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add a repeat binding quantification module to the chipseq workflow

ChIP-Seq

enhancement

Status: Open.

#1172 In maxplanck-ie/snakepipes;

· katsikora opened on Jul 13, 2026

fix chipqc issues for mm39

bug

ChIP-Seq

Status: Open.

#1170 In maxplanck-ie/snakepipes;

· katsikora opened on Jul 8, 2026

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

bug

WGBS

Status: Open.

#1168 In maxplanck-ie/snakepipes;

· katsikora opened on Jun 23, 2026

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

Status: Open.

#1167 In maxplanck-ie/snakepipes;

· katsikora opened on Jun 22, 2026

conda build clashing with python versions

CICD

conda

Status: Open.

#1166 In maxplanck-ie/snakepipes;

· katsikora opened on Jun 3, 2026

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

RNA-seq

Status: Open.

#1165 In maxplanck-ie/snakepipes;

· katsikora opened on May 13, 2026

add 10x v4 to scRNAseq STARsolo

enhancement

scRNA-seq

Status: Open.

#1161 In maxplanck-ie/snakepipes;

· katsikora opened on Mar 20, 2026

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

documentation

enhancement

RNA-seq

Status: Open.

#1160 In maxplanck-ie/snakepipes;

· NderBinf opened on Feb 18, 2026

consider renaming bw files after the applied normalization method

Status: Open.

#1157 In maxplanck-ie/snakepipes;

· katsikora opened on Dec 1, 2025

update documentation on normalization for bamCoverage files

Status: Open.

#1155 In maxplanck-ie/snakepipes;

· katsikora opened on Dec 1, 2025

ATACseq fixes and extentions

Status: Open.

#1150 In maxplanck-ie/snakepipes;

· katsikora opened on Nov 17, 2025

deprecate allelic counting mode in mRNAseq

Status: Open.

#1146 In maxplanck-ie/snakepipes;

· katsikora opened on Nov 13, 2025