:
+        - "chr22"
+    - path: output/picard/test.unlifted.vcf.gz
+    - path: output/picard/versions.yml

tests/modules/prinseqplusplus/main.nf

@@ -0,0 +1,24 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PRINSEQPLUSPLUS } from '../../../modules/prinseqplusplus/main.nf'
+
+workflow test_prinseqplusplus_single_end {
+
+        input = [ [ id:'test', single_end:true ], // meta map
+            [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+        ]
+
+    PRINSEQPLUSPLUS ( input )
+}
+
+workflow test_prinseqplusplus_paired_end {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+            [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+        ]
+
+    PRINSEQPLUSPLUS ( input )
+}

tests/modules/prinseqplusplus/nextflow.config

@@ -0,0 +1,9 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: PRINSEQPLUSPLUS {
+        ext.args = "-lc_entropy=0.8"
+    }
+
+}

tests/modules/prinseqplusplus/test.yml

@@ -0,0 +1,27 @@
+- name: prinseqplusplus test_prinseqplusplus_single_end
+  command: nextflow run tests/modules/prinseqplusplus -entry test_prinseqplusplus_single_end -c tests/config/nextflow.config
+  tags:
+    - prinseqplusplus
+  files:
+    - path: output/prinseqplusplus/test.log
+      contains:
+        - "reads removed by -lc_entropy"
+    - path: output/prinseqplusplus/test_bad_out.fastq.gz
+    - path: output/prinseqplusplus/test_good_out.fastq.gz
+    - path: output/prinseqplusplus/versions.yml
+
+- name: prinseqplusplus test_prinseqplusplus_paired_end
+  command: nextflow run tests/modules/prinseqplusplus -entry test_prinseqplusplus_paired_end -c tests/config/nextflow.config
+  tags:
+    - prinseqplusplus
+  files:
+    - path: output/prinseqplusplus/test.log
+      contains:
+        - "reads removed by -lc_entropy"
+    - path: output/prinseqplusplus/test_bad_out_R1.fastq.gz
+    - path: output/prinseqplusplus/test_bad_out_R2.fastq.gz
+    - path: output/prinseqplusplus/test_good_out_R1.fastq.gz
+    - path: output/prinseqplusplus/test_good_out_R2.fastq.gz
+    - path: output/prinseqplusplus/test_single_out_R1.fastq.gz
+    - path: output/prinseqplusplus/test_single_out_R2.fastq.gz
+    - path: output/prinseqplusplus/versions.yml

tests/modules/snapaligner/index/main.nf

@@ -0,0 +1,9 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SNAPALIGNER_INDEX } from '../../../../modules/snapaligner/index/main.nf'
+
+workflow test_snapaligner_index {
+    SNAPALIGNER_INDEX ( file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),[],[],[])
+}

tests/modules/snapaligner/index/nextflow.config

@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    
+}

tests/modules/snapaligner/index/test.yml

@@ -0,0 +1,13 @@
+- name: snapaligner index test_snapaligner_index
+  command: nextflow run tests/modules/snapaligner/index -entry test_snapaligner_index -c tests/config/nextflow.config
+  tags:
+    - snapaligner/index
+    - snapaligner
+  files:
+    - path: output/snapaligner/snap/Genome
+      md5sum: 7e189c954142ba37460332b467e34ed4
+    - path: output/snapaligner/snap/GenomeIndex
+      md5sum: 298da8bcb1134f7b24379a792a7a46f8
+    - path: output/snapaligner/snap/GenomeIndexHash
+    - path: output/snapaligner/snap/OverflowTable
+    - path: output/snapaligner/versions.yml

tests/modules/stadeniolib/scramble/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { STADENIOLIB_SCRAMBLE } from '../../../../modules/stadeniolib/scramble/main.nf'
+
+workflow test_stadeniolib {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    STADENIOLIB_SCRAMBLE ( input, file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true), file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true), [])
+}

tests/modules/stadeniolib/scramble/nextflow.config

@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    
+}

tests/modules/stadeniolib/scramble/test.yml

@@ -0,0 +1,7 @@
+- name: stadeniolib test_stadeniolib
+  command: nextflow run tests/modules/stadeniolib -entry test_stadeniolib -c tests/config/nextflow.config
+  tags:
+    - stadeniolib
+  files:
+    - path: output/stadeniolib/test.cram
+    - path: output/stadeniolib/versions.yml

tests/subworkflows/nf-core/homer/groseq/main.nf

@@ -0,0 +1,24 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HOMER_GROSEQ as HOMER_GROSEQ_BAM
+          HOMER_GROSEQ as HOMER_GROSEQ_BED } from '../../../../../subworkflows/nf-core/homer/groseq/main'
+
+workflow test_homer_groseq_bam {
+    def input = []
+    input = [[ id: 'test' ],
+            [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)]]
+    def fasta = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+    HOMER_GROSEQ_BAM ( input, fasta )
+}
+
+workflow test_homer_groseq_bed {
+    def input = []
+    input = [[ id: 'test' ],
+            [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)]]
+    def fasta = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+    HOMER_GROSEQ_BED ( input, fasta )
+}

tests/subworkflows/nf-core/homer/groseq/nextflow.config

@@ -0,0 +1,9 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: '.*:HOMER_GROSEQ_BED:HOMER_MAKETAGDIRECTORY' {
+        ext.args = "-checkGC -format bed"
+    }
+
+}

tests/subworkflows/nf-core/homer/groseq/test.yml

@@ -0,0 +1,27 @@
+- name: subworkflow homer_groseq bam
+  command: nextflow run ./tests/subworkflows/nf-core/homer/groseq/ -entry test_homer_groseq_bam -c tests/config/nextflow.config -c tests/subworkflows/nf-core/homer/groseq/nextflow.config
+  tags:
+    - homer
+  files:
+    - path: output/homer/test.bed
+      md5sum: 8d40034dfe22c5cf973071aa1e8d3617
+    - path: output/homer/test.bedGraph.gz
+      md5sum: de2b2f8ab90a909b8bfbe755bdaba407
+    - path: output/homer/test.peaks.txt
+      md5sum: 8d40034dfe22c5cf973071aa1e8d3617
+    - path: output/homer/versions.yml
+      md5sum: c85dee03f1afabe406a87743a4c5506d
+
+- name: subworkflow homer_groseq bed
+  command: nextflow run ./tests/subworkflows/nf-core/homer/groseq/ -entry test_homer_groseq_bed -c tests/config/nextflow.config -c tests/subworkflows/nf-core/homer/groseq/nextflow.config
+  tags:
+    - homer
+  files:
+    - path: output/homer/test.bed
+      md5sum: 25e8b64946012d1c4567a04062e90fae
+    - path: output/homer/test.bedGraph.gz
+      md5sum: 2d2d1c2d3242ff74c7a922695accb9d2
+    - path: output/homer/test.peaks.txt
+      md5sum: 25e8b64946012d1c4567a04062e90fae
+    - path: output/homer/versions.yml
+      md5sum: c9b5f1248d28c216b000cba8da738455