Mercurial > repos > dfornika > snippy
changeset 6:84a619014025 draft
planemo upload for repository https://github.com/tseemann/snippy commit 73ec6ea773b1b88f7c32a2e8bc57b644b82f7ff9-dirty
| author | dfornika |
|---|---|
| date | Mon, 21 Jan 2019 17:46:30 -0500 |
| parents | b9eacd069df6 |
| children | ab3026667cdc |
| files | snippy.xml |
| diffstat | 1 files changed, 2 insertions(+), 2 deletions(-) [+] |
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--- a/snippy.xml Mon Jan 21 15:46:37 2019 -0500 +++ b/snippy.xml Mon Jan 21 17:46:30 2019 -0500 @@ -54,11 +54,11 @@ #import re #if str( $fastq_input.fastq_input_selector ) == "paired_collection" - #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.forward.element_identifier) + #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.forward.name) #else #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.element_identifier) #end if - mkdir -p ${dir_name}/reference && cp out/snps.tab out/snps.aligned.fa ${dir_name}/ && cp out/reference/ref.fa ${dir_name}/reference/ && + mkdir -p ${dir_name} && cp -r out/reference out/snps.tab out/snps.aligned.fa out/snps.vcf ${dir_name}/ && tar -czf out.tgz ${dir_name}