Scalable DNA sequencing analysis suite powered by the Swift parallel scripting language
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djf604 and JasonJPitt V1.0.1 (#10)
* Small bug fixes

* Bumped up version number

* Changed - to /dev/stdin on some wrappers

* Added ''-o /dev/stdout' to RG merge sort

* Workflow json now highest precedence for swift config app block walltime, then global app config, then global default walltime

* Added sambamba merge step to contig merge-sort and RG merge-sort

* Removed '--out' from sambamba merge step since specifying that flag is not necessary

* Minor RgMergeSort edits

* Merge sort wrappers now only do merge since bams will have already been sorted. For RG merge, if only a single bam present samtools view will be used instead of sambamba merge.

* Samtools fix for RG merge step

* Samtools fix for contig merge step

* Removed '--out=' from sambamba merge in contig merge step

* Added exe_samtools to wrapper format call
Latest commit 5edf271 Nov 13, 2017

README.rst

SwiftSeq

Scalable DNA sequencing analysis suite powered by the Swift parallel scripting language