Mercurial > repos > kkonganti > cfsan_centriflaken
comparison cfsan_centriflaken.xml @ 129:1bb0dacefa6d
planemo upload
author | kkonganti |
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date | Wed, 03 Jul 2024 15:02:23 -0400 |
parents | d4439431d12c |
children | 04f6ac8ca13c |
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128:d4439431d12c | 129:1bb0dacefa6d |
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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> |