workflows

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Arriba

1

Adding support for Arriba. The most controversial thing is likely to be the changes I made to the STAR defaults. Some are required to output chimeric alignments. Others are likely...

adthrasher

Split tasks to a new repository

1

Finally, we plan to migrate the WDL `tools` to a new repository. There are several tasks required before we can make the change. - [ ] Review open PRs on...

adthrasher

a-frantz

Implements a workflow to generate an unaligned BAM (uBAM) and a `.hic` file for analysis. Users who want control can choose to perform their own analysis starting from the unaligned...

adthrasher

Adding more in-depth checks of file contents, particularly for BAM and FASTQ format output.

adthrasher

1) All quotes that can be double quotes should be (only use single quotes where necessary, such as when nesting quotes) - I don't like this phrasing, but I'm not...

a-frantz

investigate appropriate `disk_size`s

1

a-frantz

Chipseq updates

2

Updates to reflect changes to SEAseq and add support for SEAseq's paired-end mode.

adthrasher

I'll single the 3 worst offenders out: `util.wdl`, `samtools.wdl`, and `picard.wdl` have so many tasks in them it becomes difficult to find the one you're looking for. At least that's...

a-frantz

a-frantz