Skip to content

Pull requests: broadinstitute/viral-pipelines

New pull request New
15 Open 499 Closed
15 Open 499 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
Reviews
Filter by reviews
No reviews Review required Approved review Changes requested
Assignee
Filter by who’s assigned
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Pull requests list

initial WIP commit of a task and workflow to run delphy
#560 opened Oct 10, 2024 by tomkinsc Loading…
attempt at fixing OpenBLAS-related nproc limit
#553 opened Aug 23, 2024 by tomkinsc Loading…
Adding Kraken to Krona conversion to blastoff.wdl
#544 opened Jun 25, 2024 by golu099 Loading…
19
in create_or_update_sample_tables, use the sample_original from demux as the key value for rows rather than sample (i.e. use IDs with forward slashes not dashes)
#539 opened May 15, 2024 by tomkinsc Loading…
add workflow to download multiple SRA accessions to multiple bams: fetch_multiple_sra_to_bams
#537 opened May 3, 2024 by tomkinsc Loading…
1
In align_and_count, change default to count only properly-paired reads
#534 opened Apr 24, 2024 by tomkinsc Loading…
parameterize table names in create_or_update_sample_tables task
#533 opened Apr 23, 2024 by tomkinsc Loading…
bugfix output location of fasta in download_annotations; pass NCBI API key to tasks: download_fasta, download_annotations
#481 opened Aug 10, 2023 by tomkinsc Loading…
add workflow: fetch_sra_bams_for_genbank_accession
#475 opened Jul 6, 2023 by tomkinsc • Draft
Integration of taxonomic classifier trainer wdl
#459 opened Mar 24, 2023 by golu099 Loading…
@golu099
16
merge samples across lanes in demux deplete
#369 opened Sep 28, 2021 by tomkinsc Loading…
use lofreq call-parallel; option to output positions not called
#339 opened Jul 21, 2021 by tomkinsc Loading…
include generate_author_sbt in sarscov2_illumina_full wdl workflow
#259 opened Apr 14, 2021 by tomkinsc Loading…
allow custom placeholder for missing data in tsv_join task
#227 opened Mar 11, 2021 by tomkinsc Loading…
3
merge_bams_bulk
#6 opened Dec 15, 2019 by lakras Loading…
12
ProTip! What’s not been updated in a month: updated:<2024-11-20.