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Add smart format selection to module

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This commit is contained in:
Thomas A. Christensen II 2022-07-18 09:56:46 -05:00
parent 09f9a09304
commit 8c1b2a34f2
Signed by: millironx
GPG key ID: 139C07724802BC5D
1 changed files with 2 additions and 1 deletions
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3
modules/emboss/seqret/main.nf
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@ -21,13 +21,14 @@ process EMBOSS_SEQRET {
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 osformat = args.contains('-osformat') ? '' : "-osformat ${out_ext}"
""" """
seqret \\ seqret \\
${args} \\ ${args} \\
-sequence ${sequence} \\ -sequence ${sequence} \\
${osformat} \\
-outseq ${prefix}.${out_ext} -outseq ${prefix}.${out_ext}
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":
emboss: \$(echo \$(seqret -version 2>&1) | sed 's/EMBOSS://') emboss: \$(echo \$(seqret -version 2>&1) | sed 's/EMBOSS://')