Mercurial > repos > kkonganti > hfp_nowayout

comparison hfp_nowayout.xml @ 10:74ac6f6a9526 tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload
author kkonganti
date Tue, 01 Apr 2025 11:08:01 -0400
parents 5734210632d8
children
comparison
equal deleted inserted replaced
9:9c603577838a 10:74ac6f6a9526
46 --db_mode $nowo_db_mode 46 --db_mode $nowo_db_mode
47 --nowo_thresholds $nowo_thresholds 47 --nowo_thresholds $nowo_thresholds
48 --fq_filename_delim '${fq_filename_delim}' 48 --fq_filename_delim '${fq_filename_delim}'
49 --fq_filename_delim_idx $fq_filename_delim_idx 49 --fq_filename_delim_idx $fq_filename_delim_idx
50 -profile gxkubernetes; 50 -profile gxkubernetes;
51 mv './cpipes-output/nowayout-multiqc/multiqc_report.html' './multiqc_report.html' || exit 1; 51 mv './cpipes-output/nowayout-multiqc/CPIPES-Report_multiqc_report.html' './multiqc_report.html' || exit 1;
52 mv './cpipes-output/krona_ktimporttext/CPIPES_nowayout_krona.html' './CPIPES_nowayout_krona.html' || exit 1; 52 if [ -e './cpipes-output/krona_ktimporttext/CPIPES_nowayout_krona.html' ]; then mv './cpipes-output/krona_ktimporttext/CPIPES_nowayout_krona.html' './CPIPES_nowayout_krona.html'; else echo '<html><h1>No mitochondrial reads detected in any of the samples</h1></html>' > './CPIPES_nowayout_krona.html'; fi;
53 rm -rf ./cpipes-output || exit 1; 53 rm -rf ./cpipes-output || exit 1;
54 rm -rf ./work || exit 1; 54 rm -rf ./work || exit 1;
55 ]]></command> 55 ]]></command>
56 <inputs> 56 <inputs>
57 <conditional name="input_read_type_cond"> 57 <conditional name="input_read_type_cond">