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74 Open 232 Closed
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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
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