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make use of dependent on input array size

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This commit is contained in:
Matthias De Smet 2022-04-22 14:33:16 +02:00
parent a6e7ecb3a3
commit 413980e93a
1 changed files with 12 additions and 9 deletions
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21
modules/bamtools/split/main.nf
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@ -9,7 +9,6 @@ process BAMTOOLS_SPLIT {
input:
tuple val(meta), path(bam)
path(bam_list)
output:
tuple val(meta), path("*.bam"), emit: bam
@ -21,18 +20,22 @@ process BAMTOOLS_SPLIT {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def input_list = bam.collect{"-in $it"}.join(' ')
if (bam_list) {
input_list += " -list $bam_list"
}
if (!args.contains("-stub")) {
args += " -stub ${prefix}"
def stub_cmd = !args.contains("-stub") : " -stub ${prefix}" : ""
if (size(bam) > 1){
def bamtools_merge_cmd = "bamtools merge ${input_list} |"
} else {
def split_input = input_list
}
"""
bamtools merge \\
${input_list} \\
| bamtools split \\
${bamtools_merge_cmd} \\
bamtools split \\
$split_input \\
$stub_cmd \\
$args
cat <<-END_VERSIONS > versions.yml