Merge branch 'nf-core:master' into master

modules/bbmap/align/main.nf

@@ -2,10 +2,10 @@ process BBMAP_ALIGN {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::bbmap=38.92 bioconda::samtools=1.13 pigz=2.6" : null)
+    conda (params.enable_conda ? "bioconda::bbmap=38.92 bioconda::samtools=1.15.1 pigz=2.6" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:f5f55fc5623bb7b3f725e8d2f86bedacfd879510-0' :
+        'https://depot.galaxyproject.org/singularity/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0' :
-        'quay.io/biocontainers/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:f5f55fc5623bb7b3f725e8d2f86bedacfd879510-0' }"
+        'quay.io/biocontainers/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0' }"
 
     input:
     tuple val(meta), path(fastq)

modules/bbmap/pileup/main.nf

@@ -2,10 +2,10 @@ process BBMAP_PILEUP {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::bbmap=38.92 bioconda::samtools=1.13 pigz=2.6" : null)
+    conda (params.enable_conda ? "bioconda::bbmap=38.92 bioconda::samtools=1.15.1 pigz=2.6" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:f5f55fc5623bb7b3f725e8d2f86bedacfd879510-0' :
+        'https://depot.galaxyproject.org/singularity/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0' :
-        'quay.io/biocontainers/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:f5f55fc5623bb7b3f725e8d2f86bedacfd879510-0' }"
+        'quay.io/biocontainers/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:2fee0e0facec1dfe32a1ee4aa516aef7d0296ebf-0' }"
 
     input:
     tuple val(meta), path(bam)

modules/bowtie/align/main.nf

@@ -2,10 +2,10 @@ process BOWTIE_ALIGN {
     tag "$meta.id"
     label 'process_high'
 
-    conda (params.enable_conda ? 'bioconda::bowtie=1.3.0 bioconda::samtools=1.11' : null)
+    conda (params.enable_conda ? 'bioconda::bowtie=1.3.0 bioconda::samtools=1.15.1' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:9e14e16c284d6860574cf5b624bbc44c793cb024-0' :
+        'https://depot.galaxyproject.org/singularity/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0' :
-        'quay.io/biocontainers/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:9e14e16c284d6860574cf5b624bbc44c793cb024-0' }"
+        'quay.io/biocontainers/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:676c5bcfe34af6097728fea60fb7ea83f94a4a5f-0' }"
 
     input:
     tuple val(meta), path(reads)

modules/bowtie2/align/main.nf

@@ -2,10 +2,10 @@ process BOWTIE2_ALIGN {
     tag "$meta.id"
     label 'process_high'
 
-    conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4 bioconda::samtools=1.14 conda-forge::pigz=2.6' : null)
+    conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4 bioconda::samtools=1.15.1 conda-forge::pigz=2.6' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:4d235f41348a00533f18e47c9669f1ecb327f629-0' :
+        'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0' :
-        'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:4d235f41348a00533f18e47c9669f1ecb327f629-0' }"
+        'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0' }"
 
     input:
     tuple val(meta), path(reads)

modules/bwa/mem/main.nf

@@ -2,10 +2,10 @@ process BWA_MEM {
     tag "$meta.id"
     label 'process_high'
 
-    conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15" : null)
+    conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:c56a3aabc8d64e52d5b9da1e8ecec2031668596d-0' :
+        'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0' :
-        'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:c56a3aabc8d64e52d5b9da1e8ecec2031668596d-0' }"
+        'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0' }"
 
     input:
     tuple val(meta), path(reads)

modules/bwa/sampe/main.nf

@@ -2,10 +2,10 @@ process BWA_SAMPE {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15" : null)
+    conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:c56a3aabc8d64e52d5b9da1e8ecec2031668596d-0' :
+        'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0' :
-        'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:c56a3aabc8d64e52d5b9da1e8ecec2031668596d-0' }"
+        'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0' }"
 
     input:
     tuple val(meta), path(reads), path(sai)

modules/bwa/samse/main.nf

@@ -2,10 +2,10 @@ process BWA_SAMSE {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15" : null)
+    conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:c56a3aabc8d64e52d5b9da1e8ecec2031668596d-0' :
+        'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0' :
-        'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:c56a3aabc8d64e52d5b9da1e8ecec2031668596d-0' }"
+        'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0' }"
 
     input:
     tuple val(meta), path(reads), path(sai)

modules/bwamem2/mem/main.nf

@@ -2,10 +2,10 @@ process BWAMEM2_MEM {
     tag "$meta.id"
     label 'process_high'
 
-    conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1 bioconda::samtools=1.15" : null)
+    conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1 bioconda::samtools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:8ee25ae85d7a2bacac3e3139db209aff3d605a18-0' :
+        'https://depot.galaxyproject.org/singularity/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:38aed4501da19db366dc7c8d52d31d94e760cfaf-0' :
-        'quay.io/biocontainers/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:8ee25ae85d7a2bacac3e3139db209aff3d605a18-0' }"
+        'quay.io/biocontainers/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:38aed4501da19db366dc7c8d52d31d94e760cfaf-0' }"
 
     input:
     tuple val(meta), path(reads)

modules/chromap/chromap/main.nf

@@ -2,10 +2,10 @@ process CHROMAP_CHROMAP {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::chromap=0.2.1 bioconda::samtools=1.15" : null)
+    conda (params.enable_conda ? "bioconda::chromap=0.2.1 bioconda::samtools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:bd74d08a359024829a7aec1638a28607bbcd8a58-0' :
+        'https://depot.galaxyproject.org/singularity/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:963e4fe6a85c548a4018585660aed79780a175d3-0' :
-        'quay.io/biocontainers/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:bd74d08a359024829a7aec1638a28607bbcd8a58-0' }"
+        'quay.io/biocontainers/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:963e4fe6a85c548a4018585660aed79780a175d3-0' }"
 
     input:
     tuple val(meta), path(reads)

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/dragmap/align/main.nf

@@ -2,10 +2,10 @@ process DRAGMAP_ALIGN {
     tag "$meta.id"
     label 'process_high'
 
-    conda (params.enable_conda ? "bioconda::dragmap=1.2.1 bioconda::samtools=1.14 conda-forge::pigz=2.3.4" : null)
+    conda (params.enable_conda ? "bioconda::dragmap=1.2.1 bioconda::samtools=1.15.1 conda-forge::pigz=2.3.4" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:f7aad9060cde739c95685fc5ff6d6f7e3ec629c8-0':
+        'https://depot.galaxyproject.org/singularity/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:5ebebbc128cd624282eaa37d2c7fe01505a91a69-0':
-        'quay.io/biocontainers/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:f7aad9060cde739c95685fc5ff6d6f7e3ec629c8-0' }"
+        'quay.io/biocontainers/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:5ebebbc128cd624282eaa37d2c7fe01505a91a69-0' }"
 
     input:
     tuple val(meta), path(reads)

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/hisat2/align/main.nf

@@ -4,10 +4,10 @@ process HISAT2_ALIGN {
     tag "$meta.id"
     label 'process_high'
 
-    conda (params.enable_conda ? "bioconda::hisat2=2.2.0 bioconda::samtools=1.10" : null)
+    conda (params.enable_conda ? "bioconda::hisat2=2.2.0 bioconda::samtools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2880dd9d8ad0a7b221d4eacda9a818e92983128d-0' :
+        'https://depot.galaxyproject.org/singularity/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:0e773bb207600fcb4d38202226eb20a33c7909b6-0' :
-        'quay.io/biocontainers/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2880dd9d8ad0a7b221d4eacda9a818e92983128d-0' }"
+        'quay.io/biocontainers/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:0e773bb207600fcb4d38202226eb20a33c7909b6-0' }"
 
     input:
     tuple val(meta), path(reads)

modules/megan/rma2info/main.nf

@@ -0,0 +1,38 @@
+process MEGAN_RMA2INFO {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::megan=6.21.7" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/megan:6.21.7--h9ee0642_0':
+        'quay.io/biocontainers/megan:6.21.7--h9ee0642_0' }"
+
+    input:
+    tuple val(meta), path(rma6)
+    val(megan_summary)
+
+    output:
+    tuple val(meta), path("*.txt.gz")               , emit: txt
+    tuple val(meta), path("*.megan"), optional: true, emit: megan_summary
+    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 summary = megan_summary ? "-es ${prefix}.megan" : ""
+    """
+    rma2info \\
+        -i ${rma6} \\
+        -o ${prefix}.txt.gz \\
+        ${summary} \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        megan: \$(echo \$(rma2info 2>&1) | grep version | sed 's/.*version //g;s/, built.*//g')
+    END_VERSIONS
+    """
+}

modules/megan/rma2info/meta.yml

@@ -0,0 +1,51 @@
+name: "megan_rma2info"
+description: Analyses an RMA file and exports information in text format
+keywords:
+  - megan
+  - rma6
+  - classification
+  - conversion
+tools:
+  - "megan":
+      description: "A tool for studying the taxonomic content of a set of DNA reads"
+      homepage: "https://uni-tuebingen.de/fakultaeten/mathematisch-naturwissenschaftliche-fakultaet/fachbereiche/informatik/lehrstuehle/algorithms-in-bioinformatics/software/megan6/"
+      documentation: "https://software-ab.informatik.uni-tuebingen.de/download/megan6/welcome.html"
+      tool_dev_url: "https://github.com/husonlab/megan-ce"
+      doi: "10.1371/journal.pcbi.1004957"
+      licence: "['GPL >=3']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - rma6:
+      type: file
+      description: RMA6 file from MEGAN or MALT
+      pattern: "*.rma6"
+  - megan_summary:
+      type: boolean
+      description: Specify whether to generate an MEGAN summary file
+
+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"
+  - txt:
+      type: file
+      description: Compressed text file
+      pattern: "*.txt.gz"
+  - megan_summary:
+      type: file
+      description: Optionally generated MEGAN summary file
+      pattern: "*.megan"
+
+authors:
+  - "@jfy133"

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/qualimap/bamqccram/main.nf

@@ -2,10 +2,10 @@ process QUALIMAP_BAMQCCRAM {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::qualimap=2.2.2d bioconda::samtools=1.15" : null)
+    conda (params.enable_conda ? "bioconda::qualimap=2.2.2d bioconda::samtools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:9838874d42d4477d5042782ee019cec9854da7d5-0' :
+        'https://depot.galaxyproject.org/singularity/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:61f6d4658ac88635fc37623af50bba77561988ab-0' :
-        'quay.io/biocontainers/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:9838874d42d4477d5042782ee019cec9854da7d5-0' }"
+        'quay.io/biocontainers/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:61f6d4658ac88635fc37623af50bba77561988ab-0' }"
 
     input:
     tuple val(meta), path(cram), path(crai)

modules/samblaster/main.nf

@@ -2,10 +2,10 @@ process SAMBLASTER {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::samblaster=0.1.26 bioconda::samtools=1.14" : null)
+    conda (params.enable_conda ? "bioconda::samblaster=0.1.26 bioconda::samtools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:ba4a02b56f3e524a6e006bcd99fe8cc1d7fe09eb-0' :
+        'https://depot.galaxyproject.org/singularity/mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:fff03944e664bbf9a139f7b174b9cb2d4163271a-0' :
-        'quay.io/biocontainers/mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:ba4a02b56f3e524a6e006bcd99fe8cc1d7fe09eb-0' }"
+        'quay.io/biocontainers/mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:fff03944e664bbf9a139f7b174b9cb2d4163271a-0' }"
 
     input:
     tuple val(meta), path(bam)

modules/samtools/ampliconclip/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_AMPLICONCLIP {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
-        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
+        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
 
     input:
     tuple val(meta), path(bam)

modules/samtools/bam2fq/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_BAM2FQ {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
-        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
+        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
 
     input:
     tuple val(meta), path(inputbam)

modules/samtools/depth/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_DEPTH {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
-        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
+        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
 
     input:
     tuple val(meta), path(bam)

modules/samtools/faidx/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_FAIDX {
     tag "$fasta"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
-        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
+        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
 
     input:
     tuple val(meta), path(fasta)

modules/samtools/fastq/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_FASTQ {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
-        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
+        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
 
     input:
     tuple val(meta), path(bam)

modules/samtools/fixmate/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_FIXMATE {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
-        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
+        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
 
     input:
     tuple val(meta), path(bam)

modules/samtools/flagstat/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_FLAGSTAT {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
-        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
+        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
 
     input:
     tuple val(meta), path(bam), path(bai)

modules/samtools/idxstats/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_IDXSTATS {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
-        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
+        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
 
     input:
     tuple val(meta), path(bam), path(bai)

modules/samtools/index/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_INDEX {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
-        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
+        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
 
     input:
     tuple val(meta), path(input)

modules/samtools/merge/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_MERGE {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
-        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
+        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
 
     input:
     tuple val(meta), path(input_files)

modules/samtools/mpileup/main.nf

@@ -2,11 +2,10 @@ process SAMTOOLS_MPILEUP {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
-        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
+        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
-
     input:
     tuple val(meta), path(input), path(intervals)
     path  fasta

modules/samtools/sort/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_SORT {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
-        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
+        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
 
     input:
     tuple val(meta), path(bam)

modules/samtools/stats/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_STATS {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
-        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
+        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
 
     input:
     tuple val(meta), path(input), path(input_index)

modules/samtools/view/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_VIEW {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
-        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
+        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
 
     input:
     tuple val(meta), path(input)

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/star/genomegenerate/main.nf

@@ -3,10 +3,10 @@ process STAR_GENOMEGENERATE {
     label 'process_high'
 
     // Note: 2.7X indices incompatible with AWS iGenomes.
-    conda (params.enable_conda ? "bioconda::star=2.7.9a bioconda::samtools=1.13 conda-forge::gawk=5.1.0" : null)
+    conda (params.enable_conda ? "bioconda::star=2.7.9a bioconda::samtools=1.15.1 conda-forge::gawk=5.1.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:a7908dfb0485a80ca94e4d17b0ac991532e4e989-0' :
+        'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1c4c32d87798d425c970ececfbadd155e7560277-0' :
-        'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:a7908dfb0485a80ca94e4d17b0ac991532e4e989-0' }"
+        'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1c4c32d87798d425c970ececfbadd155e7560277-0' }"
 
     input:
     path fasta

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)

modules/yara/mapper/main.nf

@@ -2,10 +2,10 @@ process YARA_MAPPER {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::yara=1.0.2 bioconda::samtools=1.12" : null)
+    conda (params.enable_conda ? "bioconda::yara=1.0.2 bioconda::samtools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-f13549097a0d1ca36f9d4f017636fb3609f6c083:f794a548b8692f29264c8984ff116c2141b90d9e-0' :
+        'https://depot.galaxyproject.org/singularity/mulled-v2-f13549097a0d1ca36f9d4f017636fb3609f6c083:d6c969c1e20cc02a9234961c07a24bb0887f05ea-0' :
-        'quay.io/biocontainers/mulled-v2-f13549097a0d1ca36f9d4f017636fb3609f6c083:f794a548b8692f29264c8984ff116c2141b90d9e-0' }"
+        'quay.io/biocontainers/mulled-v2-f13549097a0d1ca36f9d4f017636fb3609f6c083:d6c969c1e20cc02a9234961c07a24bb0887f05ea-0' }"
 
     input:
     tuple val(meta), path(reads)

tests/config/pytest_modules.yml

@@ -1138,6 +1138,10 @@ megahit:
   - modules/megahit/**
   - tests/modules/megahit/**
 
+megan/rma2info:
+  - modules/megan/rma2info/**
+  - tests/modules/megan/rma2info/**
+
 meningotype:
   - modules/meningotype/**
   - tests/modules/meningotype/**
@@ -1343,6 +1347,10 @@ 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/**
@@ -1351,6 +1359,10 @@ 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/**
@@ -1659,6 +1671,10 @@ sistr:
   - modules/sistr/**
   - tests/modules/sistr/**
 
+snapaligner/index:
+  - modules/snapaligner/index/**
+  - tests/modules/snapaligner/index/**
+
 snpdists:
   - modules/snpdists/**
   - tests/modules/snpdists/**
@@ -1699,6 +1715,10 @@ 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/bbmap/align/test.yml

@@ -5,7 +5,7 @@
     - bbmap/align
   files:
     - path: output/bbmap/test.bam
-      md5sum: e0ec7f1eec537acf146fac1cbdd868d1
+      md5sum: 8549040067d23949bddb6fe2ad211c92
     - path: output/bbmap/test.bbmap.log
 
 - name: bbmap align paired end index ref
@@ -15,7 +15,7 @@
     - bbmap/align
   files:
     - path: output/bbmap/test.bam
-      md5sum: 345a72a0d58366d75dd263b107caa460
+      md5sum: aeb842491ca6c7806aa7103b5223620f
     - path: output/bbmap/test.bbmap.log
 
 - name: bbmap align single end index ref
@@ -25,7 +25,7 @@
     - bbmap/align
   files:
     - path: output/bbmap/test.bam
-      md5sum: 95f690636581ce9b27cf8568c715ae4d
+      md5sum: b6a41cb344a343d46244d8f94eb66ec0
     - path: output/bbmap/test.bbmap.log
 
 - name: bbmap align paired end index ref pigz
@@ -35,5 +35,5 @@
     - bbmap/align
   files:
     - path: output/bbmap/test.bam
-      md5sum: 441c4f196b9a82c7b224903538064308
+      md5sum: 74944e24acccb8c5abc316dcdd623c84
     - path: output/bbmap/test.bbmap.log

tests/modules/bbmap/pileup/test.yml

@@ -9,4 +9,4 @@
     - path: "output/bbmap/test.coverage.hist.txt"
       md5sum: 96915920ef42ddc9483457dd4585a088
     - path: output/bbmap/versions.yml
-      md5sum: 894acc38bdc167dc22851df15e5a8453
+      md5sum: e2bc51873b24e7fea269b7c1501de060

tests/modules/bwa/sampe/test.yml

@@ -5,4 +5,4 @@
     - bwa/sampe
   files:
     - path: output/bwa/test.bam
-      md5sum: 01d1d71c88b6de07ed51d1d06e9e970b
+      md5sum: 67528d633a1a78e3d0e8d1486c1a960a

tests/modules/bwa/samse/test.yml

@@ -5,4 +5,4 @@
     - bwa/samse
   files:
     - path: output/bwa/test.bam
-      md5sum: ddfa4a8f6b65d44704a2d9528abc7e79
+      md5sum: 9a0ca9678a03e6fa4bda459c04c99bd6

tests/modules/chromap/chromap/test.yml

@@ -8,7 +8,6 @@
     - path: output/chromap/test.bed.gz
       md5sum: 25e40bde24c7b447292cd68573728694
     - path: output/chromap/versions.yml
-      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 +19,6 @@
     - path: output/chromap/test.bed.gz
       md5sum: 7cdc8448882b75811e0c784f5f20aef2
     - path: output/chromap/versions.yml
-      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 +28,5 @@
   files:
     - path: output/chromap/genome.index
     - path: output/chromap/test.bam
-      md5sum: df467417407408e42992dc3dd15b22f5
+      md5sum: 0cb45628d1abe4b4359650040c501aef
     - path: output/chromap/versions.yml
-      md5sum: ea732b4c6f1312d09745b66c3963dd3f

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/megan/rma2info/main.nf

@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MEGAN_RMA2INFO } from '../../../../modules/megan/rma2info/main.nf'
+
+workflow test_megan_rma2info {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file('https://github.com/nf-core/test-datasets/raw/a7e61654553887475a2f7178108587ecd9b54608/data/delete_me/malt/test.rma6', checkIfExists: true)
+    ]
+    megan_summary = true
+
+    MEGAN_RMA2INFO ( input, megan_summary )
+}

tests/modules/megan/rma2info/nextflow.config

@@ -0,0 +1,9 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: MEGAN_RMA2INFO {
+        ext.args = "-c2c Taxonomy"
+    }
+
+}

tests/modules/megan/rma2info/test.yml

@@ -0,0 +1,12 @@
+- name: megan rma2info test_megan_rma2info
+  command: nextflow run tests/modules/megan/rma2info -entry test_megan_rma2info -c tests/config/nextflow.config
+  tags:
+    - megan
+    - megan/rma2info
+  files:
+    - path: output/megan/test.megan
+      contains:
+        - "@Creator"
+    - path: output/megan/test.txt.gz
+      md5sum: 5c3b876aa0abef12158bcd7c3702740f
+    - path: output/megan/versions.yml

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/samblaster/test.yml

@@ -4,4 +4,4 @@
     - samblaster
   files:
     - path: output/samblaster/test.processed.bam
-      md5sum: 950f23d85f75be1cf872f45c0144bdf4
+      md5sum: 3009528be9f69e7fc8951921583b0016

tests/modules/samtools/ampliconclip/test.yml

@@ -5,7 +5,7 @@
     - samtools/ampliconclip
   files:
     - path: output/samtools/test.bam
-      md5sum: 5d0e8bc9e6059ef3a63ee6328a3935c7
+      md5sum: d270363a7fb3d96be2df211099efc75b
 
 - name: samtools ampliconclip no stats with rejects
   command: nextflow run ./tests/modules/samtools/ampliconclip -entry test_samtools_ampliconclip_no_stats_with_rejects -c ./tests/config/nextflow.config -c ./tests/modules/samtools/ampliconclip/nextflow.config
@@ -14,9 +14,9 @@
     - samtools/ampliconclip
   files:
     - path: output/samtools/test.bam
-      md5sum: 2c998295d624c59620b7ffdb0cc080e2
+      md5sum: e7c4e64c259212e1670f6de96a5549b4
     - path: output/samtools/test.cliprejects.bam
-      md5sum: f3ebba8d91ad29cc4d2d00943e6f6bab
+      md5sum: b7c057b11950c2271a0c92236bee94b7
 
 - name: samtools ampliconclip with stats with rejects
   command: nextflow run ./tests/modules/samtools/ampliconclip -entry test_samtools_ampliconclip_with_stats_with_rejects -c ./tests/config/nextflow.config -c ./tests/modules/samtools/ampliconclip/nextflow.config
@@ -25,8 +25,8 @@
     - samtools/ampliconclip
   files:
     - path: output/samtools/test.bam
-      md5sum: 87882973b425ab27aad6ef18faf11f25
+      md5sum: e75992d4ff69cbaed9a089231be86b5e
     - path: output/samtools/test.cliprejects.bam
-      md5sum: eb5e186e1a69864dc2e99a290f02ff78
+      md5sum: 729f03e7a2801d2c56c32bef8f3d6ead
     - path: output/samtools/test.clipstats.txt
       md5sum: fc23355e1743d47f2541f2cb1a7a0cda

tests/modules/samtools/faidx/test.yml

@@ -7,4 +7,3 @@
     - path: output/samtools/genome.fasta.fai
       md5sum: 9da2a56e2853dc8c0b86a9e7229c9fe5
     - path: output/samtools/versions.yml
-      md5sum: 6a16b2148a0ab43e6d0506056e6a0409

tests/modules/samtools/fixmate/test.yml

@@ -5,4 +5,4 @@
     - samtools/fixmate
   files:
     - path: output/samtools/test.bam
-      md5sum: c7f574bb0c469e0ccfecb6b7210e03c5
+      md5sum: 13805ea1a9212496a8cb4ce395b25119

tests/modules/samtools/mpileup/test.yml

@@ -7,7 +7,6 @@
     - path: output/samtools/test.mpileup
       md5sum: 958e6bead4103d72026f80153b6b5150
     - path: output/samtools/versions.yml
-      md5sum: 26350e1e145451f0b807911db029861e
 
 - name: samtools mpileup test_samtools_mpileup_intervals
   command: nextflow run tests/modules/samtools/mpileup -entry test_samtools_mpileup_intervals -c tests/config/nextflow.config
@@ -18,4 +17,3 @@
     - path: output/samtools/test.mpileup
       md5sum: 958e6bead4103d72026f80153b6b5150
     - path: output/samtools/versions.yml
-      md5sum: 11d8118a558efb9db6798453862d719c

tests/modules/samtools/sort/test.yml

@@ -5,4 +5,4 @@
     - samtools/sort
   files:
     - path: output/samtools/test.sorted.bam
-      md5sum: a73238d6b896a3a946025d6b13fe9525
+      md5sum: f00f5d392fd5c531e1fd528d9f57b32b

tests/modules/samtools/stats/test.yml

@@ -5,7 +5,7 @@
     - samtools
   files:
     - path: output/samtools/test.paired_end.sorted.bam.stats
-      md5sum: 6e3ca28b3e98dade14992dd7ea5fc886
+      md5sum: c1e9ad551281b0bca32be1c832d125af
 
 - name: samtools stats test_samtools_stats_cram
   command: nextflow run ./tests/modules/samtools/stats -entry test_samtools_stats_cram -c ./tests/config/nextflow.config -c ./tests/modules/samtools/stats/nextflow.config
@@ -14,4 +14,4 @@
     - samtools
   files:
     - path: output/samtools/test.paired_end.recalibrated.sorted.cram.stats
-      md5sum: 985455b573444c3743510d603ed41f8c
+      md5sum: 103cd7b19743c42dab9ce570144c6f36

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