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scRNAseq txt files with barcode whitelists are not installed

Status: Open.

#1120 In maxplanck-ie/snakepipes;

· katsikora opened on Sep 11, 2025

change bowtie2 default setting to <code>--local</code>

Status: Open.

#1118 In maxplanck-ie/snakepipes;

· katsikora opened on Sep 1, 2025

deprecation list

Status: Open.

#1114 In maxplanck-ie/snakepipes;

· katsikora opened on Aug 4, 2025

multiqc errors out ( in mRNAseq) when freshly pulled from conda

External ToolAn update/modification of an external tool is neededAn update/modification of an external tool is needed

Status: Open.

Bug

#1113 In maxplanck-ie/snakepipes;

· katsikora opened on Aug 4, 2025

histoneHMM_qc rule is triggered while histoneHMM is not , for broad samples

Status: Open.

#1109 In maxplanck-ie/snakepipes;

· katsikora opened on Jul 29, 2025

Mem / resource allocation - retries

Status: Open.

#1108 In maxplanck-ie/snakepipes;

· WardDeb opened on Jul 28, 2025

Big Help in create envs

Status: Open.

#1106 In maxplanck-ie/snakepipes;

· younng367 opened on Jul 16, 2025

add size-factor-normalized bw to DNAmapping and ChIPseq workflows

ChIP-Seq

DNA-mapping

enhancement

Status: Open.

Feature

#1105 In maxplanck-ie/snakepipes;

· katsikora opened on Jun 24, 2025

chipqc Error in ChIPseq snakePipe

ChIP-Seq

Status: Open.

#1103 In maxplanck-ie/snakepipes;

· skhassafi opened on Jun 3, 2025

createIndices is missing --userYAML

Status: Open.

#1102 In maxplanck-ie/snakepipes;

· katsikora opened on Jun 3, 2025

add LRT as an option to DESeq2

enhancement

RNA-seq

Status: Open.

#1097 In maxplanck-ie/snakepipes;

· katsikora opened on Apr 15, 2025

ValueError: 'group' is not in list

bug

RNA-seq

Status: Open.

#1094 In maxplanck-ie/snakepipes;

· malszycki opened on Mar 20, 2025