add align_and_count_multiple_report workflow to aggregate multiple sp… #91
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…ike-in/alignment count reports from the align_and_count task add align_and_count_multiple_report workflow to aggregate multiple spike-in/alignment count reports from the align_and_count task; bump viral-core dependency 2.0.21 -> 2.1.0 to have reports.py::aggregate_alignment_counts()
…/viral-pipelines into ct-spikein-workflow
update docker modules requirements for broadinstitute/viral-assemble,broadinstitute/viral-classify,broadinstitute/viral-phylo to allow for layer sharing and speed up build time
dpark01
approved these changes
May 29, 2020
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align_and_count_multiple_reportworkflow to aggregate multiple spike-in/alignment count reports from thealign_and_counttask (input multiple bam files, output two aggregate reports: one with all counts, one with top-3 counts per bam);This should also fix an issue where count reports would result in empty summary output if they did not end with
*.spike_count.txt.