Skip to content

Issues: broadinstitute/viral-pipelines

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

23 Open 35 Closed
23 Open 35 Closed
Author
Filter by author
Loading
Label
Filter by label
Loading
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Loading
Milestones
Filter by milestone
Loading
Assignee
Filter by who’s assigned
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Issues list

change demux_deplete to accept multiple biosample_map input files
#559 opened Oct 4, 2024 by tomkinsc
add grimer visualization to merge_metagenomics workflow
#550 opened Aug 15, 2024 by dpark01
update / make new Terra-friendly genbank prep workflow
#531 opened Apr 2, 2024 by dpark01
1
update nextclade 2 -> 3
#530 opened Apr 2, 2024 by dpark01
workflow-ify lab data model maintenance scripts enhancement New feature or request
#496 opened Oct 26, 2023 by dpark01
@tomkinsc
add workflow for megablast reads to LCA tab file
#491 opened Sep 28, 2023 by golu099
Fetch_SRA_to_BAM retrieves incorrect run_date
#479 opened Aug 10, 2023 by dpark01
Expose kraken2 --minimum-hit-groups param
#472 opened May 8, 2023 by tomkinsc
Add task to convert Illumina-formatted sample sheet to tab-delimited version with extra columns
#471 opened May 5, 2023 by tomkinsc
Detect when i5 indices need to be rev-comp'ed
#469 opened Apr 20, 2023 by tomkinsc
1
Specify (short) input names in call to MultiQC
#466 opened Apr 19, 2023 by tomkinsc
2
rename amplicon16S_analysis to classify_qiime2_multi
#463 opened Apr 13, 2023 by dpark01
@golu099
task illumina_demux does not tolerate spaces in input filenames
#460 opened Mar 29, 2023 by dpark01
WDL task samplesheet_rename_ids does not accept Illumina-style csv sample sheets
#305 opened Jun 14, 2021 by tomkinsc
tsv_join wdl task fails on gzipped tsv input
#202 opened Jan 27, 2021 by dpark01
docker error on augur_from_assemblies call-draft_augur_tree: "This node is not a swarm manager..."
#177 opened Dec 2, 2020 by mark-fathom
7
output reads per million
#166 opened Oct 19, 2020 by tomkinsc
purge supplementary alignments prior to indel realignment in refbased assembly
#165 opened Oct 15, 2020 by tomkinsc
ensure preservation of RX tag; UMI-aware ref-based assembly
#164 opened Oct 15, 2020 by tomkinsc
3
BEAST WDL emit checkpoint and/or logs/trees in case of premature termination
#130 opened Jun 24, 2020 by dpark01
1
convert more coverage stats to samtools
#119 opened Jun 17, 2020 by dpark01
new Genbank download WDL
#109 opened Jun 10, 2020 by dpark01
@cmloreth
remux_plus
#49 opened Apr 24, 2020 by dpark01
1
ProTip! Exclude everything labeled bug with -label:bug.