Merge branch 'nf-core:master' into master

modules/bcftools/norm/main.nf

@@ -34,4 +34,15 @@ process BCFTOOLS_NORM {
         bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.vcf.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
+    """
 }

modules/bcftools/view/main.nf

@@ -41,4 +41,15 @@ process BCFTOOLS_VIEW {
         bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.vcf.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
+    """
 }

modules/bwamem2/index/main.nf

@@ -31,4 +31,19 @@ process BWAMEM2_INDEX {
         bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //')
     END_VERSIONS
     """
+
+    stub:
+    """
+    mkdir bwamem2
+    touch bwamem2/${fasta}.0123
+    touch bwamem2/${fasta}.ann
+    touch bwamem2/${fasta}.pac
+    touch bwamem2/${fasta}.amb
+    touch bwamem2/${fasta}.bwt.2bit.64
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //')
+    END_VERSIONS
+    """
 }

modules/bwamem2/mem/main.nf

@@ -43,4 +43,15 @@ process BWAMEM2_MEM {
         samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.bam
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //')
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
 }

modules/cat/cat/main.nf

@@ -47,4 +47,14 @@ process CAT_CAT {
         pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
     END_VERSIONS
     """
+
+    stub:
+    """
+    touch $prefix
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
+    END_VERSIONS
+    """
 }

modules/chromap/chromap/main.nf

@@ -2,10 +2,10 @@ process CHROMAP_CHROMAP {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::chromap=0.2.0 bioconda::samtools=1.14" : null)
+    conda (params.enable_conda ? "bioconda::chromap=0.2.1 bioconda::samtools=1.15" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:ed3529ef5253d7ccbc688b6a4c5c447152685757-0' :
-        'quay.io/biocontainers/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:ed3529ef5253d7ccbc688b6a4c5c447152685757-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:bd74d08a359024829a7aec1638a28607bbcd8a58-0' :
+        'quay.io/biocontainers/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:bd74d08a359024829a7aec1638a28607bbcd8a58-0' }"
 
     input:
     tuple val(meta), path(reads)

modules/chromap/index/main.nf

@@ -1,11 +1,11 @@
 process CHROMAP_INDEX {
-    tag '$fasta'
+    tag "$fasta"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::chromap=0.2.0" : null)
+    conda (params.enable_conda ? "bioconda::chromap=0.2.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/chromap:0.2.0--hd03093a_1' :
-        'quay.io/biocontainers/chromap:0.2.0--hd03093a_1' }"
+        'https://depot.galaxyproject.org/singularity/chromap:0.2.1--hd03093a_0' :
+        'quay.io/biocontainers/chromap:0.2.1--hd03093a_0' }"
 
     input:
     path fasta

modules/dastool/scaffolds2bin/main.nf

@@ -22,9 +22,10 @@ process DASTOOL_SCAFFOLDS2BIN {
     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 $fasta"
     """
-    gunzip -f *.${file_extension}.gz
+    $decompress_fasta
 
     Fasta_to_Scaffolds2Bin.sh \\
         $args \\

modules/dastool/scaffolds2bin/meta.yml

@@ -30,14 +30,11 @@ input:
         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,fas,fasta}"
-  - binner:
-      type: val
-      description: Name of the binning software (optional)
+      description: Fasta or 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 | ...)
+      description: Fasta file extension (fa | fas | fasta | ...), but without .gz suffix, even if gzipped input.
 
 output:
   - meta:

modules/deepvariant/main.nf

@@ -44,4 +44,16 @@ process DEEPVARIANT {
         deepvariant: \$(echo \$(/opt/deepvariant/bin/run_deepvariant --version) | sed 's/^.*version //; s/ .*\$//' )
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.vcf.gz
+    touch ${prefix}.g.vcf.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        deepvariant: \$(echo \$(/opt/deepvariant/bin/run_deepvariant --version) | sed 's/^.*version //; s/ .*\$//' )
+    END_VERSIONS
+    """
 }

modules/expansionhunter/main.nf

@@ -37,4 +37,15 @@ process EXPANSIONHUNTER {
         expansionhunter: \$( echo \$(ExpansionHunter --version 2>&1) | sed 's/^.*ExpansionHunter v//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.vcf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        expansionhunter: \$( echo \$(ExpansionHunter --version 2>&1) | sed 's/^.*ExpansionHunter v//')
+    END_VERSIONS
+    """
 }

modules/fastqc/main.nf

@@ -44,4 +44,16 @@ process FASTQC {
         END_VERSIONS
         """
     }
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.html
+    touch ${prefix}.zip
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
+    END_VERSIONS
+    """
 }

modules/gatk4/bedtointervallist/main.nf

@@ -39,4 +39,15 @@ process GATK4_BEDTOINTERVALLIST {
         gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.interval_list
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
+    """
 }

modules/gatk4/createsequencedictionary/main.nf

@@ -37,4 +37,15 @@ process GATK4_CREATESEQUENCEDICTIONARY {
         gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.dict
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
+    """
 }

modules/gatk4/intervallisttools/main.nf

@@ -51,4 +51,22 @@ process GATK4_INTERVALLISTTOOLS {
         gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    mkdir -p ${prefix}_split/temp_0001_of_6
+    mkdir -p ${prefix}_split/temp_0002_of_6
+    mkdir -p ${prefix}_split/temp_0003_of_6
+    mkdir -p ${prefix}_split/temp_0004_of_6
+    touch ${prefix}_split/temp_0001_of_6/1scattered.interval_list
+    touch ${prefix}_split/temp_0002_of_6/2scattered.interval_list
+    touch ${prefix}_split/temp_0003_of_6/3scattered.interval_list
+    touch ${prefix}_split/temp_0004_of_6/4scattered.interval_list
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
+    """
 }

modules/glnexus/main.nf

@@ -42,4 +42,15 @@ process GLNEXUS {
         glnexus: \$( echo \$(glnexus_cli 2>&1) | head -n 1 | sed 's/^.*release v//; s/ .*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.bcf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        glnexus: \$( echo \$(glnexus_cli 2>&1) | head -n 1 | sed 's/^.*release v//; s/ .*\$//')
+    END_VERSIONS
+    """
 }

modules/multiqc/main.nf

@@ -28,4 +28,16 @@ process MULTIQC {
         multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
     END_VERSIONS
     """
+
+    stub:
+    """
+    touch multiqc_data
+    touch multiqc_plots
+    touch multiqc_report.html
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
+    END_VERSIONS
+    """
 }

modules/picard/collecthsmetrics/main.nf

@@ -48,4 +48,15 @@ process PICARD_COLLECTHSMETRICS {
         picard: \$(echo \$(picard CollectHsMetrics --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_collecthsmetrics.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        picard: \$(echo \$(picard CollectHsMetrics --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
+    END_VERSIONS
+    """
 }

modules/picard/collectmultiplemetrics/main.nf

@@ -42,4 +42,24 @@ process PICARD_COLLECTMULTIPLEMETRICS {
         picard: \$(picard CollectMultipleMetrics --version 2>&1 | grep -o 'Version.*' | cut -f2- -d:)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.CollectMultipleMetrics.alignment_summary_metrics
+    touch ${prefix}.CollectMultipleMetrics.insert_size_metrics
+    touch ${prefix}.CollectMultipleMetrics.quality_distribution.pdf
+    touch ${prefix}.CollectMultipleMetrics.base_distribution_by_cycle_metrics
+    touch ${prefix}.CollectMultipleMetrics.quality_by_cycle_metrics
+    touch ${prefix}.CollectMultipleMetrics.read_length_histogram.pdf
+    touch ${prefix}.CollectMultipleMetrics.base_distribution_by_cycle.pdf
+    touch ${prefix}.CollectMultipleMetrics.quality_by_cycle.pdf
+    touch ${prefix}.CollectMultipleMetrics.insert_size_histogram.pdf
+    touch ${prefix}.CollectMultipleMetrics.quality_distribution_metrics
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        picard: \$(echo \$(picard CollectMultipleMetrics --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
+    END_VERSIONS
+    """
 }

modules/picard/markduplicates/main.nf

@@ -42,4 +42,17 @@ process PICARD_MARKDUPLICATES {
         picard: \$(echo \$(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.bam
+    touch ${prefix}.bam.bai
+    touch ${prefix}.MarkDuplicates.metrics.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        picard: \$(echo \$(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
+    END_VERSIONS
+    """
 }

modules/picard/sortvcf/main.nf

@@ -46,4 +46,17 @@ process PICARD_SORTVCF {
         picard: \$(picard SortVcf --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_sorted.vcf.gz
+    touch ${prefix}.bam.bai
+    touch ${prefix}.MarkDuplicates.metrics.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        picard: \$(picard SortVcf --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:)
+    END_VERSIONS
+    """
 }

modules/qualimap/bamqc/main.nf

@@ -52,4 +52,72 @@ process QUALIMAP_BAMQC {
         qualimap: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//')
     END_VERSIONS
     """
+
+    stub:
+    prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
+    """
+    mkdir -p $prefix/css
+    mkdir $prefix/images_qualimapReport
+    mkdir $prefix/raw_data_qualimapReport
+    cd $prefix/css
+    touch agogo.css
+    touch basic.css
+    touch bgtop.png
+    touch comment-close.png
+    touch doctools.js
+    touch down-pressed.png
+    touch jquery.js
+    touch plus.png
+    touch qualimap_logo_small.png
+    touch searchtools.js
+    touch up.png
+    touch websupport.js
+    touch ajax-loader.gif
+    touch bgfooter.png
+    touch comment-bright.png
+    touch comment.png
+    touch down.png
+    touch file.png
+    touch minus.png
+    touch pygments.css
+    touch report.css
+    touch underscore.js
+    touch up-pressed.png
+    cd ../images_qualimapReport/
+    touch genome_coverage_0to50_histogram.png
+    touch genome_coverage_quotes.png
+    touch genome_insert_size_across_reference.png
+    touch genome_mapping_quality_histogram.png
+    touch genome_uniq_read_starts_histogram.png
+    touch genome_coverage_across_reference.png
+    touch genome_gc_content_per_window.png
+    touch genome_insert_size_histogram.png
+    touch genome_reads_clipping_profile.png
+    touch genome_coverage_histogram.png
+    touch genome_homopolymer_indels.png
+    touch genome_mapping_quality_across_reference.png
+    touch genome_reads_content_per_read_position.png
+    cd ../raw_data_qualimapReport
+    touch coverage_across_reference.txt
+    touch genome_fraction_coverage.txt
+    touch insert_size_histogram.txt
+    touch mapped_reads_nucleotide_content.txt
+    touch coverage_histogram.txt
+    touch homopolymer_indels.txt
+    touch mapped_reads_clipping_profile.txt
+    touch mapping_quality_across_reference.txt
+    touch duplication_rate_histogram.txt
+    touch insert_size_across_reference.txt
+    touch mapped_reads_gc-content_distribution.txt
+    touch mapping_quality_histogram.txt
+    cd ../
+    touch genome_results.txt
+    touch qualimapReport.html
+    cd ../
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        qualimap: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//')
+    END_VERSIONS
+    """
 }

modules/samtools/faidx/main.nf

@@ -29,4 +29,14 @@ process SAMTOOLS_FAIDX {
         samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """
+
+    stub:
+    """
+    touch ${fasta}.fai
+    cat <<-END_VERSIONS > versions.yml
+
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
 }

modules/samtools/index/main.nf

@@ -33,4 +33,16 @@ process SAMTOOLS_INDEX {
         samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """
+
+    stub:
+    """
+    touch ${input}.bai
+    touch ${input}.crai
+    touch ${input}.csi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
 }

modules/samtools/merge/main.nf

@@ -38,4 +38,16 @@ process SAMTOOLS_MERGE {
         samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """
+
+    stub:
+    prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
+    def file_type = input_files[0].getExtension()
+    """
+    touch ${prefix}.${file_type}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
 }

modules/samtools/sort/main.nf

@@ -28,4 +28,15 @@ process SAMTOOLS_SORT {
         samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.bam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
 }

modules/samtools/stats/main.nf

@@ -34,4 +34,15 @@ process SAMTOOLS_STATS {
         samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${input}.stats
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
 }

modules/svdb/query/main.nf

@@ -70,5 +70,4 @@ process SVDB_QUERY {
         svdb: \$( echo \$(svdb) | head -1 | sed 's/usage: SVDB-\\([0-9]\\.[0-9]\\.[0-9]\\).*/\\1/' )
     END_VERSIONS
     """
-
 }

modules/tabix/bgziptabix/main.nf

@@ -30,4 +30,16 @@ process TABIX_BGZIPTABIX {
         tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.gz
+    touch ${prefix}.gz.tbi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
+    END_VERSIONS
+    """
 }

modules/tabix/tabix/main.nf

@@ -27,4 +27,15 @@ process TABIX_TABIX {
         tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${tab}.tbi
+    cat <<-END_VERSIONS > versions.yml
+
+    "${task.process}":
+        tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
+    END_VERSIONS
+    """
 }

modules/tiddit/cov/main.nf

@@ -36,4 +36,16 @@ process TIDDIT_COV {
         tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*TIDDIT-//; s/ .*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch $prefix.wig
+    touch $prefix.tab
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*TIDDIT-//; s/ .*\$//')
+    END_VERSIONS
+    """
 }

modules/tiddit/sv/main.nf

@@ -38,4 +38,17 @@ process TIDDIT_SV {
         tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*TIDDIT-//; s/ .*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch $prefix.vcf
+    touch $prefix.ploidy.tab
+    touch $prefix.signals.tab
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*TIDDIT-//; s/ .*\$//')
+    END_VERSIONS
+    """
 }

modules/ucsc/wigtobigwig/main.nf

@@ -35,4 +35,15 @@ process UCSC_WIGTOBIGWIG {
         ucsc: $VERSION
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.bw
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        ucsc: $VERSION
+    END_VERSIONS
+    """
 }

modules/untar/main.nf

@@ -33,4 +33,15 @@ process UNTAR {
         untar: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//')
     END_VERSIONS
     """
+
+    stub:
+    untar     = archive.toString() - '.tar.gz'
+    """
+    touch $untar
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        untar: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//')
+    END_VERSIONS
+    """
 }

modules/vcfanno/main.nf

@@ -39,4 +39,15 @@ process VCFANNO {
         vcfanno: \$(echo \$(vcfanno 2>&1 | grep version | cut -f3 -d' ' ))
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_annotated.vcf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        vcfanno: \$(echo \$(vcfanno 2>&1 | grep version | cut -f3 -d' ' ))
+    END_VERSIONS
+    """
 }

tests/modules/chromap/chromap/test.yml

@@ -8,7 +8,7 @@
     - path: output/chromap/test.bed.gz
       md5sum: 25e40bde24c7b447292cd68573728694
     - path: output/chromap/versions.yml
-      md5sum: 2d3d2959ac20d98036807964896829e7
+      md5sum: d24cfc35ad958206a5bc5694221b4fae
 
 - name: chromap chromap test_chromap_chromap_paired_end
   command: nextflow run ./tests/modules/chromap/chromap -entry test_chromap_chromap_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/chromap/chromap/nextflow.config
@@ -20,7 +20,7 @@
     - path: output/chromap/test.bed.gz
       md5sum: 7cdc8448882b75811e0c784f5f20aef2
     - path: output/chromap/versions.yml
-      md5sum: 51cff66779161d8a602cce5989017395
+      md5sum: 68ffe268a9d460956de4aad2a55ffd68
 
 - name: chromap chromap test_chromap_chromap_paired_bam
   command: nextflow run ./tests/modules/chromap/chromap -entry test_chromap_chromap_paired_bam -c ./tests/config/nextflow.config -c ./tests/modules/chromap/chromap/nextflow.config
@@ -30,6 +30,6 @@
   files:
     - path: output/chromap/genome.index
     - path: output/chromap/test.bam
-      md5sum: f255c7441d5a1f307fc642d2aa19647e
+      md5sum: df467417407408e42992dc3dd15b22f5
     - path: output/chromap/versions.yml
-      md5sum: f91910c44169549c3923931de5c3afcb
+      md5sum: ea732b4c6f1312d09745b66c3963dd3f

tests/modules/chromap/index/test.yml

@@ -6,4 +6,4 @@
   files:
     - path: output/chromap/genome.index
     - path: output/chromap/versions.yml
-      md5sum: b75dec647f9dc5f4887f36d1db7a9ccd
+      md5sum: fc5c80190d0622ea3e979e6862f8e32b

tests/modules/dastool/scaffolds2bin/main.nf

@@ -2,9 +2,10 @@
 
 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 { 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_SCAFFOLDS2BIN                 } from '../../../../modules/dastool/scaffolds2bin/main.nf'
 
 workflow test_dastool_scaffolds2bin {
 
@@ -22,4 +23,26 @@ workflow test_dastool_scaffolds2bin {
     METABAT2_METABAT2 ( input_metabat2 )
 
     DASTOOL_SCAFFOLDS2BIN ( METABAT2_METABAT2.out.fasta.collect(), "fa")
-}
+}
+
+workflow test_dastool_scaffolds2bin_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_scaffolds2bin = GUNZIP( METABAT2_METABAT2.out.fasta  ).gunzip
+
+    DASTOOL_SCAFFOLDS2BIN ( ch_input_2_scaffolds2bin, "fa")
+}

tests/modules/dastool/scaffolds2bin/test.yml

@@ -1,14 +1,20 @@
 - name: dastool scaffolds2bin test_dastool_scaffolds2bin
-  command: nextflow run ./tests/modules/dastool/scaffolds2bin -entry test_dastool_scaffolds2bin -c ./tests/config/nextflow.config -c ./tests/modules/dastool/scaffolds2bin/nextflow.config
+  command: nextflow run tests/modules/dastool/scaffolds2bin -entry test_dastool_scaffolds2bin -c tests/config/nextflow.config
   tags:
     - dastool
     - dastool/scaffolds2bin
   files:
     - path: output/dastool/test.tsv
       md5sum: 6e46c0be14dded7cb13af38f54feea47
-    - 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/versions.yml
+      md5sum: d0831ed159eb5a1a1565d1d211012ad6
+- name: dastool scaffolds2bin test_dastool_scaffolds2bin_ungzipped
+  command: nextflow run tests/modules/dastool/scaffolds2bin -entry test_dastool_scaffolds2bin_ungzipped -c tests/config/nextflow.config
+  tags:
+    - dastool
+    - dastool/scaffolds2bin
+  files:
+    - path: output/dastool/test.tsv
+      md5sum: 6e46c0be14dded7cb13af38f54feea47
+    - path: output/dastool/versions.yml
+      md5sum: da58e477b7f4c16a9ea495ec1a4a4d4f

tests/modules/expansionhunter/main.nf

@@ -7,8 +7,8 @@ include { EXPANSIONHUNTER } from '../../../modules/expansionhunter/main.nf'
 workflow test_expansionhunter {
 
     input = [ [ id:'test', gender:'male' ], // meta map
-              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
-              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
+              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
             ]
     fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
     variant_catalog = file(params.test_data['homo_sapiens']['genome']['repeat_expansions'], checkIfExists: true)

tests/modules/expansionhunter/test.yml

@@ -4,4 +4,4 @@
     - expansionhunter
   files:
     - path: output/expansionhunter/test.vcf
-      md5sum: ef6c2101d7bd67211bb5a5a132690e02
+      md5sum: cfd4a1d35c0e469b99eb6aaa6d22de76