Skip to content

Issues: genome/analysis-workflows

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

74 Open 232 Closed
74 Open 232 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

filter_vcf_depth.cwl problems handling DNPs?
#1081 opened Nov 26, 2022 by zlskidmore
1
How to run immuno.cwl pipeline
#1076 opened Aug 16, 2022 by dxkeac
1
Pangenome: RNA-seq Pipeline Requirements Pangenome
#1055 opened Nov 3, 2021 by jasonwalker80
@chad388
1
Pangenome: ATAC-seq Pipeline Pangenome
#1054 opened Nov 3, 2021 by jasonwalker80
@ebelter
Build HCC1395 test input for CNVKit
#1052 opened Oct 15, 2021 by jasonwalker80
Add cwltool requirement InlineJavascriptRequirement
#1051 opened Oct 15, 2021 by jasonwalker80
1
Location of FASTQ files
#1050 opened Oct 15, 2021 by jasonwalker80
1
Should we pass Omni to BQSR?
#1049 opened Oct 15, 2021 by jasonwalker80
Problem with merge_bams
#1045 opened Aug 19, 2021 by tgambin
4
update germline workflows to produce genome vcfs and genotyped vcf
#1040 opened Jul 13, 2021 by apaul7
Add jigv for pre-computed IGV views in a clean HTML format
#1032 opened Jun 8, 2021 by chrisamiller
1
Validate 2.0 workflows
#1004 opened Feb 10, 2021 by chrisamiller 2.0
Update biscuit QC scripts in bisulfite pipeline
#993 opened Jan 13, 2021 by chrisamiller
Update AnnotSV filtration according to the 3.0 version of the tool
#985 opened Dec 22, 2020 by serge2016
1
MMQS filter is overly strict in fp_filter
#972 opened Dec 2, 2020 by chrisamiller
1
Write equivalent sequence_align_and_tag.cwl for rnaseq, rnaseq_star_fusion, and rnaseq_star_fursion_xenosplit pipelines.
#970 opened Nov 18, 2020 by Sam16711 2.0
@sridhar0605
Write equivalent sequence_align_and_tag.cwl for the bisulfite sequencing pipeline.
#967 opened Nov 12, 2020 by Sam16711 2.0
@chrisamiller
Validate Workflow Examples with cwltool
#958 opened Oct 6, 2020 by tmooney 2.0
@gschang
6
docm filter should work the same in the somatic and tumor-only pipelines
#953 opened Sep 17, 2020 by chrisamiller
example rnaseq data yields no gene expression with stringtie
#951 opened Sep 8, 2020 by chrisamiller
Review software for upgrades
#948 opened Sep 2, 2020 by chrisamiller
21 of 24 tasks
2.0
8
Implement bam-readcount CRAM support
#942 opened Sep 1, 2020 by jasonwalker80 2.0
@johnegarza @Matthew-Mosior
3
Replace links to broad FTP server in "Gather Inputs" wiki
#941 opened Sep 1, 2020 by chrisamiller
Create a CWL workflow that creates an annotation bundle
#940 opened Aug 31, 2020 by chrisamiller
Compile inputs into "annotation bundles" that are downloadable
#938 opened Aug 28, 2020 by chrisamiller
5
ProTip! no:milestone will show everything without a milestone.