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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: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)
path(bam_list)
output: output:
tuple val(meta), path("*.bam"), emit: bam tuple val(meta), path("*.bam"), emit: bam
@ -21,18 +20,22 @@ process BAMTOOLS_SPLIT {
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
def input_list = bam.collect{"-in $it"}.join(' ') def input_list = bam.collect{"-in $it"}.join(' ')
if (bam_list) { def stub_cmd = !args.contains("-stub") : " -stub ${prefix}" : ""
input_list += " -list $bam_list"
} if (size(bam) > 1){
if (!args.contains("-stub")) { def bamtools_merge_cmd = "bamtools merge ${input_list} |"
args += " -stub ${prefix}" } else {
def split_input = input_list
} }
""" """
bamtools merge \\ ${bamtools_merge_cmd} \\
${input_list} \\ bamtools split \\
| bamtools split \\ $split_input \\
$stub_cmd \\
$args $args
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml