Mercurial > repos > jjohnson > defuse
diff defuse.xml @ 13:3a4876d01c7e draft
Uploaded
| author | jjohnson |
|---|---|
| date | Tue, 12 Dec 2017 10:01:42 -0500 |
| parents | 4fe2e80d4ae1 |
| children | bdd93719cede |
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--- a/defuse.xml Tue May 03 15:18:11 2016 -0400 +++ b/defuse.xml Tue Dec 12 10:01:42 2017 -0500 @@ -626,7 +626,8 @@ mkdir -p output_dir #end if ## run defuse.pl -perl \${DEFUSE_PATH}/scripts/defuse.pl -name "$library_name" -c $defuse_config -1 data_dir/reads_1.fastq -2 data_dir/reads_2.fastq -o output_dir -p \$GALAXY_SLOTS +perl \${DEFUSE_PATH}/scripts/defuse.pl -name "$library_name" -c $defuse_config -1 data_dir/reads_1.fastq -2 data_dir/reads_2.fastq -o output_dir -p \$GALAXY_SLOTS; +exit_code_for_galaxy=\$?; ## copy primary results to output datasets if [ -e output_dir/log/defuse.log ]; then cp output_dir/log/defuse.log $defuse_log; fi ## if [ -e output_dir/results.tsv ]; then cp output_dir/results.tsv $results_tsv; fi @@ -666,6 +667,7 @@ results2html output_dir/results.filtered.tsv $fusion_reads $fusion_reads.dataset.extra_files_path fi #end if +(exit \$exit_code_for_galaxy) </configfile> </configfiles>