Mercurial > repos > kkonganti > cfsan_centriflaken

comparison cfsan_centriflaken.xml @ 62:770ce74dfc47

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"planemo upload"
author kkonganti
date Wed, 13 Jul 2022 13:03:50 -0400
parents 29fec32b8f47
children d1efe888e1ed
comparison
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61:29fec32b8f47 62:770ce74dfc47
52 #end if 52 #end if
53 --fq_filename_delim '${fq_filename_delim}' 53 --fq_filename_delim '${fq_filename_delim}'
54 --fq_filename_delim_idx $fq_filename_delim_idx 54 --fq_filename_delim_idx $fq_filename_delim_idx
55 --centrifuge_extract_bug '${centrifuge_extract_bug}' 55 --centrifuge_extract_bug '${centrifuge_extract_bug}'
56 -profile kondagac; 56 -profile kondagac;
57 mv './cpipes-output/${pipeline}-multiqc/multiqc_report.html' './multiqc_report.html' || exit 1; 57 mv './cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-multiqc/multiqc_report.html' './multiqc_report.html' || exit 1;
58 mv './cpipes-output/${pipeline}-results/kraken2_extract_contigs' kraken2_extract_contigs || exit 1; 58 mv './cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-results/kraken2_extract_contigs' kraken2_extract_contigs || exit 1;
59 rm -rf ./cpipes-output || exit 1; 59 rm -rf ./cpipes-output || exit 1;
60 rm -rf ./work || exit 1 60 rm -rf ./work || exit 1
61 ]]></command> 61 ]]></command>
62 <inputs> 62 <inputs>
63 <conditional name="input_read_type_cond"> 63 <conditional name="input_read_type_cond">