Published December 4, 2020
| Version v2.1.10.0
Software
Open
broadinstitute/viral-pipelines: v2.1.10.0
Authors/Creators
- 1. Broad Institute
- 2. Broad Institute of MIT and Harvard
- 3. MIT
- 4. @broadinstitute
- 5. Columbia University Medical Center
- 6. Aalborg University
- 7. @gitlabhq
Description
New or changed WDL workflows:
- new workflow: subsample_by_metadata_with_focal [#161]
Changes:
- rename workflow augur_from_newick to augur_export_only, add new workflow augur_from_mltree [#151]
- drop support for trinity (pinned version) assembler [#168]
- bump upstream docker images [#169, #163]
- README changes [#162]
Fixes:
- bugfix: isnvs_per_sample when specifying optional parameters [#160]
- bugfixes for use of
set -o pipefail[#175, #173] - bugfix: optional input handling in filter_bam_to_taxa [#171]
VM shape parameterization or changes to defaults:
- mafft parameterization [#170]
- memory increase to task filter_sequences_to_list [#159]
- parameterize BEAST GPU settings [#158]
- memory increase to assemble_refbased (specifically to task align_reads) [#157]
- memory increase to task multi_align_mafft [#155]
- memory increase & cpu decrease to task refine_augur_tree and ancestral_tree (the timetree invocations) [#153]
- parameterize CPU count for task draft_augur_tree (iqtree) [#150]
DNAnexus:
- update DNAnexus demux_launcher to v2 instance types [#156]
- update instance types to v2 [#167]
Files
broadinstitute/viral-pipelines-v2.1.10.0.zip
Files
(19.8 MB)
| Name | Size | Download all |
|---|---|---|
|
md5:184bf3b76165e80b1ffbf43419aec420
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19.8 MB | Preview Download |
Additional details
Related works
- Is supplement to
- https://github.com/broadinstitute/viral-pipelines/tree/v2.1.10.0 (URL)