nf-core_modules/modules/qualimap/bamqccram/main.nf
FriederikeHanssen 950700bcdc
Update samtools version (#1361)
* Update samtools version

* update checksums
2022-02-28 23:13:11 +01:00

60 lines
1.9 KiB
Text

process QUALIMAP_BAMQCCRAM {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::qualimap=2.2.2d bioconda::samtools=1.15" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:9838874d42d4477d5042782ee019cec9854da7d5-0' :
'quay.io/biocontainers/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:9838874d42d4477d5042782ee019cec9854da7d5-0' }"
input:
tuple val(meta), path(cram), path(crai)
path gff
path fasta
path fasta_fai
output:
tuple val(meta), path("${prefix}"), emit: results
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
def collect_pairs = meta.single_end ? '' : '--collect-overlap-pairs'
def memory = task.memory.toGiga() + "G"
def regions = gff ? "--gff $gff" : ''
def strandedness = 'non-strand-specific'
if (meta.strandedness == 'forward') {
strandedness = 'strand-specific-forward'
} else if (meta.strandedness == 'reverse') {
strandedness = 'strand-specific-reverse'
}
"""
unset DISPLAY
mkdir tmp
export _JAVA_OPTIONS=-Djava.io.tmpdir=./tmp
samtools view -hb -T ${fasta} ${cram} |
qualimap \\
--java-mem-size=$memory \\
bamqc \\
$args \\
-bam /dev/stdin \\
$regions \\
-p $strandedness \\
$collect_pairs \\
-outdir $prefix \\
-nt $task.cpus
cat <<-END_VERSIONS > versions.yml
"${task.process}":
qualimap: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//')
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}