Mercurial > repos > trinity_ctat > ctat_star_fusion
changeset 2:3268b5e6ab4a draft
Trying to fix problems with ctat_star_fusion and ctat_metagenomics.
| author | trinity_ctat |
|---|---|
| date | Fri, 13 Apr 2018 14:59:28 -0400 |
| parents | dc3454ad7e09 |
| children | 853bfaeea21c |
| files | ctat_star_fusion.xml |
| diffstat | 1 files changed, 11 insertions(+), 9 deletions(-) [+] |
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--- a/ctat_star_fusion.xml Thu Apr 12 14:19:02 2018 -0400 +++ b/ctat_star_fusion.xml Fri Apr 13 14:59:28 2018 -0400 @@ -8,8 +8,8 @@ are not in it at the current time. --> <requirement type="package">perl-carp</requirement> - <requirement type="package">perl-json-xs<plrequirement> - <requirement type="package">perl-io-gzip<plrequirement> + <requirement type="package">perl-json-xs</requirement> + <requirement type="package">perl-io-gzip</requirement> <requirement type="package">samtools</requirement> <!-- FIX - If samtools is really a requirement, shouldn't it be a star-fusion dependency? @@ -18,6 +18,15 @@ <requirement type="package" version="1.3">samtools</requirement> --> </requirements> + <!-- Using command's detect_errors instead of below. + <stdio> + <exit_code range="1:" level="fatal" description="Error returned from pipeline" /> + </stdio> + <regex match="Must investigate error above." + source="stderr" + level="fatal" + description="Unknown error encountered" /> + --> <command detect_errors="default"> <![CDATA[ STAR-Fusion @@ -27,13 +36,6 @@ --output_dir subdir ]]> </command> - <stdio> - <exit_code range="1:" level="fatal" description="Error returned from pipeline" /> - </stdio> - <regex match="Must investigate error above." - source="stderr" - level="fatal" - description="Unknown error encountered" /> <inputs> <param format="fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/>