Mercurial > repos > kkonganti > cfsan_centriflaken
diff cfsan_centriflaken.xml @ 131:45900148ca9e
planemo upload
| author | kkonganti |
|---|---|
| date | Fri, 05 Jul 2024 09:31:14 -0400 |
| parents | 04f6ac8ca13c |
| children | cbb06f201be5 |
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--- a/cfsan_centriflaken.xml Wed Jul 03 15:16:39 2024 -0400 +++ b/cfsan_centriflaken.xml Fri Jul 05 09:31:14 2024 -0400 @@ -5,8 +5,6 @@ </requirements> <version_command>nextflow -version</version_command> <command detect_errors="exit_code"><![CDATA[ - time_stamp=\$(date +%Y-%m-%d-%s); - work_dir="/galaxy/nf-work-dirs/centriflaken_work_dir-"\${time_stamp}; input_path=\$(pwd)"/cpipes-input"; mkdir -p "\${input_path}" || exit 1; #import re @@ -71,8 +69,8 @@ --seqkit_rmdup_run true #end if -profile gxkubernetes; - mv "./cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-multiqc/multiqc_report.html" './multiqc_report.html' || exit 1; - mv "./cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-results/kraken2_extract_contigs" kraken2_extract_contigs || exit 1; + mv "./cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-multiqc/multiqc_report.html" "./multiqc_report.html" || exit 1; + mv "./cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-results/kraken2_extract_contigs" "kraken2_extract_contigs" || exit 1; ]]></command> <inputs> <conditional name="input_read_type_cond">