mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
Remove fasta requirement from module
This commit is contained in:
parent
0d8bd42cca
commit
dcb1dc5cd9
1 changed files with 4 additions and 3 deletions
|
@ -21,7 +21,6 @@ process BWA_MEM {
|
|||
input:
|
||||
tuple val(meta), path(reads)
|
||||
path index
|
||||
path fasta
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.bam"), emit: bam
|
||||
|
@ -32,13 +31,15 @@ process BWA_MEM {
|
|||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
|
||||
"""
|
||||
INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`
|
||||
|
||||
bwa mem \\
|
||||
$options.args \\
|
||||
$read_group \\
|
||||
-t $task.cpus \\
|
||||
$fasta \\
|
||||
\$INDEX \\
|
||||
$reads \\
|
||||
| samtools view $options.args2 -@ $task.cpus -bS -o ${prefix}.bam -
|
||||
| samtools view $options.args2 -@ $task.cpus -bhS -o ${prefix}.bam -
|
||||
|
||||
echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//' > ${software}.version.txt
|
||||
"""
|
||||
|
|
Loading…
Reference in a new issue