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samtools subsampling (#1194)

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Co-authored-by: Subazini Thankaswamy Kosalai <sth036@orcus.orebroll.se>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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Subazini TK 2022-01-11 22:39:21 +01:00 committed by GitHub
parent 30e64becaa
commit 05ba4d901d
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modules/samtools/view/main.nf
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@ -18,6 +18,7 @@ process SAMTOOLS_VIEW {
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
def reference = fasta ? "--reference ${fasta} -C" : "" def reference = fasta ? "--reference ${fasta} -C" : ""
def file_type = input.getExtension() def file_type = input.getExtension()
@ -29,6 +30,7 @@ process SAMTOOLS_VIEW {
${reference} \\ ${reference} \\
$args \\ $args \\
$input \\ $input \\
$args2 \\
> ${prefix}.${file_type} > ${prefix}.${file_type}
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml