Issues

• filter_vcf_depth.cwl problems handling DNPs?

  genome/analysis-workflows#1081 · Filter by author zlskidmore opened on Nov 26, 2022
  1

• How to run immuno.cwl pipeline

  genome/analysis-workflows#1076 · Filter by author dxkeac opened on Aug 16, 2022
  1

• Pangenome: RNA-seq Pipeline Requirements

  Pangenome
  genome/analysis-workflows#1055 · Filter by author jasonwalker80 opened on Nov 3, 2021
  1

  

• Pangenome: ATAC-seq Pipeline

  Pangenome
  genome/analysis-workflows#1054 · Filter by author jasonwalker80 opened on Nov 3, 2021
  

• Build HCC1395 test input for CNVKit

  genome/analysis-workflows#1052 · Filter by author jasonwalker80 opened on Oct 15, 2021

• Add cwltool requirement InlineJavascriptRequirement

  genome/analysis-workflows#1051 · Filter by author jasonwalker80 opened on Oct 15, 2021
  1

• Location of FASTQ files

  genome/analysis-workflows#1050 · Filter by author jasonwalker80 opened on Oct 15, 2021
  1

• Should we pass Omni to BQSR?

  genome/analysis-workflows#1049 · Filter by author jasonwalker80 opened on Oct 15, 2021

• Problem with merge_bams

  genome/analysis-workflows#1045 · Filter by author tgambin opened on Aug 19, 2021
  4

• update germline workflows to produce genome vcfs and genotyped vcf

  genome/analysis-workflows#1040 · Filter by author apaul7 opened on Jul 13, 2021

• Add jigv for pre-computed IGV views in a clean HTML format

  genome/analysis-workflows#1032 · Filter by author chrisamiller opened on Jun 8, 2021
  1

• Validate 2.0 workflows

  genome/analysis-workflows#1004 · Filter by author chrisamiller opened on Feb 10, 2021 · 2.0

• Update biscuit QC scripts in bisulfite pipeline

  genome/analysis-workflows#993 · Filter by author chrisamiller opened on Jan 13, 2021

• Update AnnotSV filtration according to the 3.0 version of the tool

  genome/analysis-workflows#985 · Filter by author serge2016 opened on Dec 22, 2020
  1

• MMQS filter is overly strict in fp_filter

  genome/analysis-workflows#972 · Filter by author chrisamiller opened on Dec 2, 2020
  1

• Write equivalent sequence_align_and_tag.cwl for rnaseq, rnaseq_star_fusion, and rnaseq_star_fursion_xenosplit pipelines.

  genome/analysis-workflows#970 · Filter by author Sam16711 opened on Nov 18, 2020 · 2.0
  

• Write equivalent sequence_align_and_tag.cwl for the bisulfite sequencing pipeline.

  genome/analysis-workflows#967 · Filter by author Sam16711 opened on Nov 12, 2020 · 2.0
  

• Validate Workflow Examples with cwltool

  genome/analysis-workflows#958 · Filter by author tmooney opened on Oct 6, 2020 · 2.0
  6

  

• docm filter should work the same in the somatic and tumor-only pipelines

  genome/analysis-workflows#953 · Filter by author chrisamiller opened on Sep 17, 2020

• example rnaseq data yields no gene expression with stringtie

  genome/analysis-workflows#951 · Filter by author chrisamiller opened on Sep 8, 2020

• Review software for upgrades

  genome/analysis-workflows#948 · Filter by author chrisamiller opened on Sep 2, 2020 · 2.0
  8

• Implement bam-readcount CRAM support

  genome/analysis-workflows#942 · Filter by author jasonwalker80 opened on Sep 1, 2020 · 2.0
  3

  

• Replace links to broad FTP server in "Gather Inputs" wiki

  genome/analysis-workflows#941 · Filter by author chrisamiller opened on Sep 1, 2020

• Create a CWL workflow that creates an annotation bundle

  genome/analysis-workflows#940 · Filter by author chrisamiller opened on Aug 31, 2020

• Compile inputs into "annotation bundles" that are downloadable

  genome/analysis-workflows#938 · Filter by author chrisamiller opened on Aug 28, 2020
  5