Merge branch 'nf-core:master' into master

modules/cat/cat/main.nf

@@ -30,7 +30,7 @@ process CAT_CAT {
     // | ungzipped | gzipped    | cat      | pigz     |
 
     // Use input file ending as default
-    prefix = task.ext.prefix ?: "${meta.id}${file_list[0].substring(file_list[0].lastIndexOf('.'))}"
+    prefix   = task.ext.prefix ?: "${meta.id}${file_list[0].substring(file_list[0].lastIndexOf('.'))}"
     out_zip  = prefix.endsWith('.gz')
     in_zip   = file_list[0].endsWith('.gz')
     command1 = (in_zip && !out_zip) ? 'zcat' : 'cat'
@@ -49,6 +49,8 @@ process CAT_CAT {
     """
 
     stub:
+    def file_list = files_in.collect { it.toString() }
+    prefix   = task.ext.prefix ?: "${meta.id}${file_list[0].substring(file_list[0].lastIndexOf('.'))}"
     """
     touch $prefix
 

modules/cnvpytor/callcnvs/main.nf

@@ -4,7 +4,7 @@ process CNVPYTOR_CALLCNVS {
 
     conda (params.enable_conda ? "bioconda::cnvpytor=1.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/cnvpytor:A1.0--py39h6a678da_2':
+        'https://depot.galaxyproject.org/singularity/cnvpytor:1.0--py39h6a678da_2':
         'quay.io/biocontainers/cnvpytor:1.0--py39h6a678da_2' }"
 
     input:
@@ -30,4 +30,15 @@ process CNVPYTOR_CALLCNVS {
         cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' ))
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' ))
+    END_VERSIONS
+    """
 }

modules/cnvpytor/histogram/main.nf

@@ -4,7 +4,7 @@ process CNVPYTOR_HISTOGRAM {
 
     conda (params.enable_conda ? "bioconda::cnvpytor=1.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/cnvpytor:A1.0--py39h6a678da_2':
+        'https://depot.galaxyproject.org/singularity/cnvpytor:1.0--py39h6a678da_2':
         'quay.io/biocontainers/cnvpytor:1.0--py39h6a678da_2' }"
 
     input:
@@ -29,4 +29,14 @@ process CNVPYTOR_HISTOGRAM {
         cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' ))
     END_VERSIONS
     """
+
+    stub:
+    """
+    touch test.pytor
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' ))
+    END_VERSIONS
+    """
 }

modules/cnvpytor/importreaddepth/main.nf

@@ -4,7 +4,7 @@ process CNVPYTOR_IMPORTREADDEPTH {
 
     conda (params.enable_conda ? "bioconda::cnvpytor=1.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/cnvpytor:A1.0--py39h6a678da_2':
+        'https://depot.galaxyproject.org/singularity/cnvpytor:1.0--py39h6a678da_2':
         'quay.io/biocontainers/cnvpytor:1.0--py39h6a678da_2' }"
 
     input:
@@ -35,4 +35,15 @@ process CNVPYTOR_IMPORTREADDEPTH {
         cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' ))
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.pytor
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' ))
+    END_VERSIONS
+    """
 }

modules/cnvpytor/partition/main.nf

@@ -4,7 +4,7 @@ process CNVPYTOR_PARTITION {
 
     conda (params.enable_conda ? "bioconda::cnvpytor=1.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/cnvpytor:A1.0--py39h6a678da_2':
+        'https://depot.galaxyproject.org/singularity/cnvpytor:1.0--py39h6a678da_2':
         'quay.io/biocontainers/cnvpytor:1.0--py39h6a678da_2' }"
 
     input:
@@ -18,7 +18,7 @@ process CNVPYTOR_PARTITION {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: '1000'
+    def args = task.ext.args ?: ''
     """
     cnvpytor \\
         -root $pytor \\
@@ -29,4 +29,14 @@ process CNVPYTOR_PARTITION {
         cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' ))
     END_VERSIONS
     """
+
+    stub:
+    """
+    touch test.pytor
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' ))
+    END_VERSIONS
+    """
 }

modules/dastool/dastool/main.nf

@@ -2,27 +2,28 @@ process DASTOOL_DASTOOL {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::das_tool=1.1.3" : null)
+    conda (params.enable_conda ? "bioconda::das_tool=1.1.4" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/das_tool:1.1.3--r41hdfd78af_0' :
-        'quay.io/biocontainers/das_tool:1.1.3--r41hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/das_tool:1.1.4--r41hdfd78af_1' :
+        'quay.io/biocontainers/das_tool:1.1.4--r41hdfd78af_1' }"
 
     input:
     tuple val(meta), path(contigs), path(bins)
     path(proteins)
     path(db_directory)
-    val(search_engine)
 
     output:
     tuple val(meta), path("*.log")                                      , emit: log
-    tuple val(meta), path("*_summary.txt")                              , emit: summary
-    tuple val(meta), path("*_DASTool_scaffolds2bin.txt")                , emit: scaffolds2bin
+    tuple val(meta), path("*_summary.tsv")                              , emit: summary
+    tuple val(meta), path("*_DASTool_contig2bin.tsv")                   , 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
-    tuple val(meta), path("*.proteins.faa")             , optional: true, emit: fasta_proteins
+    tuple val(meta), path("*.candidates.faa")           , optional: true, emit: fasta_proteins
+    tuple val(meta), path("*.faa")                      , optional: true, emit: candidates_faa
     tuple val(meta), path("*.archaea.scg")              , optional: true, emit: fasta_archaea_scg
     tuple val(meta), path("*.bacteria.scg")             , optional: true, emit: fasta_bacteria_scg
+    tuple val(meta), path("*.b6")                       , optional: true, emit: b6
     tuple val(meta), path("*.seqlength")                , optional: true, emit: seqlength
     path "versions.yml"                                 , emit: versions
 
@@ -33,17 +34,12 @@ process DASTOOL_DASTOOL {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def bin_list = bins instanceof List ? bins.join(",") : "$bins"
-    def engine = search_engine ? "--search_engine $search_engine" : "--search_engine diamond"
     def db_dir = db_directory ? "--db_directory $db_directory" : ""
     def clean_contigs = contigs.toString() - ".gz"
     def decompress_contigs = contigs.toString() == clean_contigs ? "" : "gunzip -q -f $contigs"
-    def decompress_proteins = proteins ? "gunzip -f $proteins" : ""
     def clean_proteins = proteins ? proteins.toString() - ".gz" : ""
-    def proteins_pred = proteins ? "--proteins $clean_proteins" : ""
-
-    if (! search_engine) {
-        log.info('[DAS_Tool] Default search engine (USEARCH) is proprietary software and not available in bioconda. Using DIAMOND as alternative.')
-    }
+    def decompress_proteins = proteins ? "gunzip -f $proteins" : ""
+    def proteins_pred = proteins ? "-p $clean_proteins" : ""
 
     """
     $decompress_proteins
@@ -53,15 +49,14 @@ process DASTOOL_DASTOOL {
         $args \\
         $proteins_pred \\
         $db_dir \\
-        $engine \\
         -t $task.cpus \\
-        --bins $bin_list \\
+        -i $bin_list \\
         -c $clean_contigs \\
         -o $prefix
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        dastool: \$( DAS_Tool --version 2>&1 | grep "DAS Tool" | sed 's/DAS Tool version //' )
+        dastool: \$( DAS_Tool --version 2>&1 | grep "DAS Tool" | sed 's/DAS Tool //' )
     END_VERSIONS
     """
 }

modules/dastool/dastool/meta.yml

@@ -34,8 +34,8 @@ input:
       pattern: "*.{fa.gz,fas.gz,fasta.gz}"
   - bins:
       type: file
-      description: "Scaffolds2bin tabular file generated with dastool/scaffolds2bin"
-      pattern: "*.scaffolds2bin.tsv"
+      description: "FastaToContig2Bin tabular file generated with dastool/fastatocontig2bin"
+      pattern: "*.tsv"
   - proteins:
       type: file
       description: Predicted proteins in prodigal fasta format (>scaffoldID_geneNo)
@@ -43,9 +43,6 @@ input:
   - db_directory:
       type: file
       description: (optional) Directory of single copy gene database.
-  - search_engine:
-      type: val
-      description: Engine used for single copy gene identification. USEARCH is not supported due to it being proprietary [blast/diamond]
 
 output:
   - meta:
@@ -65,14 +62,17 @@ output:
       type: file
       description: Summary of output bins including quality and completeness estimates
       pattern: "*summary.txt"
-  - scaffolds2bin:
+  - contig2bin:
       type: file
       description: Scaffolds to bin file of output bins
-      pattern: "*.scaffolds2bin.txt"
+      pattern: "*.contig2bin.txt"
   - eval:
       type: file
       description: Quality and completeness estimates of input bin sets
       pattern: "*.eval"
+  - bins:
+      description: Final refined bins in fasta format
+      pattern: "*.fa"
   - pdfs:
       type: file
       description: Plots showing the amount of high quality bins and score distribution of bins per method
@@ -89,6 +89,10 @@ output:
       type: file
       description: Results of bacterial single-copy-gene prediction
       pattern: "*.bacteria.scg"
+  - b6:
+      type: file
+      description: Results in b6 format
+      pattern: "*.b6"
   - seqlength:
       type: file
       description: Summary of contig lengths

modules/dastool/fastatocontig2bin/main.nf

@@ -0,0 +1,41 @@
+process DASTOOL_FASTATOCONTIG2BIN {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::das_tool=1.1.4" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/das_tool:1.1.4--r41hdfd78af_1' :
+        'quay.io/biocontainers/das_tool:1.1.4--r41hdfd78af_1' }"
+
+    input:
+    tuple val(meta), path(fasta)
+    val(extension)
+
+    output:
+    tuple val(meta), path("*.tsv"), emit: fastatocontig2bin
+    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 file_extension = extension ? extension : "fasta"
+    def clean_fasta = fasta.toString() - ".gz"
+    def decompress_fasta = fasta.toString() == clean_fasta ? "" : "gunzip -q -f $fasta"
+    """
+    $decompress_fasta
+
+    Fasta_to_Contig2Bin.sh \\
+        $args \\
+        -i . \\
+        -e $file_extension \\
+        > ${prefix}.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        dastool: \$( DAS_Tool --version 2>&1 | grep "DAS Tool" | sed 's/DAS Tool //' )
+    END_VERSIONS
+    """
+}

modules/dastool/fastatocontig2bin/meta.yml

@@ -0,0 +1,56 @@
+name: dastool_fastatocontig2bin
+description: Helper script to convert a set of bins in fasta format to tabular scaffolds2bin format
+keywords:
+  - binning
+  - das tool
+  - table
+  - de novo
+  - bins
+  - contigs
+  - assembly
+  - das_tool
+tools:
+  - dastool:
+      description: |
+        DAS Tool is an automated method that integrates the results
+        of a flexible number of binning algorithms to calculate an optimized, non-redundant
+        set of bins from a single assembly.
+
+      homepage: https://github.com/cmks/DAS_Tool
+      documentation: https://github.com/cmks/DAS_Tool
+      tool_dev_url: https://github.com/cmks/DAS_Tool
+      doi: "10.1038/s41564-018-0171-1"
+      licence: ["BSD"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - fasta:
+      type: file
+      description: Fasta of list of fasta files recommended to be gathered via with .collect() of bins
+      pattern: "*.{fa,fa.gz,fas,fas.gz,fna,fna.gz,fasta,fasta.gz}"
+  - extension:
+      type: val
+      description: Fasta file extension (fa | fas | fasta | ...), without .gz suffix, if gzipped input.
+
+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"
+  - fastatocontig2bin:
+      type: file
+      description: tabular contig2bin file for DAS tool input
+      pattern: "*.tsv"
+
+authors:
+  - "@maxibor"
+  - "@jfy133"

modules/deepvariant/main.nf

@@ -46,7 +46,7 @@ process DEEPVARIANT {
     """
 
     stub:
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.vcf.gz
     touch ${prefix}.g.vcf.gz

modules/gatk4/createsequencedictionary/main.nf

@@ -39,9 +39,8 @@ process GATK4_CREATESEQUENCEDICTIONARY {
     """
 
     stub:
-    def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}.dict
+    touch test.dict
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/gstama/polyacleanup/main.nf

@@ -0,0 +1,40 @@
+process GSTAMA_POLYACLEANUP {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::gs-tama=1.0.3" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/gs-tama:1.0.3--hdfd78af_0':
+        'quay.io/biocontainers/gs-tama:1.0.3--hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path("*_tama.fa.gz")                   , emit: fasta
+    tuple val(meta), path("*_tama_polya_flnc_report.txt.gz"), emit: report
+    tuple val(meta), path("*_tama_tails.fa.gz")             , emit: tails
+    path "versions.yml"                                     , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    if( "$fasta" == "${prefix}.fasta" | "$fasta" == "${prefix}.fa" ) error "Input and output names are the same, set prefix in module configuration"
+    """
+    tama_flnc_polya_cleanup.py \\
+        -f $fasta \\
+        -p ${prefix} \\
+        $args
+    gzip ${prefix}.fa
+    gzip ${prefix}_polya_flnc_report.txt
+    gzip ${prefix}_tails.fa
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gstama: \$( tama_collapse.py -version | grep 'tc_version_date_'|sed 's/tc_version_date_//g' )
+    END_VERSIONS
+    """
+}

modules/gstama/polyacleanup/meta.yml

@@ -0,0 +1,55 @@
+name: gstama_polyacleanup
+description: Helper script, remove remaining polyA sequences from Full Length Non Chimeric reads (Pacbio isoseq3)
+keywords:
+  - gstama
+  - gstama/polyacleanup
+  - long-read
+  - isoseq
+  - tama
+  - trancriptome
+  - annotation
+tools:
+  - gstama:
+      description: Gene-Switch Transcriptome Annotation by Modular Algorithms
+      homepage: https://github.com/sguizard/gs-tama
+      documentation: https://github.com/GenomeRIK/tama/wiki
+      tool_dev_url: https://github.com/sguizard/gs-tama
+      doi: "https://doi.org/10.1186/s12864-020-07123-7"
+      licence: ["GPL v3 License"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - fasta:
+      type: file
+      description: Full Length Non Chimeric reads in fasta format
+      pattern: "*.{fa,fasta}"
+
+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"
+  - fasta:
+      type: file
+      description: The Full Length Non Chimeric reads clened from remaining polyA tails. The sequences are in FASTA format compressed with gzip.
+      pattern: "*_tama.fa.gz"
+  - report:
+      type: file
+      description: A text file describing the number of polyA tails removed and their length. Compressed with gzip.
+      pattern: "*_tama_polya_flnc_report.txt.gz"
+  - tails:
+      type: file
+      description: A gzip compressed FASTA file of trimmed polyA tails.
+      pattern: "*_tama_tails.fa.gz"
+
+authors:
+  - "@sguizard"

modules/manta/germline/main.nf

@@ -8,9 +8,10 @@ process MANTA_GERMLINE {
         'quay.io/biocontainers/manta:1.6.0--h9ee0642_1' }"
 
     input:
-    tuple val(meta), path(input), path(index), path(target_bed), path(target_bed_tbi)
+    tuple val(meta), path(input), path(index)
     path fasta
     path fasta_fai
+    tuple path(target_bed), path(target_bed_tbi)
 
 
     output:

modules/phantompeakqualtools/main.nf

@@ -26,7 +26,7 @@ process PHANTOMPEAKQUALTOOLS {
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     RUN_SPP=`which run_spp.R`
-    Rscript -e "library(caTools); source(\\"\$RUN_SPP\\")" -c="$bam" -savp="${prefix}.spp.pdf" -savd="${prefix}.spp.Rdata" -out="${prefix}.spp.out" -p=$task.cpus
+    Rscript $args -e "library(caTools); source(\\"\$RUN_SPP\\")" -c="$bam" -savp="${prefix}.spp.pdf" -savd="${prefix}.spp.Rdata" -out="${prefix}.spp.out" -p=$task.cpus
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/phantompeakqualtools/meta.yml

@@ -0,0 +1,60 @@
+name: "phantompeakqualtools"
+
+description:
+keywords:
+  - "ChIP-Seq"
+  - "QC"
+  - "phantom peaks"
+tools:
+  - "phantompeakqualtools":
+      description: |
+        "This package computes informative enrichment and quality measures
+        for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used
+        to obtain robust estimates of the predominant fragment length or
+        characteristic tag shift values in these assays."
+      homepage: "None"
+      documentation: "https://github.com/kundajelab/phantompeakqualtools"
+      tool_dev_url: "https://github.com/kundajelab/phantompeakqualtools"
+      doi: "https://doi.org/10.1101/gr.136184.111"
+      licence: "['BSD-3-clause']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+
+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"
+  - spp:
+      type: file
+      description: |
+        A ChIP-Seq Processing Pipeline file containing
+        peakshift/phantomPeak results
+      pattern: "*.{out}"
+  - pdf:
+      type: file
+      description: A pdf containing save cross-correlation plots
+      pattern: "*.{pdf}"
+  - rdata:
+      type: file
+      description: Rdata file containing the R session
+      pattern: "*.{Rdata}"
+
+authors:
+  - "@drpatelh"
+  - "@Emiller88"
+  - "@JoseEspinosa"

modules/pydamage/analyze/main.nf

@@ -2,10 +2,10 @@ process PYDAMAGE_ANALYZE {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::pydamage=0.62" : null)
+    conda (params.enable_conda ? "bioconda::pydamage=0.70" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pydamage:0.62--pyhdfd78af_0' :
-        'quay.io/biocontainers/pydamage:0.62--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/pydamage:0.70--pyhdfd78af_0' :
+        'quay.io/biocontainers/pydamage:0.70--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam), path(bai)

modules/pydamage/filter/main.nf

@@ -2,10 +2,10 @@ process PYDAMAGE_FILTER {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::pydamage=0.62" : null)
+    conda (params.enable_conda ? "bioconda::pydamage=0.70" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pydamage:0.62--pyhdfd78af_0' :
-        'quay.io/biocontainers/pydamage:0.62--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/pydamage:0.70--pyhdfd78af_0' :
+        'quay.io/biocontainers/pydamage:0.70--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(csv)

modules/seqkit/stats/main.nf

@@ -0,0 +1,34 @@
+process SEQKIT_STATS {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::seqkit=2.2.0" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/seqkit:2.2.0--h9ee0642_0':
+        'quay.io/biocontainers/seqkit:2.2.0--h9ee0642_0' }"
+
+    input:
+    tuple val(meta), path(reads)
+
+    output:
+    tuple val(meta), path("*.tsv"), emit: stats
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: '--all'
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    seqkit stats \\
+        --tabular \\
+        $args \\
+        $reads > '${prefix}.tsv'
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        seqkit: \$( seqkit version | sed 's/seqkit v//' )
+    END_VERSIONS
+    """
+}

modules/seqkit/stats/meta.yml

@@ -0,0 +1,44 @@
+name: "seqkit_stats"
+description: simple statistics of FASTA/Q files
+keywords:
+  - seqkit
+  - stats
+tools:
+  - "seqkit":
+      description: Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.
+      homepage: https://bioinf.shenwei.me/seqkit/usage/
+      documentation: https://bioinf.shenwei.me/seqkit/usage/
+      tool_dev_url: https://github.com/shenwei356/seqkit/
+      doi: "10.1371/journal.pone.0163962"
+      licence: ["MIT"]
+
+input:
+  - meta:
+      type: map
+      description: >
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - reads:
+      type: file
+      description: >
+        Either FASTA or FASTQ files.
+      pattern: "*.{fa,fna,faa,fasta,fq,fastq}[.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"
+  - stats:
+      type: file
+      description: >
+        Tab-separated output file with basic sequence statistics.
+      pattern: "*.tsv"
+
+authors:
+  - "@Midnighter"

modules/svdb/merge/main.nf

@@ -2,10 +2,10 @@ process SVDB_MERGE {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::svdb=2.5.2" : null)
+    conda (params.enable_conda ? "bioconda::svdb=2.6.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/svdb:2.5.2--py39h5371cbf_0':
-        'quay.io/biocontainers/svdb:2.5.2--py39h5371cbf_0' }"
+        'https://depot.galaxyproject.org/singularity/svdb:2.6.0--py39h5371cbf_0':
+        'quay.io/biocontainers/svdb:2.6.0--py39h5371cbf_0' }"
 
     input:
     tuple val(meta), path(vcfs)

modules/svdb/query/main.nf

@@ -2,10 +2,10 @@ process SVDB_QUERY {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::svdb=2.5.2" : null)
+    conda (params.enable_conda ? "bioconda::svdb=2.6.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/svdb:2.5.2--py39h5371cbf_0':
-        'quay.io/biocontainers/svdb:2.5.2--py39h5371cbf_0' }"
+        'https://depot.galaxyproject.org/singularity/svdb:2.6.0--py39h5371cbf_0':
+        'quay.io/biocontainers/svdb:2.6.0--py39h5371cbf_0' }"
 
     input:
     tuple val(meta), path(vcf)

modules/tiddit/cov/main.nf

@@ -40,8 +40,8 @@ process TIDDIT_COV {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch $prefix.wig
-    touch $prefix.tab
+    touch ${prefix}.wig
+    touch ${prefix}.tab
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/tiddit/sv/main.nf

@@ -42,9 +42,9 @@ process TIDDIT_SV {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch $prefix.vcf
-    touch $prefix.ploidy.tab
-    touch $prefix.signals.tab
+    touch ${prefix}.vcf
+    touch ${prefix}.ploidy.tab
+    touch ${prefix}.signals.tab
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

tests/config/pytest_modules.yml

@@ -487,6 +487,10 @@ dastool/dastool:
   - modules/dastool/dastool/**
   - tests/modules/dastool/dastool/**
 
+dastool/fastatocontig2bin:
+  - modules/dastool/fastatocontig2bin/**
+  - tests/modules/dastool/fastatocontig2bin/**
+
 dastool/scaffolds2bin:
   - modules/dastool/scaffolds2bin/**
   - tests/modules/dastool/scaffolds2bin/**
@@ -811,6 +815,10 @@ gstama/merge:
   - modules/gstama/merge/**
   - tests/modules/gstama/merge/**
 
+gstama/polyacleanup:
+  - modules/gstama/polyacleanup/**
+  - tests/modules/gstama/polyacleanup/**
+
 gtdbtk/classifywf:
   - modules/gtdbtk/classifywf/**
   - tests/modules/gtdbtk/classifywf/**
@@ -1299,6 +1307,10 @@ peddy:
   - modules/peddy/**
   - tests/modules/peddy/**
 
+phantompeakqualtools:
+  - modules/phantompeakqualtools/**
+  - tests/modules/phantompeakqualtools/**
+
 phyloflash:
   - modules/phyloflash/**
   - tests/modules/phyloflash/**
@@ -1591,6 +1603,10 @@ seqkit/split2:
   - modules/seqkit/split2/**
   - tests/modules/seqkit/split2/**
 
+seqkit/stats:
+  - modules/seqkit/stats/**
+  - tests/modules/seqkit/stats/**
+
 seqsero2:
   - modules/seqsero2/**
   - tests/modules/seqsero2/**

tests/modules/cat/cat/test.yml

@@ -7,6 +7,14 @@
     - path: output/cat/test.fasta
       md5sum: f44b33a0e441ad58b2d3700270e2dbe2
 
+- name: cat unzipped unzipped stub
+  command: nextflow run ./tests/modules/cat/cat -entry test_cat_unzipped_unzipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config -stub-run
+  tags:
+    - cat
+    - cat/cat
+  files:
+    - path: output/cat/test.fasta
+
 - name: cat zipped zipped
   command: nextflow run ./tests/modules/cat/cat -entry test_cat_zipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config
   tags:
@@ -15,6 +23,14 @@
   files:
     - path: output/cat/test.gz
 
+- name: cat zipped zipped stub
+  command: nextflow run ./tests/modules/cat/cat -entry test_cat_zipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config -stub-run
+  tags:
+    - cat
+    - cat/cat
+  files:
+    - path: output/cat/test.gz
+
 - name: cat zipped unzipped
   command: nextflow run ./tests/modules/cat/cat -entry test_cat_zipped_unzipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config
   tags:
@@ -24,6 +40,14 @@
     - path: output/cat/cat.txt
       md5sum: c439d3b60e7bc03e8802a451a0d9a5d9
 
+- name: cat zipped unzipped stub
+  command: nextflow run ./tests/modules/cat/cat -entry test_cat_zipped_unzipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config -stub-run
+  tags:
+    - cat
+    - cat/cat
+  files:
+    - path: output/cat/cat.txt
+
 - name: cat unzipped zipped
   command: nextflow run ./tests/modules/cat/cat -entry test_cat_unzipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config
   tags:
@@ -32,6 +56,14 @@
   files:
     - path: output/cat/cat.txt.gz
 
+- name: cat unzipped zipped stub
+  command: nextflow run ./tests/modules/cat/cat -entry test_cat_unzipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config -stub-run
+  tags:
+    - cat
+    - cat/cat
+  files:
+    - path: output/cat/cat.txt.gz
+
 - name: cat one file unzipped zipped
   command: nextflow run ./tests/modules/cat/cat -entry test_cat_one_file_unzipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config
   tags:
@@ -39,3 +71,11 @@
     - cat/cat
   files:
     - path: output/cat/cat.txt.gz
+
+- name: cat one file unzipped zipped stub
+  command: nextflow run ./tests/modules/cat/cat -entry test_cat_one_file_unzipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config -stub-run
+  tags:
+    - cat
+    - cat/cat
+  files:
+    - path: output/cat/cat.txt.gz

tests/modules/cnvpytor/callcnvs/test.yml

@@ -4,7 +4,17 @@
     - cnvpytor
     - cnvpytor/callcnvs
   files:
-    - path: output/cnvpytor/calls.10000.tsv
+    - path: output/cnvpytor/test.tsv
       md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: output/cnvpytor/versions.yml
-      md5sum: 5fe6ca3ef5c40f9dbf487f28db237821
+      md5sum: 0bea08a253fcb2ff0ff79b99df77b9fa
+
+- name: cnvpytor callcnvs test_cnvpytor_callcnvs stub
+  command: nextflow run tests/modules/cnvpytor/callcnvs -entry test_cnvpytor_callcnvs -c tests/config/nextflow.config -stub-run
+  tags:
+    - cnvpytor
+    - cnvpytor/callcnvs
+  files:
+    - path: output/cnvpytor/test.tsv
+    - path: output/cnvpytor/versions.yml
+      md5sum: 0bea08a253fcb2ff0ff79b99df77b9fa

tests/modules/cnvpytor/histogram/test.yml

@@ -7,4 +7,14 @@
     - path: output/cnvpytor/test.pytor
       md5sum: aa03a8fa15b39f77816705a48e10312a
     - path: output/cnvpytor/versions.yml
-      md5sum: 9a4b176afd5f1a3edeb37eeb301cf464
+      md5sum: 0f4d75c4f3a3eb26c22616d12b0b78b2
+
+- name: cnvpytor histogram test_cnvpytor_histogram stub
+  command: nextflow run tests/modules/cnvpytor/histogram -entry test_cnvpytor_histogram -c tests/config/nextflow.config -stub-run
+  tags:
+    - cnvpytor
+    - cnvpytor/histogram
+  files:
+    - path: output/cnvpytor/test.pytor
+    - path: output/cnvpytor/versions.yml
+      md5sum: 0f4d75c4f3a3eb26c22616d12b0b78b2

tests/modules/cnvpytor/importreaddepth/nextflow.config

@@ -8,5 +8,5 @@ process {
 }
 
 params {
-    cnvpytor_chr = '' // specifies chromosome name(s) the same way as they are described in the sam/bam/cram header e.g. '1 2' or 'chr1 chr2'.
+    cnvpytor_chr = null // specifies chromosome name(s) the same way as they are described in the sam/bam/cram header e.g. '1 2' or 'chr1 chr2'.
     }

tests/modules/cnvpytor/importreaddepth/test.yml

@@ -0,0 +1,39 @@
+- name: cnvpytor importreaddepth test_cnvpytor_importreaddepth
+  command: nextflow run tests/modules/cnvpytor/importreaddepth -entry test_cnvpytor_importreaddepth -c tests/config/nextflow.config
+  tags:
+    - cnvpytor
+    - cnvpytor/importreaddepth
+  files:
+    - path: output/cnvpytor/test.pytor
+    - path: output/cnvpytor/versions.yml
+      md5sum: 5834495324c08a37f3fd73ccdd881dc8
+
+- name: cnvpytor importreaddepth test_cnvpytor_importreaddepth stub
+  command: nextflow run tests/modules/cnvpytor/importreaddepth -entry test_cnvpytor_importreaddepth -c tests/config/nextflow.config -stub-run
+  tags:
+    - cnvpytor
+    - cnvpytor/importreaddepth
+  files:
+    - path: output/cnvpytor/test.pytor
+    - path: output/cnvpytor/versions.yml
+      md5sum: 5834495324c08a37f3fd73ccdd881dc8
+
+- name: cnvpytor importreaddepth test_cnvpytor_importreaddepth_cram
+  command: nextflow run tests/modules/cnvpytor/importreaddepth -entry test_cnvpytor_importreaddepth_cram -c tests/config/nextflow.config
+  tags:
+    - cnvpytor
+    - cnvpytor/importreaddepth
+  files:
+    - path: output/cnvpytor/test.pytor
+    - path: output/cnvpytor/versions.yml
+      md5sum: dfa0afb0982d985b96d1633f71ebb82a
+
+- name: cnvpytor importreaddepth test_cnvpytor_importreaddepth_cram stub
+  command: nextflow run tests/modules/cnvpytor/importreaddepth -entry test_cnvpytor_importreaddepth_cram -c tests/config/nextflow.config -stub-run
+  tags:
+    - cnvpytor
+    - cnvpytor/importreaddepth
+  files:
+    - path: output/cnvpytor/test.pytor
+    - path: output/cnvpytor/versions.yml
+      md5sum: dfa0afb0982d985b96d1633f71ebb82a

tests/modules/cnvpytor/partition/test.yml

@@ -7,4 +7,14 @@
     - path: output/cnvpytor/test.pytor
       md5sum: aa03a8fa15b39f77816705a48e10312a
     - path: output/cnvpytor/versions.yml
-      md5sum: 8a04506554c58cd170cc050fd9904c6f
+      md5sum: 7fd6ec952a316463bcd324f176b46b64
+
+- name: cnvpytor partition test_cnvpytor_partition stub
+  command: nextflow run tests/modules/cnvpytor/partition -entry test_cnvpytor_partition -c tests/config/nextflow.config -stub-run
+  tags:
+    - cnvpytor
+    - cnvpytor/partition
+  files:
+    - path: output/cnvpytor/test.pytor
+    - path: output/cnvpytor/versions.yml
+      md5sum: 7fd6ec952a316463bcd324f176b46b64

tests/modules/dastool/dastool/main.nf

@@ -3,7 +3,7 @@ nextflow.enable.dsl = 2
 
 include { METABAT2_METABAT2 } from '../../../../modules/metabat2/metabat2/main.nf'
 include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../modules/metabat2/jgisummarizebamcontigdepths/main.nf'
-include { DASTOOL_SCAFFOLDS2BIN } from '../../../../modules/dastool/scaffolds2bin/main.nf'
+include { DASTOOL_FASTATOCONTIG2BIN } from '../../../../modules/dastool/fastatocontig2bin/main.nf'
 include { DASTOOL_DASTOOL } from '../../../../modules/dastool/dastool/main.nf'
 
 workflow test_dastool_dastool {
@@ -21,13 +21,13 @@ workflow test_dastool_dastool {
 
     METABAT2_METABAT2 ( input_metabat2 )
 
-    DASTOOL_SCAFFOLDS2BIN ( METABAT2_METABAT2.out.fasta.collect(), "fa")
+    DASTOOL_FASTATOCONTIG2BIN ( METABAT2_METABAT2.out.fasta.collect(), "fa")
 
     Channel.of([ [ id:'test', single_end:false ], // meta map
                       file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)])
-        .join(DASTOOL_SCAFFOLDS2BIN.out.scaffolds2bin)
+        .join( DASTOOL_FASTATOCONTIG2BIN.out.fastatocontig2bin )
         .set {input_dastool}
-    
 
-    DASTOOL_DASTOOL ( input_dastool, [], [], [] )
+
+    DASTOOL_DASTOOL ( input_dastool, [], [] )
 }

tests/modules/dastool/dastool/test.yml

@@ -1,29 +1,28 @@
 - name: dastool dastool test_dastool_dastool
-  command: nextflow run ./tests/modules/dastool/dastool -entry test_dastool_dastool -c ./tests/config/nextflow.config -c ./tests/modules/dastool/dastool/nextflow.config
+  command: nextflow run tests/modules/dastool/dastool -entry test_dastool_dastool -c tests/config/nextflow.config
   tags:
-    - dastool
     - dastool/dastool
+    - dastool
   files:
     - path: output/dastool/test.seqlength
       md5sum: b815a5811008c36808a59b1d0dcfab24
     - path: output/dastool/test.tsv
       md5sum: 6e46c0be14dded7cb13af38f54feea47
     - path: output/dastool/test_DASTool.log
-      contains:
-        - "DAS Tool run on"
-    - path: output/dastool/test_DASTool_scaffolds2bin.txt
+    - path: output/dastool/test_DASTool_contig2bin.tsv
       md5sum: 6e46c0be14dded7cb13af38f54feea47
-    - path: output/dastool/test_DASTool_summary.txt
-      md5sum: a3efa8717b30dfada78dc5ae9a3dc396
+    - path: output/dastool/test_DASTool_summary.tsv
+      md5sum: ab9dd3709a59a69bc66030b9e0ff3d5b
+    - path: output/dastool/test_proteins.faa
+    - path: output/dastool/test_proteins.faa.all.b6
+      md5sum: 39c11237ef22ac73109aaac267e185d0
     - path: output/dastool/test_proteins.faa.archaea.scg
       md5sum: e79d82eecee25821d1658ea4f082601d
     - path: output/dastool/test_proteins.faa.bacteria.scg
       md5sum: 8132cfb17cf398d41c036ead55c96ffe
-    - path: output/dastool/test_test.tsv.eval
-      md5sum: a3efa8717b30dfada78dc5ae9a3dc396
-    - path: output/metabat2/bins/test.1.fa.gz
-      md5sum: 2b297bf557cc3831b800348859331268
-    - path: output/metabat2/test.tsv.gz
-      md5sum: 619338fa5019e361d5545ce385a6961f
-    - path: output/metabat2/test.txt.gz
-      md5sum: 745a0446af6ef68b930975e9ce5a95d6
+    - path: output/dastool/test_proteins.faa.findSCG.b6
+      md5sum: 48e90e12cd6c88d00608777dbc48a82a
+    - path: output/dastool/test_proteins.faa.scg.candidates.faa
+      md5sum: d94b7bed0f8aa9cf2824d72c548c537c
+    - path: output/dastool/versions.yml
+      md5sum: 004e04c6a38652df2e0c59c44e29c9de

tests/modules/dastool/fastatocontig2bin/main.nf

@@ -0,0 +1,48 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GUNZIP                                } from '../../../../modules/gunzip/main.nf'
+include { METABAT2_METABAT2                     } from '../../../../modules/metabat2/metabat2/main.nf'
+include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS  } from '../../../../modules/metabat2/jgisummarizebamcontigdepths/main.nf'
+include { DASTOOL_FASTATOCONTIG2BIN                 } from '../../../../modules/dastool/fastatocontig2bin/main.nf'
+
+workflow test_dastool_fastatocontig2bin {
+
+    input_depth = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_sorted_bam'], checkIfExists: true),
+              file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_sorted_bam_bai'], checkIfExists: true) ]
+
+    METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS ( input_depth )
+
+    Channel.fromPath(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
+        .map { it -> [[ id:'test', single_end:false ], it] }
+        .join(METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS.out.depth)
+        .set { input_metabat2 }
+
+    METABAT2_METABAT2 ( input_metabat2 )
+
+    DASTOOL_FASTATOCONTIG2BIN ( METABAT2_METABAT2.out.fasta.collect(), "fa")
+}
+
+workflow test_dastool_fastatocontig2bin_ungzipped {
+
+    input_depth = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_sorted_bam'], checkIfExists: true),
+              file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_sorted_bam_bai'], checkIfExists: true) ]
+
+
+    METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS ( input_depth )
+
+    Channel.fromPath(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
+        .map { it -> [[ id:'test', single_end:false ], it] }
+        .join(METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS.out.depth)
+        .set { input_metabat2 }
+
+    METABAT2_METABAT2 ( input_metabat2 )
+
+    // TODO test unzipped input files
+    ch_input_2_fastatocontig2bin = GUNZIP( METABAT2_METABAT2.out.fasta  ).gunzip
+
+    DASTOOL_FASTATOCONTIG2BIN ( ch_input_2_fastatocontig2bin, "fa")
+}

tests/modules/dastool/fastatocontig2bin/nextflow.config

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

tests/modules/dastool/fastatocontig2bin/test.yml

@@ -0,0 +1,20 @@
+- name: dastool fastatocontig2bin test_dastool_fastatocontig2bin
+  command: nextflow run tests/modules/dastool/fastatocontig2bin -entry test_dastool_fastatocontig2bin -c tests/config/nextflow.config
+  tags:
+    - dastool
+    - dastool/fastatocontig2bin
+  files:
+    - path: output/dastool/test.tsv
+      md5sum: 6e46c0be14dded7cb13af38f54feea47
+    - path: output/dastool/versions.yml
+      md5sum: ff4b6f14bee4548bf09b5e602c306595
+
+- name: dastool fastatocontig2bin test_dastool_fastatocontig2bin_ungzipped
+  command: nextflow run tests/modules/dastool/fastatocontig2bin -entry test_dastool_fastatocontig2bin_ungzipped -c tests/config/nextflow.config
+  tags:
+    - dastool
+    - dastool/fastatocontig2bin
+  files:
+    - path: output/dastool/test.tsv
+      md5sum: 6e46c0be14dded7cb13af38f54feea47
+    - path: output/dastool/versions.yml

tests/modules/gstama/polyacleanup/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GSTAMA_POLYACLEANUP } from '../../../../modules/gstama/polyacleanup/main.nf'
+
+workflow test_gstama_polyacleanup {
+
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['homo_sapiens']['genome']['transcriptome_fasta'], checkIfExists: true)
+    ]
+
+    GSTAMA_POLYACLEANUP ( input )
+}

tests/modules/gstama/polyacleanup/nextflow.config

@@ -0,0 +1,6 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    ext.prefix = { "${meta.id}_tama" }
+
+}

tests/modules/gstama/polyacleanup/test.yml

@@ -0,0 +1,14 @@
+- name: gstama polyacleanup test_gstama_polyacleanup
+  command: nextflow run tests/modules/gstama/polyacleanup -entry test_gstama_polyacleanup -c tests/config/nextflow.config
+  tags:
+    - gstama
+    - gstama/polyacleanup
+  files:
+    - path: output/gstama/test_tama.fa.gz
+      md5sum: 9c768387478e5f966a42c369c0270b09
+    - path: output/gstama/test_tama_polya_flnc_report.txt.gz
+      md5sum: fe3606979ed11538aacd83159f4cff03
+    - path: output/gstama/test_tama_tails.fa.gz
+      md5sum: ba21256c0afe0bda71b3ee66b4c761bf
+    - path: output/gstama/versions.yml
+      md5sum: 07ebb812ae13a350d955fab7600b2542

tests/modules/manta/germline/main.nf

@@ -7,28 +7,30 @@ include { MANTA_GERMLINE } from '../../../../modules/manta/germline/main.nf'
 workflow test_manta_germline {
     input = [
         [ id:'test'], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
-        [],[]
+        [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true)],
+        [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)]
     ]
     fasta   = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
     fai     = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    bed     = [[],[]]
 
-    MANTA_GERMLINE ( input, fasta, fai )
+    MANTA_GERMLINE ( input, fasta, fai, bed )
 }
 
 workflow test_manta_germline_target_bed {
     input = [
         [ id:'test'], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true)
+        [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true)],
+        [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)]
     ]
     fasta   = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
     fai     = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    bed     = [
+        file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true),
+    ]
 
-    MANTA_GERMLINE ( input, fasta, fai )
+    MANTA_GERMLINE ( input, fasta, fai, bed )
 }
 
 workflow test_manta_germline_target_bed_jointcalling {
@@ -37,12 +39,14 @@ workflow test_manta_germline_target_bed_jointcalling {
         [file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
         file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram'], checkIfExists: true)],
         [file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram_crai'], checkIfExists: true),],
-        file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true)
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram_crai'], checkIfExists: true),]
     ]
     fasta   = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
     fai     = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    bed     = [
+        file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true),
+    ]
 
-    MANTA_GERMLINE ( input, fasta, fai )
+    MANTA_GERMLINE ( input, fasta, fai, bed )
 }

tests/modules/phantompeakqualtools/main.nf

@@ -0,0 +1,25 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PHANTOMPEAKQUALTOOLS } from '../../../modules/phantompeakqualtools/main.nf'
+
+workflow test_phantompeakqualtools_single_end {
+
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
+    ]
+
+    PHANTOMPEAKQUALTOOLS ( input )
+}
+
+workflow test_phantompeakqualtools_paired_end {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    PHANTOMPEAKQUALTOOLS ( input )
+}

tests/modules/phantompeakqualtools/nextflow.config

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

tests/modules/phantompeakqualtools/test.yml

@@ -0,0 +1,23 @@
+- name: phantompeakqualtools test_phantompeakqualtools_single_end
+  command: nextflow run tests/modules/phantompeakqualtools -entry test_phantompeakqualtools_single_end -c tests/config/nextflow.config
+  tags:
+    - phantompeakqualtools
+  files:
+    - path: output/phantompeakqualtools/test.spp.Rdata
+    - path: output/phantompeakqualtools/test.spp.out
+      md5sum: b01d976506b6fe45b66c821b1e8a1d15
+    - path: output/phantompeakqualtools/test.spp.pdf
+    - path: output/phantompeakqualtools/versions.yml
+      md5sum: 6c2ede1aac4c574e3c72fbe09f15c03f
+
+- name: phantompeakqualtools test_phantompeakqualtools_paired_end
+  command: nextflow run tests/modules/phantompeakqualtools -entry test_phantompeakqualtools_paired_end -c tests/config/nextflow.config
+  tags:
+    - phantompeakqualtools
+  files:
+    - path: output/phantompeakqualtools/test.spp.Rdata
+    - path: output/phantompeakqualtools/test.spp.out
+      md5sum: eed46e75eab119224f397a7a8b5924e6
+    - path: output/phantompeakqualtools/test.spp.pdf
+    - path: output/phantompeakqualtools/versions.yml
+      md5sum: 383d2dd583fcb40451bde0d3840bdb72

tests/modules/seqkit/stats/main.nf

@@ -0,0 +1,58 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SEQKIT_STATS } from '../../../../modules/seqkit/stats/main.nf'
+
+workflow test_seqkit_stats_single_end {
+
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    ]
+
+    SEQKIT_STATS ( input )
+}
+
+workflow test_seqkit_stats_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)
+        ]
+    ]
+
+    SEQKIT_STATS ( input )
+}
+
+workflow test_seqkit_stats_nanopore {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true),
+    ]
+
+    SEQKIT_STATS ( input )
+}
+
+workflow test_seqkit_stats_genome_fasta {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
+    ]
+
+    SEQKIT_STATS ( input )
+}
+
+workflow test_seqkit_stats_transcriptome_fasta {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true),
+    ]
+
+    SEQKIT_STATS ( input )
+}

tests/modules/seqkit/stats/nextflow.config

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

tests/modules/seqkit/stats/test.yml

@@ -0,0 +1,54 @@
+- name: seqkit stats test_seqkit_stats_single_end
+  command: nextflow run tests/modules/seqkit/stats -entry test_seqkit_stats_single_end -c tests/config/nextflow.config
+  tags:
+    - seqkit/stats
+    - seqkit
+  files:
+    - path: output/seqkit/test.tsv
+      md5sum: e23227d089a7e04b0ec0cb547c4aadff
+    - path: output/seqkit/versions.yml
+      md5sum: d67f0c16feb9df77b11f6c91bbdf9926
+
+- name: seqkit stats test_seqkit_stats_paired_end
+  command: nextflow run tests/modules/seqkit/stats -entry test_seqkit_stats_paired_end -c tests/config/nextflow.config
+  tags:
+    - seqkit/stats
+    - seqkit
+  files:
+    - path: output/seqkit/test.tsv
+      md5sum: 9de20dc39fb01285e3f0c382fda9db52
+    - path: output/seqkit/versions.yml
+      md5sum: bd8881933b953d07f2600e2e6a88ebf3
+
+- name: seqkit stats test_seqkit_stats_nanopore
+  command: nextflow run tests/modules/seqkit/stats -entry test_seqkit_stats_nanopore -c tests/config/nextflow.config
+  tags:
+    - seqkit/stats
+    - seqkit
+  files:
+    - path: output/seqkit/test.tsv
+      md5sum: 5da1709eb5ae64fa3b2d624bffe2e7aa
+    - path: output/seqkit/versions.yml
+      md5sum: 565632701fbe048f7ba99f1865bd48ca
+
+- name: seqkit stats test_seqkit_stats_genome_fasta
+  command: nextflow run tests/modules/seqkit/stats -entry test_seqkit_stats_genome_fasta -c tests/config/nextflow.config
+  tags:
+    - seqkit/stats
+    - seqkit
+  files:
+    - path: output/seqkit/test.tsv
+      md5sum: f64489767a4e769539ef3faf83260184
+    - path: output/seqkit/versions.yml
+      md5sum: 782fcdeaa922c8bb532ffa5808849d87
+
+- name: seqkit stats test_seqkit_stats_transcriptome_fasta
+  command: nextflow run tests/modules/seqkit/stats -entry test_seqkit_stats_transcriptome_fasta -c tests/config/nextflow.config
+  tags:
+    - seqkit/stats
+    - seqkit
+  files:
+    - path: output/seqkit/test.tsv
+      md5sum: fbb975b665a08c8862fcd1268613a945
+    - path: output/seqkit/versions.yml
+      md5sum: db99b016d986d26102ec398264a58410