comparison cfsan_centriflaken.xml @ 129:1bb0dacefa6d

planemo upload
author kkonganti
date Wed, 03 Jul 2024 15:02:23 -0400
parents d4439431d12c
children 04f6ac8ca13c
comparison
equal deleted inserted replaced
128:d4439431d12c 129:1bb0dacefa6d
71 #if (str($input_read_type_cond.pipeline_cond.rm_dup_seqs) == "true"): 71 #if (str($input_read_type_cond.pipeline_cond.rm_dup_seqs) == "true"):
72 --seqkit_rmdup_run true 72 --seqkit_rmdup_run true
73 #end if 73 #end if
74 -work-dir \${work_dir} 74 -work-dir \${work_dir}
75 -profile gxkubernetes; 75 -profile gxkubernetes;
76 mv "\${work_dir}/cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-multiqc/multiqc_report.html" './multiqc_report.html' > /dev/null 2>&1 || exit 1; 76 mv "\${work_dir}/cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-multiqc/multiqc_report.html" './multiqc_report.html' || exit 1;
77 mv "\${work_dir}/cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-results/kraken2_extract_contigs" kraken2_extract_contigs > /dev/null 2>&1 || exit 1; 77 mv "\${work_dir}/cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-results/kraken2_extract_contigs" kraken2_extract_contigs > /dev/null 2>&1 || exit 1;
78 rm -rf "\${work_dir}/cpipes-output" > /dev/null 2>&1 || exit 1; 78 rm -rf "\${work_dir}/cpipes-output" || exit 1;
79 ]]></command> 79 ]]></command>
80 <inputs> 80 <inputs>
81 <conditional name="input_read_type_cond"> 81 <conditional name="input_read_type_cond">
82 <param name="input_read_type" type="select" label="Select the read collection type"> 82 <param name="input_read_type" type="select" label="Select the read collection type">
83 <option value="single_long" selected="true">Unpaired reads (i.e. Single-End short reads or Long reads)</option> 83 <option value="single_long" selected="true">Unpaired reads (i.e. Single-End short reads or Long reads)</option>