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fix formatting, fix code style

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This commit is contained in:
Matthias De Smet 2022-04-22 11:39:22 +02:00
parent b4d2e374a0
commit c4072f274c
1 changed files with 5 additions and 6 deletions
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11
modules/elprep/merge/main.nf
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@ -18,12 +18,10 @@ process ELPREP_MERGE {
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
if (meta.single_end) {
args += " --single-end"
}
def suffix = args.contains("--output-type sam") ? "sam" : "bam"
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def suffix = args.contains("--output-type sam") ? "sam" : "bam"
def single_end = meta.single_end ? " --single-end" : ""
"""
# create directory and move all input so elprep can find and merge them before splitting
@ -34,6 +32,7 @@ process ELPREP_MERGE {
input \\
${prefix}.${suffix} \\
$args \\
${single_end} \\
--nr-of-threads $task.cpus
cat <<-END_VERSIONS > versions.yml