Mercurial > repos > kkonganti > cfsan_centriflaken

comparison cfsan_centriflaken.xml @ 102:4425d68a184c

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"planemo upload"
author kkonganti
date Thu, 04 Aug 2022 10:54:24 -0400
parents ce6d9548fe89
children 96a34c382154
comparison
equal deleted inserted replaced
101:ce6d9548fe89 102:4425d68a184c
64 --fq_filter_by_len $fq_filter_by_len 64 --fq_filter_by_len $fq_filter_by_len
65 #end if 65 #end if
66 --fq_filename_delim '${fq_filename_delim}' 66 --fq_filename_delim '${fq_filename_delim}'
67 --fq_filename_delim_idx $fq_filename_delim_idx 67 --fq_filename_delim_idx $fq_filename_delim_idx
68 --centrifuge_extract_bug '${centrifuge_extract_bug}' 68 --centrifuge_extract_bug '${centrifuge_extract_bug}'
69 #if ($input_read_type_cond.pipeline_cond.rm_dup_seqs == "true"): 69 #if (str($input_read_type_cond.pipeline_cond.rm_dup_seqs) == "true"):
70 --seqkit_rmdup_run true 70 --seqkit_rmdup_run true
71 #end if 71 #end if
72 -profile kondagac; 72 -profile kondagac;
73 mv './cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-multiqc/multiqc_report.html' './multiqc_report.html' > /dev/null 2>&1 || exit 1; 73 mv './cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-multiqc/multiqc_report.html' './multiqc_report.html' > /dev/null 2>&1 || exit 1;
74 mv './cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-results/kraken2_extract_contigs' kraken2_extract_contigs > /dev/null 2>&1 || exit 1; 74 mv './cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-results/kraken2_extract_contigs' kraken2_extract_contigs > /dev/null 2>&1 || exit 1;