mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 02:58:17 +00:00
Fix version commands (#749)
* Fix version commands * Fix version commands: again
This commit is contained in:
Harshil Patel
GitHub
parent
4ec8b025bd
commit
43c2779258
79 changed files with 159 additions and 142 deletions
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@ -42,7 +42,7 @@ process ABACAS {
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mv unused_contigs.out ${prefix}.abacas.unused.contigs.out
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(abacas.pl -v 2>&1 | sed 's/^.*ABACAS.//; s/ .*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(abacas.pl -v 2>&1) | sed 's/^.*ABACAS.//; s/ .*\$//')
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END_VERSIONS
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"""
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}
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@ -36,7 +36,7 @@ process AGRVATE {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(agrvate -v 2>&1 | sed 's/agrvate //;')
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${getSoftwareName(task.process)}: \$(echo \$(agrvate -v 2>&1) | sed 's/agrvate v//;')
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END_VERSIONS
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"""
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}
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@ -35,7 +35,7 @@ process BANDAGE_IMAGE {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(Bandage --version 2>&1 | sed 's/^.*Version: //; s/ .*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(Bandage --version 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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@ -41,7 +41,7 @@ process BISMARK_ALIGN {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(bismark -v 2>&1 | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
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END_VERSIONS
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"""
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}
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@ -38,7 +38,7 @@ process BISMARK_DEDUPLICATE {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(bismark -v 2>&1 | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
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END_VERSIONS
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"""
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}
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@ -34,7 +34,7 @@ process BISMARK_GENOMEPREPARATION {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(bismark -v 2>&1 | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
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END_VERSIONS
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"""
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}
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@ -45,7 +45,7 @@ process BISMARK_METHYLATIONEXTRACTOR {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(bismark -v 2>&1 | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
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END_VERSIONS
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"""
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}
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@ -32,7 +32,7 @@ process BISMARK_REPORT {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(bismark -v 2>&1 | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
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END_VERSIONS
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"""
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}
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@ -57,7 +57,7 @@ process BOWTIE_ALIGN {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(bowtie --version 2>&1 | sed 's/^.*bowtie-align-s version //; s/ .*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(bowtie --version 2>&1) | sed 's/^.*bowtie-align-s version //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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@ -32,7 +32,7 @@ process BOWTIE_BUILD {
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bowtie-build --threads $task.cpus $fasta bowtie/${fasta.baseName}
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(bowtie --version 2>&1 | sed 's/^.*bowtie-align-s version //; s/ .*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(bowtie --version 2>&1) | sed 's/^.*bowtie-align-s version //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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@ -39,7 +39,7 @@ process BOWTIE2_ALIGN {
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bowtie2 \\
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-x \$INDEX \\
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-U $reads \\
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--threads ${split_cpus} \\
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--threads $split_cpus \\
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$unaligned \\
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$options.args \\
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2> ${prefix}.bowtie2.log \\
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@ -47,7 +47,7 @@ process BOWTIE2_ALIGN {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(bowtie2 --version 2>&1 | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
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END_VERSIONS
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"""
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} else {
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@ -58,7 +58,7 @@ process BOWTIE2_ALIGN {
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-x \$INDEX \\
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-1 ${reads[0]} \\
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-2 ${reads[1]} \\
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--threads ${split_cpus} \\
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--threads $split_cpus \\
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$unaligned \\
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$options.args \\
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2> ${prefix}.bowtie2.log \\
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@ -72,7 +72,7 @@ process BOWTIE2_ALIGN {
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fi
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(bowtie2 --version 2>&1 | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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@ -32,7 +32,7 @@ process BOWTIE2_BUILD {
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bowtie2-build $options.args --threads $task.cpus $fasta bowtie2/${fasta.baseName}
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(bowtie2 --version 2>&1 | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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@ -24,7 +24,7 @@ process BWA_ALN {
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output:
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tuple val(meta), path("*.sai"), emit: sai
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path "versions.yml" , emit: version
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path "versions.yml" , emit: version
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script:
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def software = getSoftwareName(task.process)
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@ -43,7 +43,7 @@ process BWA_ALN {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(bwa 2>&1 | sed 's/^.*Version: //; s/Contact:.*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//')
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END_VERSIONS
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"""
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} else {
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@ -66,7 +66,7 @@ process BWA_ALN {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(bwa 2>&1 | sed 's/^.*Version: //; s/Contact:.*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//')
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END_VERSIONS
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"""
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}
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@ -22,17 +22,22 @@ process BWA_INDEX {
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path fasta
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output:
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path "bwa" , emit: index
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path "versions.yml" , emit: version
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path "bwa" , emit: index
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path "versions.yml", emit: version
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script:
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def software = getSoftwareName(task.process)
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"""
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mkdir bwa
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bwa index $options.args $fasta -p bwa/${fasta.baseName}
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bwa \\
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index \\
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$options.args \\
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$fasta \\
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-p bwa/${fasta.baseName}
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(bwa 2>&1 | sed 's/^.*Version: //; s/Contact:.*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//')
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END_VERSIONS
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"""
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}
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@ -37,14 +37,14 @@ process BWA_MEM {
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bwa mem \\
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$options.args \\
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$read_group \\
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-t ${split_cpus} \\
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-t $split_cpus \\
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\$INDEX \\
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$reads \\
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| samtools view $options.args2 -@ ${split_cpus} -bhS -o ${prefix}.bam -
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(bwa 2>&1 | sed 's/^.*Version: //; s/Contact:.*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//')
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END_VERSIONS
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"""
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}
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@ -43,7 +43,7 @@ process BWA_SAMPE {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(bwa 2>&1 | sed 's/^.*Version: //; s/Contact:.*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//')
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END_VERSIONS
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"""
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}
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@ -43,7 +43,7 @@ process BWA_SAMSE {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(bwa 2>&1 | sed 's/^.*Version: //; s/Contact:.*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//')
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END_VERSIONS
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"""
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}
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@ -29,10 +29,14 @@ process BWAMEM2_INDEX {
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def software = getSoftwareName(task.process)
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"""
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mkdir bwamem2
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bwa-mem2 index $options.args $fasta -p bwamem2/${fasta}
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bwa-mem2 \\
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index \\
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$options.args \\
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$fasta -p bwamem2/${fasta}
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(bwa-mem2 version 2>&1)
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${getSoftwareName(task.process)}: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //')
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END_VERSIONS
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"""
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}
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@ -34,17 +34,18 @@ process BWAMEM2_MEM {
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"""
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INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`
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bwa-mem2 mem \\
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bwa-mem2 \\
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mem \\
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$options.args \\
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$read_group \\
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-t ${split_cpus} \\
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-t $split_cpus \\
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\$INDEX \\
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$reads \\
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| samtools view $options.args2 -@ ${split_cpus} -bhS -o ${prefix}.bam -
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(bwa-mem2 version 2>&1)
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${getSoftwareName(task.process)}: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //')
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END_VERSIONS
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"""
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}
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@ -44,7 +44,7 @@ process BWAMETH_ALIGN {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(bwameth.py --version 2>&1 | cut -f2 -d" ")
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${getSoftwareName(task.process)}: \$(echo \$(bwameth.py --version 2>&1) | cut -f2 -d" ")
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END_VERSIONS
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"""
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}
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@ -32,7 +32,7 @@ process BWAMETH_INDEX {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(bwameth.py --version 2>&1 | cut -f2 -d" ")
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${getSoftwareName(task.process)}: \$(echo \$(bwameth.py --version 2>&1) | cut -f2 -d" ")
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END_VERSIONS
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"""
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}
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@ -75,11 +75,13 @@ process CHROMAP_CHROMAP {
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-1 ${reads.join(',')} \\
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-o ${prefix}.${file_extension}
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$compression_cmds
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo "$VERSION")
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END_VERSIONS
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""" + compression_cmds
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"""
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} else {
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"""
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chromap ${args.join(' ')} \\
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@ -90,10 +92,12 @@ process CHROMAP_CHROMAP {
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-2 ${reads[1]} \\
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-o ${prefix}.${file_extension}
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$compression_cmds
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo "$VERSION")
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END_VERSIONS
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""" + compression_cmds
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"""
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}
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}
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@ -35,6 +35,7 @@ process CHROMAP_INDEX {
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-t $task.cpus \\
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-r $fasta \\
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-o ${prefix}.index
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo "$VERSION")
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@ -44,7 +44,7 @@ process GATK4_APPLYBQSR {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
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END_VERSIONS
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"""
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}
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@ -47,7 +47,7 @@ process GATK4_BASERECALIBRATOR {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
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END_VERSIONS
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"""
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}
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@ -38,7 +38,7 @@ process GATK4_BEDTOINTERVALLIST {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
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END_VERSIONS
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"""
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}
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@ -42,7 +42,7 @@ process GATK4_CREATESEQUENCEDICTIONARY {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
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END_VERSIONS
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"""
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}
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@ -38,7 +38,7 @@ process GATK4_FASTQTOSAM {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//')
|
||||
${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -45,7 +45,7 @@ process GATK4_GETPILEUPSUMMARIES {
|
|||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//')
|
||||
${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -49,7 +49,7 @@ process GATK4_HAPLOTYPECALLER {
|
|||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//')
|
||||
${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -50,7 +50,7 @@ process GATK4_INTERVALLISTTOOLS {
|
|||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//')
|
||||
${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -41,7 +41,7 @@ process GATK4_MARKDUPLICATES {
|
|||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//')
|
||||
${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -41,7 +41,7 @@ process GATK4_MERGEBAMALIGNMENT {
|
|||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//')
|
||||
${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -46,7 +46,7 @@ process GATK4_MERGEVCFS {
|
|||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//')
|
||||
${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -74,7 +74,7 @@ process GATK4_MUTECT2 {
|
|||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//')
|
||||
${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -36,7 +36,7 @@ process GATK4_REVERTSAM {
|
|||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//')
|
||||
${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -37,7 +37,7 @@ process GATK4_SAMTOFASTQ {
|
|||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//')
|
||||
${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -38,7 +38,7 @@ process GATK4_SPLITNCIGARREADS {
|
|||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//')
|
||||
${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -41,7 +41,7 @@ process GATK4_VARIANTFILTRATION {
|
|||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(gatk --version 2>&1 | sed 's/^.*(GATK) v//; s/ .*\$//')
|
||||
${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -48,7 +48,7 @@ process SALMON_INDEX {
|
|||
-i salmon
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(salmon --version | sed -e "s/salmon //g")
|
||||
${getSoftwareName(task.process)}: \$(echo \$(salmon --version) | sed -e "s/salmon //g")
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -74,7 +74,7 @@ process SALMON_QUANT {
|
|||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(salmon --version | sed -e "s/salmon //g")
|
||||
${getSoftwareName(task.process)}: \$(echo \$(salmon --version) | sed -e "s/salmon //g")
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -48,7 +48,7 @@ process SAMTOOLS_AMPLICONCLIP {
|
|||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(samtools --version 2>&1 | sed 's/^.*samtools //; s/Using.*\$//')
|
||||
${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -31,7 +31,7 @@ process SAMTOOLS_FAIDX {
|
|||
samtools faidx $fasta
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(samtools --version 2>&1 | sed 's/^.*samtools //; s/Using.*\$//')
|
||||
${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -38,7 +38,7 @@ process SAMTOOLS_FASTQ {
|
|||
$bam
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(samtools --version 2>&1 | sed 's/^.*samtools //; s/Using.*\$//')
|
||||
${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -31,7 +31,7 @@ process SAMTOOLS_FLAGSTAT {
|
|||
samtools flagstat $bam > ${bam}.flagstat
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(samtools --version 2>&1 | sed 's/^.*samtools //; s/Using.*\$//')
|
||||
${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -31,7 +31,7 @@ process SAMTOOLS_IDXSTATS {
|
|||
samtools idxstats $bam > ${bam}.idxstats
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(samtools --version 2>&1 | sed 's/^.*samtools //; s/Using.*\$//')
|
||||
${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -32,7 +32,7 @@ process SAMTOOLS_INDEX {
|
|||
samtools index $options.args $bam
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(samtools --version 2>&1 | sed 's/^.*samtools //; s/Using.*\$//')
|
||||
${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -32,7 +32,7 @@ process SAMTOOLS_MERGE {
|
|||
samtools merge ${prefix}.bam $bams
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(samtools --version 2>&1 | sed 's/^.*samtools //; s/Using.*\$//')
|
||||
${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -37,7 +37,7 @@ process SAMTOOLS_MPILEUP {
|
|||
$bam
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(samtools --version 2>&1 | sed 's/^.*samtools //; s/Using.*\$//')
|
||||
${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -32,7 +32,7 @@ process SAMTOOLS_SORT {
|
|||
samtools sort $options.args -@ $task.cpus -o ${prefix}.bam -T $prefix $bam
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(samtools --version 2>&1 | sed 's/^.*samtools //; s/Using.*\$//')
|
||||
${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -31,7 +31,7 @@ process SAMTOOLS_STATS {
|
|||
samtools stats $bam > ${bam}.stats
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(samtools --version 2>&1 | sed 's/^.*samtools //; s/Using.*\$//')
|
||||
${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -32,7 +32,7 @@ process SAMTOOLS_VIEW {
|
|||
samtools view $options.args $bam > ${prefix}.bam
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(samtools --version 2>&1 | sed 's/^.*samtools //; s/Using.*\$//')
|
||||
${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -62,7 +62,8 @@ process TRIMGALORE {
|
|||
${prefix}.fastq.gz
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(trim_galore --version 2>&1 | sed 's/^.*version //; s/Last.*\$//')
|
||||
${getSoftwareName(task.process)}: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//')
|
||||
cutadapt: \$(cutadapt --version)
|
||||
END_VERSIONS
|
||||
"""
|
||||
} else {
|
||||
|
|
@ -82,7 +83,8 @@ process TRIMGALORE {
|
|||
${prefix}_2.fastq.gz
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(trim_galore --version 2>&1 | sed 's/^.*version //; s/Last.*\$//')
|
||||
${getSoftwareName(task.process)}: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//')
|
||||
cutadapt: \$(cutadapt --version)
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -5,10 +5,10 @@ nextflow.enable.dsl = 2
|
|||
include { BANDAGE_IMAGE } from '../../../../modules/bandage/image/main.nf' addParams( options: [:] )
|
||||
|
||||
workflow test_bandage_image {
|
||||
input = [ [ id:'B-3106' ], // meta map
|
||||
[ file("${launchDir}/tests/data/generic/gfa/B-3106.gfa", checkIfExists: true) ]
|
||||
//[ file("${launchDir}/tests/data/genomics/sarscov2/genome/gfa/test.gfa", checkIfExists: true) ]
|
||||
]
|
||||
input = [
|
||||
[ id:'B-3106' ], // meta map
|
||||
file( params.test_data['sarscov2']['illumina']['assembly_gfa'], checkIfExists: true)
|
||||
]
|
||||
|
||||
BANDAGE_IMAGE ( input )
|
||||
}
|
||||
|
|
|
|||
|
|
@ -7,11 +7,11 @@ include { BBMAP_ALIGN } from '../../../../modules/bbmap/align/main.nf' addParams
|
|||
include { BBMAP_ALIGN as BBMAP_ALIGN_PIGZ } from '../../../../modules/bbmap/align/main.nf' addParams( options: [args: "unpigz=t" ] )
|
||||
|
||||
workflow test_bbmap_align_paired_end_fasta_ref {
|
||||
|
||||
|
||||
input = [ [ id:'test', single_end:false ], // meta map
|
||||
[
|
||||
file( params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
|
||||
file( params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
|
||||
file( params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
|
||||
]
|
||||
]
|
||||
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
||||
|
|
@ -20,11 +20,11 @@ workflow test_bbmap_align_paired_end_fasta_ref {
|
|||
}
|
||||
|
||||
workflow test_bbmap_align_paired_end_index_ref {
|
||||
|
||||
|
||||
input = [ [ id:'test', single_end:false ], // meta map
|
||||
[
|
||||
file( params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
|
||||
file( params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
|
||||
file( params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
|
||||
]
|
||||
]
|
||||
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
||||
|
|
@ -34,7 +34,7 @@ workflow test_bbmap_align_paired_end_index_ref {
|
|||
}
|
||||
|
||||
workflow test_bbmap_align_single_end_index_ref {
|
||||
|
||||
|
||||
input = [ [ id:'test', single_end:true ], // meta map
|
||||
file( params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
|
||||
]
|
||||
|
|
@ -45,11 +45,11 @@ workflow test_bbmap_align_single_end_index_ref {
|
|||
}
|
||||
|
||||
workflow test_bbmap_align_paired_end_index_ref_pigz {
|
||||
|
||||
|
||||
input = [ [ id:'test', single_end:false ], // meta map
|
||||
[
|
||||
file( params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
|
||||
file( params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
|
||||
file( params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
|
||||
]
|
||||
]
|
||||
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
- name: Run bismark align single-end test workflow
|
||||
- name: bismark align single-end test workflow
|
||||
command: nextflow run ./tests/modules/bismark/align -entry test_bismark_align_single_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bismark
|
||||
|
|
@ -8,7 +8,7 @@
|
|||
md5sum: dca4ba9ff705b70446f812e59bdb1a32
|
||||
- path: output/test_single_end/test.methylated_1_bismark_bt2_SE_report.txt
|
||||
|
||||
- name: Run bismark align paired-end test workflow
|
||||
- name: bismark align paired-end test workflow
|
||||
command: nextflow run ./tests/modules/bismark/align -entry test_bismark_align_paired_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bismark
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
- name: Run bismark deduplicate test workflow
|
||||
- name: bismark deduplicate test workflow
|
||||
command: nextflow run ./tests/modules/bismark/deduplicate -entry test_bismark_deduplicate -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bismark
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
- name: Run bismark_genomepreparation test workflow
|
||||
- name: bismark genomepreparation test workflow
|
||||
command: nextflow run ./tests/modules/bismark/genomepreparation -entry test_bismark_genomepreparation -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bismark
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
- name: Run bismark methylation extractor test workflow
|
||||
- name: bismark methylation extractor test workflow
|
||||
command: nextflow run ./tests/modules/bismark/methylationextractor -entry test_bismark_methylationextractor -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bismark
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
- name: Run bismark report test workflow
|
||||
- name: bismark report test workflow
|
||||
command: nextflow run ./tests/modules/bismark/report -entry test_bismark_report -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bismark
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
- name: Run bismark summary test workflow
|
||||
- name: bismark summary test workflow
|
||||
command: nextflow run ./tests/modules/bismark/summary -entry test_bismark_summary -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bismark
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { BOWTIE_BUILD } from '../../../../modules/bowtie/build/main.nf' addParams( options: [:] )
|
||||
include { BOWTIE_BUILD } from '../../../../modules/bowtie/build/main.nf' addParams( options: [publish_dir:'bowtie'] )
|
||||
|
||||
workflow test_bowtie_build {
|
||||
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
||||
|
|
|
|||
|
|
@ -4,15 +4,15 @@
|
|||
- bowtie
|
||||
- bowtie/build
|
||||
files:
|
||||
- path: ./output/index/bowtie/genome.3.ebwt
|
||||
- path: ./output/bowtie/bowtie/genome.3.ebwt
|
||||
md5sum: 4ed93abba181d8dfab2e303e33114777
|
||||
- path: ./output/index/bowtie/genome.2.ebwt
|
||||
- path: ./output/bowtie/bowtie/genome.2.ebwt
|
||||
md5sum: 02b44af9f94c62ecd3c583048e25d4cf
|
||||
- path: ./output/index/bowtie/genome.rev.2.ebwt
|
||||
- path: ./output/bowtie/bowtie/genome.rev.2.ebwt
|
||||
md5sum: 9e6b0c4c1ddb99ae71ff8a4fe5ec6459
|
||||
- path: ./output/index/bowtie/genome.4.ebwt
|
||||
- path: ./output/bowtie/bowtie/genome.4.ebwt
|
||||
md5sum: c25be5f8b0378abf7a58c8a880b87626
|
||||
- path: ./output/index/bowtie/genome.rev.1.ebwt
|
||||
- path: ./output/bowtie/bowtie/genome.rev.1.ebwt
|
||||
md5sum: b37aaf11853e65a3b13561f27a912b06
|
||||
- path: ./output/index/bowtie/genome.1.ebwt
|
||||
- path: ./output/bowtie/bowtie/genome.1.ebwt
|
||||
md5sum: d9b76ecf9fd0413240173273b38d8199
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { BOWTIE2_BUILD } from '../../../../modules/bowtie2/build/main.nf' addParams( options: [:] )
|
||||
include { BOWTIE2_BUILD } from '../../../../modules/bowtie2/build/main.nf' addParams( options: [publish_dir:'bowtie2'] )
|
||||
|
||||
workflow test_bowtie2_build {
|
||||
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
||||
|
|
|
|||
|
|
@ -4,15 +4,15 @@
|
|||
- bowtie2
|
||||
- bowtie2/build
|
||||
files:
|
||||
- path: ./output/index/bowtie2/genome.3.bt2
|
||||
- path: ./output/bowtie2/bowtie2/genome.3.bt2
|
||||
md5sum: 4ed93abba181d8dfab2e303e33114777
|
||||
- path: ./output/index/bowtie2/genome.2.bt2
|
||||
- path: ./output/bowtie2/bowtie2/genome.2.bt2
|
||||
md5sum: 47b153cd1319abc88dda532462651fcf
|
||||
- path: ./output/index/bowtie2/genome.1.bt2
|
||||
- path: ./output/bowtie2/bowtie2/genome.1.bt2
|
||||
md5sum: cbe3d0bbea55bc57c99b4bfa25b5fbdf
|
||||
- path: ./output/index/bowtie2/genome.4.bt2
|
||||
- path: ./output/bowtie2/bowtie2/genome.4.bt2
|
||||
md5sum: c25be5f8b0378abf7a58c8a880b87626
|
||||
- path: ./output/index/bowtie2/genome.rev.1.bt2
|
||||
- path: ./output/bowtie2/bowtie2/genome.rev.1.bt2
|
||||
md5sum: 52be6950579598a990570fbcf5372184
|
||||
- path: ./output/index/bowtie2/genome.rev.2.bt2
|
||||
- path: ./output/bowtie2/bowtie2/genome.rev.2.bt2
|
||||
md5sum: e3b4ef343dea4dd571642010a7d09597
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf' addParams( options: [:] )
|
||||
include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf' addParams( options: [publish_dir:'bwa'] )
|
||||
|
||||
workflow test_bwa_index {
|
||||
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
||||
|
|
|
|||
|
|
@ -4,13 +4,13 @@
|
|||
- bwa
|
||||
- bwa/index
|
||||
files:
|
||||
- path: ./output/index/bwa/genome.bwt
|
||||
- path: ./output/bwa/bwa/genome.bwt
|
||||
md5sum: 0469c30a1e239dd08f68afe66fde99da
|
||||
- path: ./output/index/bwa/genome.amb
|
||||
- path: ./output/bwa/bwa/genome.amb
|
||||
md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
|
||||
- path: ./output/index/bwa/genome.sa
|
||||
- path: ./output/bwa/bwa/genome.sa
|
||||
md5sum: ab3952cabf026b48cd3eb5bccbb636d1
|
||||
- path: ./output/index/bwa/genome.pac
|
||||
- path: ./output/bwa/bwa/genome.pac
|
||||
md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
|
||||
- path: ./output/index/bwa/genome.ann
|
||||
- path: ./output/bwa/bwa/genome.ann
|
||||
md5sum: c32e11f6c859f166c7525a9c1d583567
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { BWAMEM2_INDEX } from '../../../../modules/bwamem2/index/main.nf' addParams( options: [:] )
|
||||
include { BWAMEM2_INDEX } from '../../../../modules/bwamem2/index/main.nf' addParams( options: [publish_dir:'bwamem2'] )
|
||||
|
||||
workflow test_bwamem2_index {
|
||||
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
||||
|
|
|
|||
|
|
@ -4,13 +4,13 @@
|
|||
- bwamem2
|
||||
- bwamem2/index
|
||||
files:
|
||||
- path: ./output/index/bwamem2/genome.fasta.amb
|
||||
- path: ./output/bwamem2/bwamem2/genome.fasta.amb
|
||||
md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
|
||||
- path: ./output/index/bwamem2/genome.fasta.pac
|
||||
- path: ./output/bwamem2/bwamem2/genome.fasta.pac
|
||||
md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
|
||||
- path: ./output/index/bwamem2/genome.fasta.0123
|
||||
- path: ./output/bwamem2/bwamem2/genome.fasta.0123
|
||||
md5sum: b02870de80106104abcb03cd9463e7d8
|
||||
- path: ./output/index/bwamem2/genome.fasta.bwt.2bit.64
|
||||
- path: ./output/bwamem2/bwamem2/genome.fasta.bwt.2bit.64
|
||||
md5sum: d097a1b82dee375d41a1ea69895a9216
|
||||
- path: ./output/index/bwamem2/genome.fasta.ann
|
||||
- path: ./output/bwamem2/bwamem2/genome.fasta.ann
|
||||
md5sum: c32e11f6c859f166c7525a9c1d583567
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
- name: Run bwameth single-end test workflow
|
||||
- name: bwameth align single-end test workflow
|
||||
command: nextflow run ./tests/modules/bwameth/align -entry test_bwameth_align_single_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bwameth
|
||||
|
|
@ -6,7 +6,7 @@
|
|||
files:
|
||||
- path: output/test_single_end/test.bam
|
||||
|
||||
- name: Run bwameth paired-end test workflow
|
||||
- name: bwameth align paired-end test workflow
|
||||
command: nextflow run ./tests/modules/bwameth/align -entry test_bwameth_align_paired_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bwameth
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { BWAMETH_INDEX } from '../../../../modules/bwameth/index/main.nf' addParams( options: [:] )
|
||||
include { BWAMETH_INDEX } from '../../../../modules/bwameth/index/main.nf' addParams( options: [publish_dir:'bwameth'] )
|
||||
|
||||
workflow test_bwameth_index {
|
||||
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
||||
|
|
|
|||
|
|
@ -1,18 +1,18 @@
|
|||
- name: Run bwameth index test workflow
|
||||
- name: bwameth index test workflow
|
||||
command: nextflow run ./tests/modules/bwameth/index -entry test_bwameth_index -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bwameth
|
||||
- bwameth/index
|
||||
files:
|
||||
- path: ./output/index/bwameth/genome.fasta.bwameth.c2t
|
||||
- path: ./output/bwameth/bwameth/genome.fasta.bwameth.c2t
|
||||
md5sum: 98039984526a41d04d6bd92fcc040c62
|
||||
- path: ./output/index/bwameth/genome.fasta.bwameth.c2t.pac
|
||||
- path: ./output/bwameth/bwameth/genome.fasta.bwameth.c2t.pac
|
||||
md5sum: 4d8e51cb0bbdeaf24576bdf0264d8653
|
||||
- path: ./output/index/bwameth/genome.fasta.bwameth.c2t.amb
|
||||
- path: ./output/bwameth/bwameth/genome.fasta.bwameth.c2t.amb
|
||||
md5sum: 249a4195069071ce47cd0bae68abe376
|
||||
- path: ./output/index/bwameth/genome.fasta.bwameth.c2t.ann
|
||||
- path: ./output/bwameth/bwameth/genome.fasta.bwameth.c2t.ann
|
||||
md5sum: 46524d4359dcdfb203a235ab3b930dbb
|
||||
- path: ./output/index/bwameth/genome.fasta.bwameth.c2t.bwt
|
||||
- path: ./output/bwameth/bwameth/genome.fasta.bwameth.c2t.bwt
|
||||
md5sum: 84f65df7d42dbe84c9ccfaddfdd5ea6b
|
||||
- path: ./output/index/bwameth/genome.fasta.bwameth.c2t.sa
|
||||
- path: ./output/bwameth/bwameth/genome.fasta.bwameth.c2t.sa
|
||||
md5sum: d25f6486f5134f57ed5b258f6fbb8673
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
- name: Run methyldackel extract test workflow
|
||||
- name: methyldackel extract
|
||||
command: nextflow run ./tests/modules/methyldackel/extract -entry test_methyldackel_extract -c tests/config/nextflow.config
|
||||
tags:
|
||||
- methyldackel
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
- name: Run methyldackel mbias test workflow
|
||||
- name: methyldackel mbias
|
||||
command: nextflow run ./tests/modules/methyldackel/mbias -entry test_methyldackel_mbias -c tests/config/nextflow.config
|
||||
tags:
|
||||
- methyldackel
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
- name: Run tests for minia - test_minia
|
||||
- name: minia
|
||||
command: nextflow run tests/modules/minia -entry test_minia -c tests/config/nextflow.config
|
||||
tags:
|
||||
- minia
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
- name: Run qualimap bamqc test workflow
|
||||
- name: qualimap bamqc test workflow
|
||||
command: nextflow run ./tests/modules/qualimap/bamqc -entry test_qualimap_bamqc -c tests/config/nextflow.config
|
||||
tags:
|
||||
- qualimap
|
||||
|
|
|
|||
|
|
@ -2,11 +2,11 @@
|
|||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { SALMON_INDEX } from '../../../../modules/salmon/index/main.nf' addParams( options: [:] )
|
||||
include { SALMON_INDEX } from '../../../../modules/salmon/index/main.nf' addParams( options: [publish_dir:'salmon'] )
|
||||
|
||||
workflow test_salmon_index {
|
||||
genome_fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
||||
transcript_fasta = file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)
|
||||
|
||||
|
||||
SALMON_INDEX ( genome_fasta, transcript_fasta )
|
||||
}
|
||||
|
|
|
|||
|
|
@ -4,28 +4,28 @@
|
|||
- salmon
|
||||
- salmon/index
|
||||
files:
|
||||
- path: ./output/index/salmon/ref_indexing.log
|
||||
- path: ./output/index/salmon/refseq.bin
|
||||
- path: ./output/salmon/salmon/ref_indexing.log
|
||||
- path: ./output/salmon/salmon/refseq.bin
|
||||
md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
|
||||
- path: ./output/index/salmon/versionInfo.json
|
||||
- path: ./output/salmon/salmon/versionInfo.json
|
||||
md5sum: 6c764bd219b7bc17168a99d232c0fe09
|
||||
- path: ./output/index/salmon/complete_ref_lens.bin
|
||||
- path: ./output/salmon/salmon/complete_ref_lens.bin
|
||||
md5sum: f57562f1fca3ae7b133f895ae13c3d08
|
||||
- path: ./output/index/salmon/mphf.bin
|
||||
- path: ./output/salmon/salmon/mphf.bin
|
||||
md5sum: 53669a47610e33e031faafd32703b714
|
||||
- path: ./output/index/salmon/pre_indexing.log
|
||||
- path: ./output/index/salmon/ctable.bin
|
||||
- path: ./output/index/salmon/duplicate_clusters.tsv
|
||||
- path: ./output/salmon/salmon/pre_indexing.log
|
||||
- path: ./output/salmon/salmon/ctable.bin
|
||||
- path: ./output/salmon/salmon/duplicate_clusters.tsv
|
||||
md5sum: 51b5292e3a874119c0e1aa566e95d70c
|
||||
- path: ./output/index/salmon/reflengths.bin
|
||||
- path: ./output/salmon/salmon/reflengths.bin
|
||||
md5sum: f57562f1fca3ae7b133f895ae13c3d08
|
||||
- path: ./output/index/salmon/info.json
|
||||
- path: ./output/salmon/salmon/info.json
|
||||
md5sum: 61ff4d3471134c280668355ddd39e99f
|
||||
- path: ./output/index/salmon/refAccumLengths.bin
|
||||
- path: ./output/salmon/salmon/refAccumLengths.bin
|
||||
md5sum: 8d1970505b2b08ca0eb5ff7722b48cde
|
||||
- path: ./output/index/salmon/ctg_offsets.bin
|
||||
- path: ./output/salmon/salmon/ctg_offsets.bin
|
||||
md5sum: 27a76542337df436436e66017f66dd25
|
||||
- path: ./output/index/salmon/rank.bin
|
||||
- path: ./output/salmon/salmon/rank.bin
|
||||
md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71
|
||||
- path: ./output/index/salmon/pos.bin
|
||||
- path: ./output/index/salmon/seq.bin
|
||||
- path: ./output/salmon/salmon/pos.bin
|
||||
- path: ./output/salmon/salmon/seq.bin
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
- name: Run samtools faidx test workflow
|
||||
- name: samtools faidx test workflow
|
||||
command: nextflow run tests/modules/samtools/faidx -entry test_samtools_faidx -c tests/config/nextflow.config
|
||||
tags:
|
||||
- samtools
|
||||
|
|
|
|||
Loading…
Reference in a new issue