Issues

• Tests workflow failing

  cgat-developers/cgat-flow#166 · Filter by author IanSudbery opened on Jun 19, 2025

• java VM optoins change

  cgat-developers/cgat-flow#163 · Filter by author IanSudbery opened on Dec 12, 2024
  1

• semi colons in preprocess commands

  cgat-developers/cgat-flow#162 · Filter by author IanSudbery opened on Jul 15, 2024
  2

• buildJunctions in mapping pipeline produces invalid file

  cgat-developers/cgat-flow#157 · Filter by author IanSudbery opened on Mar 23, 2022
  1

• Alternate pipeline paths and checksums

  cgat-developers/cgat-flow#149 · Filter by author IanSudbery opened on Sep 20, 2021
  2

• rnaseqqc - Error setting xlim in plotStrandednessSalmon

  cgat-developers/cgat-flow#146 · Filter by author IanSudbery opened on Sep 2, 2021
  9

• cgat-flow-pipelines.yml causes installation of cgat-apps 0.6.0

  cgat-developers/cgat-flow#143 · Filter by author IanSudbery opened on Aug 26, 2021
  12

• pipeline_genesets assumes that a genome has a miRBase entry

  cgat-developers/cgat-flow#136 · Filter by author IanSudbery opened on Feb 16, 2021
  1

• Installation breaks cgat-apps bamtools

  cgat-developers/cgat-flow#133 · Filter by author IanSudbery opened on Nov 20, 2020
  4

• MACS2 is now compatible with python3

  cgat-developers/cgat-flow#132 · Filter by author IanSudbery opened on Nov 10, 2020
  1

• bamstats counts unaligned reads as intergenic.

  cgat-developers/cgat-flow#130 · Filter by author IanSudbery opened on Sep 15, 2020
  1

• install-level script conflicts

  cgat-developers/cgat-flow#127 · Filter by author Acribbs opened on Jan 20, 2020
  1

• Updated samtools doesn't work with hisat2 in mapping pipeline

  cgat-developers/cgat-flow#124 · Filter by author microbialman opened on Dec 19, 2019
  1

• Filter HOT regions

  enhancement
  cgat-developers/cgat-flow#102 · Filter by author Acribbs opened on Jun 28, 2019

• Mapping rate no longer reported by any pipeline

  cgat-developers/cgat-flow#85 · Filter by author IanSudbery opened on Jan 3, 2019
  6

• Memory in peakcalling checkBams

  cgat-developers/cgat-flow#78 · Filter by author IanSudbery opened on Nov 5, 2018
  8

• Regex for paired sequencing in pipeline_readqc

  cgat-developers/cgat-flow#75 · Filter by author IanSudbery opened on Oct 22, 2018

• Duplication of code between bamstats.py and mappingqc.py

  cgat-developers/cgat-flow#60 · Filter by author jscaber opened on Sep 21, 2018
  2