DKFZ-ODCF/AlignmentAndQCWorkflows

Issues

• `.DepthOfCoverage_Target.txt` has odd output

  #90 opened 5 months ago by vinjana
  0

• Filename length restriction in R diffchrom script

  #63 opened 3 years ago by vinjana
  2

• _de novo_ adapter detection

  #60 opened 9 months ago by vinjana
  1

• Get fingerprinting to work with ALT-contig reference

  #86 opened 2 years ago by vinjana
  0

• Remove the biobambam sort option

  #85 opened 2 years ago by vinjana
  0

• Add bwa-postalt.js to WGBS bwa job

  #84 opened 2 years ago by vinjana
  0

• Move fingerprinting into pipeline

  #67 opened 3 years ago by vinjana
  0

• bwa-mem2 support

  #66 opened 3 years ago by vinjana
  0

• Check wait -n for task management in bash code

  #65 opened 3 years ago by vinjana
  0

• Lift methylation meta job to WFMS level

  #62 opened 3 years ago by vinjana
  0

• CRAM support

  #28 opened 6 years ago by vinjana
  6

• Calculate target region size from TARGET_REGION_FILE

  #58 opened 5 years ago by vinjana
  0

• Add for-loop to waitForRegisteredPids

  #44 opened 5 years ago by vinjana
  0

• Move Bash library code to DefaultPlugin or own repo

  #46 opened 5 years ago by vinjana
  1

• Tagmentation WGS and WES

  #54 opened 5 years ago by vinjana
  0

• Better IO checks in Perl scripts

  #53 opened 5 years ago by vinjana
  0

• Check: Chromosomes in stats file need to be subset of those in genome (index)

  #15 opened 6 years ago by vinjana
  1

• Merge without duplication marking

  #52 opened 5 years ago by vinjana
  0

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

  #48 opened 5 years ago by vinjana
  0

• checkExecutability(): adapter file for trimming exists

  #16 opened 5 years ago by vinjana
  0

• Clean-up code around adapter trimming

  #17 opened 5 years ago by vinjana
  0

• WGBS: Include Option for non-directional protocol

  #34 opened 5 years ago by vinjana
  0

• WGBS Bug: coveragePlot.R

  #33 opened 6 years ago by vinjana
  1

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

  #47 opened 5 years ago by vinjana
  0

• Switch PID registry to associative array

  #45 opened 5 years ago by vinjana
  0

• Process data from object storage

  #41 opened 5 years ago by vinjana
  0

• Single-end alignment

  #40 opened 5 years ago by vinjana
  0

• `ConfigurationValues::toStringList(String, String)` cannot deal with parentheses that are not separated by spaces from values

  #21 opened 5 years ago by vinjana
  1

• Check content of CHROM_SIZES_FILE and CHROMOSOME_INDICES against BAM file (maybe also the BWA index?)

  #23 opened 5 years ago by vinjana
  1

• Make output MultiQC-compatible

  #39 opened 5 years ago by vinjana
  0

• coveragePlot.R fix

  #26 opened 6 years ago by vinjana
  1

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

  #37 opened 6 years ago by vinjana
  0

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

  #36 opened 6 years ago by vinjana
  0

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

  #35 opened 6 years ago by vinjana
  0

• Agglomerate methylation rates over specific sets of chromosomes for QC

  #32 opened 6 years ago by vinjana
  0

• Extract library name from path in BasicCOProjectsRuntimeService#extractLibrariesFromSampleDirectory using the XML config

  #31 opened 6 years ago by vinjana
  0

• Move alignment files from temporary to final location only after the BWA checks have finished

  #30 opened 6 years ago by vinjana
  1

• Benchmark the tool BIS-Sniper for Methylation- and SNP-Calling

  #29 opened 6 years ago by vinjana
  0

• Check all read BAM files for MD5 sum on the fly

  #27 opened 6 years ago by vinjana
  0

• Remove FileStage Hack from LaneFile

  #25 opened 6 years ago by vinjana
  0

• Catch PIPESTATUS for pipe expressions

  #24 opened 6 years ago by vinjana
  0

• Relocate library information into the CO or Alignment Plugin

  #22 opened 6 years ago by vinjana
  0

• Metadata Table access for WES/WGS

  #19 opened 6 years ago by vinjana
  0

• Add @PG entry with parameter for sambamba merging/marking

  #20 opened 6 years ago by vinjana
  0

• Add check in checkExecutability() for correct markDuplicatesVariant.

  #18 opened 6 years ago by vinjana
  0

• Track number of reads lost by read-trimming

  #13 opened 6 years ago by vinjana
  0

• Read-count consistency check before/after processing to improve operation safety

  #14 opened 6 years ago by vinjana
  0

• methylCtools should write metadata into BAM attribute instead of identifier

  #10 opened 6 years ago by vinjana
  0

• BAM integrity check job

  #9 opened 6 years ago by vinjana
  0

• roddy.sh run fails on existing output (WGBS)

  #8 opened 6 years ago by vinjana
  0