Skip to content
Snippets Groups Projects

Crey02 master patch 25149

3 files
+ 291
4
Compare changes
  • Side-by-side
  • Inline

Files

@@ -16,7 +16,6 @@ process index_fasta {
output:
tuple val(file_id), path("${fasta}"), path("*.mmi*"), emit: index
path "*_report.txt", emit: report
script:
memory = "${task.memory}" - ~/\s*GB/
@@ -41,7 +40,6 @@ process mapping_fastq {
output:
tuple val(file_id), path("*.bam"), emit: bam
path "*_report.txt", emit: report
script:
if (file_id instanceof List){
@@ -50,7 +48,7 @@ process mapping_fastq {
file_prefix = file_id
}
memory = "${task.memory}" - ~/\s*GB/
memory = memory / (task.cpus + 1.0)
memory = memory.toInteger() / (task.cpus + 1.0)
if (reads.size() == 2)
"""
minimap2 ${params.mapping_fastq} -t ${task.cpus} -K ${memory} ${fasta} ${reads[0]} ${reads[1]} |
@@ -61,4 +59,4 @@ process mapping_fastq {
minimap2 ${params.mapping_fastq} -t ${task.cpus} -K ${memory} ${fasta} ${reads} |
samtools view -Sb - > ${pair_id}.bam
"""
}
\ No newline at end of file
}
Loading