Issues

• Voom transformation for TE normalisation

  maxplanck-ie/snakepipes#1185 · Filter by author TomLanchec opened on Sep 30, 2026
  2

• add support for a bigBed rmsk file

  createIndicesRNA-seq
  maxplanck-ie/snakepipes#1184 · Filter by author katsikora opened on Sep 28, 2026

• add support for gtf.gz

  maxplanck-ie/snakepipes#1183 · Filter by author katsikora opened on Sep 24, 2026

• rule run_eisaR fails

  bugcreateIndices
  maxplanck-ie/snakepipes#1174 · Filter by author katsikora opened on Jul 28, 2026

• trim_galore SE trimming error snakepipes-v.3.4.0

  bugRNA-seq
  maxplanck-ie/snakepipes#1173 · Filter by author NderBinf opened on Jul 21, 2026
  1

• add a repeat binding quantification module to the chipseq workflow

  ChIP-Seqenhancement
  maxplanck-ie/snakepipes#1172 · Filter by author katsikora opened on Jul 13, 2026

• fix chipqc issues for mm39

  bugChIP-Seq
  maxplanck-ie/snakepipes#1170 · Filter by author katsikora opened on Jul 8, 2026

• trimming is not invoked in WGBS although --trim is passed

  bugWGBS
  maxplanck-ie/snakepipes#1168 · Filter by author katsikora opened on Jun 23, 2026

• move setting tmpdir to snakemake profile rather than a combo of defaults.yaml + rule shell command

  maxplanck-ie/snakepipes#1167 · Filter by author katsikora opened on Jun 22, 2026

• conda build clashing with python versions

  CICDconda
  maxplanck-ie/snakepipes#1166 · Filter by author katsikora opened on Jun 3, 2026

• add --outMultimapperOrder Random --outSAMmultNmax 1 to aligner options for STAR

  RNA-seq
  maxplanck-ie/snakepipes#1165 · Filter by author katsikora opened on May 13, 2026

• add 10x v4 to scRNAseq STARsolo

  enhancementscRNA-seq
  maxplanck-ie/snakepipes#1161 · Filter by author katsikora opened on Mar 20, 2026

• STAR overwrite hard coded aligner options in case of bamRemoveDuplicatesType UniqueIdentical is not possible

  documentationenhancementRNA-seq
  maxplanck-ie/snakepipes#1160 · Filter by author NderBinf opened on Feb 18, 2026
  1

• consider renaming bw files after the applied normalization method

  maxplanck-ie/snakepipes#1157 · Filter by author katsikora opened on Dec 1, 2025
  1

• update documentation on normalization for bamCoverage files

  maxplanck-ie/snakepipes#1155 · Filter by author katsikora opened on Dec 1, 2025
  1

• ATACseq fixes and extentions

  maxplanck-ie/snakepipes#1150 · Filter by author katsikora opened on Nov 17, 2025
  1

• deprecate allelic counting mode in mRNAseq

  maxplanck-ie/snakepipes#1146 · Filter by author katsikora opened on Nov 13, 2025

• WGBS calculate conversion rate over lambda chromosome

  enhancementWGBS
  maxplanck-ie/snakepipes#1130 · Filter by author katsikora opened on Sep 26, 2025
  

• Mem / resource allocation - retries

  maxplanck-ie/snakepipes#1108 · Filter by author WardDeb opened on Jul 28, 2025

• add summary of whatshap splitting metrics

  RNA-seq
  Feature

  maxplanck-ie/snakepipes#1091 · Filter by author katsikora opened on Jan 28, 2025
  

• pairtools - multiqc enhancements

  maxplanck-ie/snakepipes#1081 · Filter by author WardDeb opened on Nov 15, 2024

• force compression of multiqc_data

  enhancementquestion
  maxplanck-ie/snakepipes#1079 · Filter by author thomasmanke opened on Nov 9, 2024

• rule histoneHMM_out_gz throws an error at workflow rerun in the same output folder

  bugChIP-Seq
  maxplanck-ie/snakepipes#1070 · Filter by author katsikora opened on Oct 18, 2024

• snakepipes - pypi

  installation/configuration
  maxplanck-ie/snakepipes#1069 · Filter by author WardDeb opened on Oct 10, 2024

• makePairs workflow cleanup

  maxplanck-ie/snakepipes#1068 · Filter by author WardDeb opened on Oct 9, 2024
  1