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Diffstat (limited to 'doc/blog/using-covid-19-pubseq-part2.org')
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diff --git a/doc/blog/using-covid-19-pubseq-part2.org b/doc/blog/using-covid-19-pubseq-part2.org index 4b827f5..d7816ba 100644 --- a/doc/blog/using-covid-19-pubseq-part2.org +++ b/doc/blog/using-covid-19-pubseq-part2.org @@ -96,6 +96,27 @@ the git repo and starts a new run calling into /data/pubseq/bh20-seq-resource/venv3/bin/bh20-seq-analyzer which is essentially [[https://github.com/arvados/bh20-seq-resource/blob/2baa88b766ec540bd34b96599014dd16e393af39/bh20seqanalyzer/main.py#L354][monitoring]] for uploads. +On ~run --help~ + +#+begin_example +optional arguments: + -h, --help show this help message and exit + --uploader-project UPLOADER_PROJECT + --pangenome-analysis-project PANGENOME_ANALYSIS_PROJECT + --fastq-project FASTQ_PROJECT + --validated-project VALIDATED_PROJECT + --workflow-def-project WORKFLOW_DEF_PROJECT + --pangenome-workflow-uuid PANGENOME_WORKFLOW_UUID + --fastq-workflow-uuid FASTQ_WORKFLOW_UUID + --exclude-list EXCLUDE_LIST + --latest-result-collection LATEST_RESULT_COLLECTION + --kickoff + --no-start-analysis + --once + --print-status PRINT_STATUS + --revalidate +#+end_example + * Wiring up CWL In above script ~bh20-seq-analyzer~ you can see that the [[https://www.commonwl.org/][Common |