Mercurial > repos > kkonganti > cfsan_centriflaken

comparison cfsan_centriflaken.xml @ 106:c02d3cf60fe0

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"planemo upload"
author kkonganti
date Thu, 27 Jun 2024 14:18:02 -0400
parents 52045ea4679d
children 2bda095a1222
comparison
equal deleted inserted replaced
105:52045ea4679d 106:c02d3cf60fe0
70 --fq_filename_delim_idx $fq_filename_delim_idx 70 --fq_filename_delim_idx $fq_filename_delim_idx
71 --centrifuge_extract_bug '${centrifuge_extract_bug}' 71 --centrifuge_extract_bug '${centrifuge_extract_bug}'
72 #if (str($input_read_type_cond.pipeline_cond.rm_dup_seqs) == "true"): 72 #if (str($input_read_type_cond.pipeline_cond.rm_dup_seqs) == "true"):
73 --seqkit_rmdup_run true 73 --seqkit_rmdup_run true
74 #end if 74 #end if
75 -profile kondagac; 75 -profile gxkubernetes;
76 mv './cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-multiqc/multiqc_report.html' './multiqc_report.html' > /dev/null 2>&1 || exit 1; 76 mv './cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-multiqc/multiqc_report.html' './multiqc_report.html' > /dev/null 2>&1 || exit 1;
77 mv './cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-results/kraken2_extract_contigs' kraken2_extract_contigs > /dev/null 2>&1 || exit 1; 77 mv './cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-results/kraken2_extract_contigs' kraken2_extract_contigs > /dev/null 2>&1 || exit 1;
78 rm -rf ./cpipes-output > /dev/null 2>&1 || exit 1; 78 rm -rf ./cpipes-output > /dev/null 2>&1 || exit 1;
79 rm -rf ./work > /dev/null 2>&1 || exit 1 79 rm -rf ./work > /dev/null 2>&1 || exit 1
80 ]]></command> 80 ]]></command>