Issues

• small number of reads / no aberrant reads triggers exception in chrom_diff.r

  bug
  DKFZ-ODCF/AlignmentAndQCWorkflows#92 · Filter by author GWarsow opened on Dec 4, 2024
  1

• Roddy cannot zip folder

  DKFZ-ODCF/AlignmentAndQCWorkflows#91 · Filter by author AndreasKienzle opened on Jun 22, 2024

• .DepthOfCoverage_Target.txt has odd output

  DKFZ-ODCF/AlignmentAndQCWorkflows#90 · Filter by author vinjana opened on Jan 31, 2024

• Get fingerprinting to work with ALT-contig reference

  DKFZ-ODCF/AlignmentAndQCWorkflows#86 · Filter by author vinjana opened on Jun 22, 2022

• Remove the biobambam sort option

  DKFZ-ODCF/AlignmentAndQCWorkflows#85 · Filter by author vinjana opened on May 4, 2022

• Add bwa-postalt.js to WGBS bwa job

  DKFZ-ODCF/AlignmentAndQCWorkflows#84 · Filter by author vinjana opened on Apr 26, 2022

• Move fingerprinting into pipeline

  DKFZ-ODCF/AlignmentAndQCWorkflows#67 · Filter by author vinjana opened on Sep 14, 2021

• bwa-mem2 support

  DKFZ-ODCF/AlignmentAndQCWorkflows#66 · Filter by author vinjana opened on Sep 14, 2021

• Check wait -n for task management in bash code

  DKFZ-ODCF/AlignmentAndQCWorkflows#65 · Filter by author vinjana opened on Sep 14, 2021

• Filename length restriction in R diffchrom script

  bug
  DKFZ-ODCF/AlignmentAndQCWorkflows#63 · Filter by author vinjana opened on Jul 13, 2021
  2

  

• Lift methylation meta job to WFMS level

  DKFZ-ODCF/AlignmentAndQCWorkflows#62 · Filter by author vinjana opened on Jun 25, 2021

• Calculate target region size from TARGET_REGION_FILE

  DKFZ-ODCF/AlignmentAndQCWorkflows#58 · Filter by author vinjana opened on Nov 5, 2019

• Tagmentation WGS and WES

  DKFZ-ODCF/AlignmentAndQCWorkflows#54 · Filter by author vinjana opened on Jun 26, 2019

• Better IO checks in Perl scripts

  DKFZ-ODCF/AlignmentAndQCWorkflows#53 · Filter by author vinjana opened on Jun 18, 2019

• Merge without duplication marking

  DKFZ-ODCF/AlignmentAndQCWorkflows#52 · Filter by author vinjana opened on Jun 18, 2019

• Allow setting the number of bases at read start that should should be ignored for conversion statistics

  DKFZ-ODCF/AlignmentAndQCWorkflows#48 · Filter by author vinjana opened on Mar 14, 2019

• Add collected ambiguously classified undirected WGBS reads in QC-JSON

  DKFZ-ODCF/AlignmentAndQCWorkflows#47 · Filter by author vinjana opened on Feb 15, 2019

• Move Bash library code to DefaultPlugin or own repo

  DKFZ-ODCF/AlignmentAndQCWorkflows#46 · Filter by author vinjana opened on Feb 15, 2019
  1

• Switch PID registry to associative array

  DKFZ-ODCF/AlignmentAndQCWorkflows#45 · Filter by author vinjana opened on Feb 15, 2019

• Process data from object storage

  DKFZ-ODCF/AlignmentAndQCWorkflows#41 · Filter by author vinjana opened on Jan 16, 2019

• Single-end alignment

  DKFZ-ODCF/AlignmentAndQCWorkflows#40 · Filter by author vinjana opened on Jan 16, 2019

• Make output MultiQC-compatible

  DKFZ-ODCF/AlignmentAndQCWorkflows#39 · Filter by author vinjana opened on Jan 16, 2019

• Safer online QC statistics on the SAM output stream for post-mortem analysis of alignment (or other processes)

  DKFZ-ODCF/AlignmentAndQCWorkflows#37 · Filter by author vinjana opened on Nov 15, 2018

• Merge Methylation Calls per library instead of performing methylation calling on merged bam

  DKFZ-ODCF/AlignmentAndQCWorkflows#36 · Filter by author vinjana opened on Nov 15, 2018

• Handle incremental addition of new lanes when dealing with multiple sequencing libraries

  DKFZ-ODCF/AlignmentAndQCWorkflows#35 · Filter by author vinjana opened on Nov 15, 2018