Release/1.4#910
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gongyixiao merged 169 commits intomasterfrom Aug 12, 2021
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…d filtering settings for multiqc to recognize facets qc files
…ble format for multiqc within the multiqc step.
…tion instead of Fraction.
….py scripts, and set the Homopolymer graph to show Percentage upon loading rather than the default
… QC option, thus avoiding a warning message for a QC operation when --QC is not specified
…n parse_alfred.py
…gnored folder; edited Facets QC value from TRUE/FALSE to PASS/FAIL; finetuned coverage pass/fail thresholds
…opy that is used for the Docker container
…tHsMetrics is not run so that downstream processes SampleRunMultiQC, CohortRunMultiQC, and QcBamAggregate can run
… that it runs with genome in addition to exome
…rouped together subsections under the sections Facets and Multiqc. Also fixed the order of Alfred subsections.
…de in parse_alfred.py
…so changed TRUE -> PASS and FALSE -> FAIL for facets qc results in the report
synchronize hotfix in master back to develop
…(of reads) in y axis rather than count
…sed the function to remove decimals from 'Homopolymer distribution' tables, which only show whole numbers
…nto feature/allowCustomTargets
combine bqsr processes into one
Bugfix/filter strandbias
Enhancement/unfiltered vcf
Custom targets
anoronh4
approved these changes
Aug 12, 2021
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Repeat of draft PR #874