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feat: remove read_group which should be set up with task.ext.args (#1521)

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* feat: remove reat_group which should be set up with ext.args

* fix: simplify dragmap command
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Maxime U. Garcia 2022-04-13 14:30:34 +02:00 committed by GitHub
parent 39b4b45ba0
commit 4f5274c3de
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3 changed files with 16 additions and 41 deletions
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2
modules/bwa/mem/main.nf
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@ -23,14 +23,12 @@ process BWA_MEM {
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: '' def args2 = task.ext.args2 ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
def samtools_command = sort_bam ? 'sort' : 'view' def samtools_command = sort_bam ? 'sort' : 'view'
""" """
INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'` INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`
bwa mem \\ bwa mem \\
$args \\ $args \\
$read_group \\
-t $task.cpus \\ -t $task.cpus \\
\$INDEX \\ \$INDEX \\
$reads \\ $reads \\

2
modules/bwamem2/mem/main.nf
View file

@ -23,7 +23,6 @@ process BWAMEM2_MEM {
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: '' def args2 = task.ext.args2 ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
def samtools_command = sort_bam ? 'sort' : 'view' def samtools_command = sort_bam ? 'sort' : 'view'
""" """
INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'` INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`
@ -31,7 +30,6 @@ process BWAMEM2_MEM {
bwa-mem2 \\ bwa-mem2 \\
mem \\ mem \\
$args \\ $args \\
$read_group \\
-t $task.cpus \\ -t $task.cpus \\
\$INDEX \\ \$INDEX \\
$reads \\ $reads \\

53
modules/dragmap/align/main.nf
View file

@ -24,44 +24,23 @@ process DRAGMAP_ALIGN {
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: '' def args2 = task.ext.args2 ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
def read_group = meta.read_group ? "--RGSM ${meta.read_group}" : "" def reads_command = meta.single_end ? "-1 $reads" : "-1 ${reads[0]} -2 ${reads[1]}"
def samtools_command = sort_bam ? 'sort' : 'view' def samtools_command = sort_bam ? 'sort' : 'view'
if (meta.single_end) {
"""
dragen-os \\
-r $hashmap \\
$args \\
$read_group \\
--num-threads $task.cpus \\
-1 $reads \\
2> ${prefix}.dragmap.log \\
| samtools $samtools_command $args2 --threads $task.cpus -o ${prefix}.bam -
cat <<-END_VERSIONS > versions.yml """
"${task.process}": dragen-os \\
dragmap: \$(echo \$(dragen-os --version 2>&1)) -r $hashmap \\
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') $args \\
pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' ) --num-threads $task.cpus \\
END_VERSIONS $reads_command \\
""" 2> ${prefix}.dragmap.log \\
} else { | samtools $samtools_command $args2 --threads $task.cpus -o ${prefix}.bam -
"""
dragen-os \\
-r $hashmap \\
$args \\
$read_group \\
--num-threads $task.cpus \\
-1 ${reads[0]} \\
-2 ${reads[1]} \\
2> ${prefix}.dragmap.log \\
| samtools $samtools_command $args2 --threads $task.cpus -o ${prefix}.bam -
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":
dragmap: \$(echo \$(dragen-os --version 2>&1)) dragmap: \$(echo \$(dragen-os --version 2>&1))
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' ) pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
END_VERSIONS END_VERSIONS
""" """
}
} }