Stephen Watts

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Results 71 comments of Stephen Watts

Foreign file staging can allow pipelines to proceed with corrupt files

Closing now that this has been addressed in the above PR, thank you all!

Differences when using cram input file versus fastqs

Closing due to inactivity, please re-open if you'd like to continue discussing

Update GRIDSS 2.13.2

Both `linux_test` job attempts failed from exceeding available disk space on the VM: ``` .02:34:18 BIOCONDA INFO (ERR) [Mar 5 02:34:18] SERR [Mar 5 02:34:18] ERRO Task processing failed: API...

Update GRIDSS 2.13.2

@BiocondaBot please fetch artifacts

Update GRIDSS 2.13.2

Please do not merge until I add the `please review & merge` label!

Update GRIDSS 2.13.2

The Docker image is missing the Dfam database: ```text $ docker run quay.io/biocontainers/gridss:2.13.2--h50ea8bc_4 cat /usr/local/share/RepeatMasker/Libraries/Dfam.h5 Placeholder file, should be replaced on Conda package installation. ``` Absence of the Dfham database...

Update GRIDSS 2.13.2

Using the GitHub 'Update with rebase' didn't work, manually rebasing and force pushing again

Update GRIDSS 2.13.2

Repeating rebase on latest `master` branch commit

Update GRIDSS 2.13.2

@BiocondaBot please fetch artifacts

Use pbzip2/pigz for asset decompression

Thanks for the suggestion @brainstorm. Given a sufficiently well-resourced executor where each job can run independently I would expect to see a runtime improvement of upwards of ~5 minutes This...