Mercurial > repos > nml > biohansel
changeset 9:e305df0b1af7 draft
planemo upload for repository https://github.com/phac-nml/biohansel commit 13f8e2ed8e9de3e1437cc9632110ce5395e34191
| author | nml |
|---|---|
| date | Mon, 22 Jul 2019 14:40:16 -0400 |
| parents | 4fa9d5e748d4 |
| children | cd6682c83b22 |
| files | biohansel.xml |
| diffstat | 1 files changed, 2 insertions(+), 1 deletions(-) [+] |
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--- a/biohansel.xml Tue May 21 15:05:40 2019 -0400 +++ b/biohansel.xml Mon Jul 22 14:40:16 2019 -0400 @@ -7,6 +7,7 @@ <![CDATA[ #import re +#import os ## Illumina FASTQ naming regular expression (https://github.com/phac-nml/biohansel/issues/38) #set global $ILLUMINA_REGEX = $re.compile(r'^([\w\-\_]+)_S\d+_L\d{3}_R(\d)_001\.fastq(\.gz)?$') @@ -52,7 +53,7 @@ ## Create symlinks from Galaxy *.dat to <sample_name>(.fasta|.fastq|.fastq.gz) #if $input.type == 'fasta' - #set $input_files = '"{}"'.format($input.fasta.name) + #set $input_files = '"{}.fasta"'.format(os.path.splitext($input.fasta.name)[0]) ln -s "$input.fasta" $input_files && #elif $input.type == 'paired' #set $forward_filename = $get_paired_fastq_filename($input.forward)