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Fix falco publication names

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This commit is contained in:
James Fellows Yates 2022-12-15 12:57:49 +01:00
parent 88589fbc53
commit 3b86a22556
2 changed files with 5 additions and 3 deletions
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4
conf/modules.config
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@ -33,7 +33,7 @@ process {
} }
withName: FALCO { withName: FALCO {
ext.prefix = { "${meta.id}_${meta.run_accession}_raw" } ext.prefix = { "${meta.id}_${meta.run_accession}_raw_falco" }
publishDir = [ publishDir = [
path: { "${params.outdir}/falco/raw" }, path: { "${params.outdir}/falco/raw" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
@ -42,7 +42,7 @@ process {
} }
withName: FALCO_PROCESSED { withName: FALCO_PROCESSED {
ext.prefix = { "${meta.id}_${meta.run_accession}_processed" } ext.prefix = { "${meta.id}_${meta.run_accession}_processed_falco" }
publishDir = [ publishDir = [
path: { "${params.outdir}/falco/processed" }, path: { "${params.outdir}/falco/processed" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,

4
modules/nf-core/falco/main.nf generated
View file

@ -33,7 +33,9 @@ process FALCO {
""" """
} else { } else {
""" """
falco $args --threads $task.cpus ${reads} [ ! -f ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
[ ! -f ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
falco $args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":