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42 Open 439 Closed
42 Open 439 Closed
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Issues list

cleanup code
#1087 opened Jan 14, 2025 by katsikora
1 task
@katsikora
the default spikeinExt doesn't get appended to spikein chromosome names in all cases bug createIndices
#1085 opened Jan 10, 2025 by katsikora
@katsikora
1
RuleException in rule validateFQ: The name 'snakePipes_cluster_logDir' is unknown in this context snakemake
#1084 opened Dec 31, 2024 by sunta3iouxos
2
WGBS: conversion rate is failing WGBS
#1083 opened Dec 17, 2024 by katsikora
1 of 2 tasks
@katsikora
methylDackel Mbias output missing External Tool An update/modification of an external tool is needed WGBS
#1082 opened Dec 6, 2024 by katsikora
@katsikora
1
pairtools - multiqc enhancements
#1081 opened Nov 15, 2024 by WardDeb
@WardDeb
force compression of multiqc_data enhancement question
#1079 opened Nov 9, 2024 by thomasmanke
@WardDeb
three-prime-seq replace "shell" with "script" directive bug RNA-seq
#1078 opened Nov 8, 2024 by katsikora
proper envs - conda versions
#1077 opened Nov 7, 2024 by WardDeb
salmonIndex seq name from genes_bed2fasta
#1076 opened Oct 29, 2024 by hanrong498
rule histoneHMM_out_gz throws an error at workflow rerun in the same output folder bug ChIP-Seq
#1070 opened Oct 18, 2024 by katsikora
snakepipes - pypi installation/configuration
#1069 opened Oct 10, 2024 by WardDeb
@WardDeb
makePairs workflow cleanup
#1068 opened Oct 9, 2024 by WardDeb
5 tasks
Clean up global args
#1066 opened Oct 9, 2024 by WardDeb
scRNA - combine_loom
#1063 opened Sep 26, 2024 by WardDeb
@katsikora
default conda env in 3.0.0
#1061 opened Sep 25, 2024 by sunta3iouxos
5
add --keep-going back to snakemake command
#1058 opened Sep 20, 2024 by katsikora
@katsikora
bowtie --cutntag -X 700, ATAC-seq, maxfragment size
#1057 opened Sep 10, 2024 by sunta3iouxos
shift read correction for ATAC/Cut&Tag
#1056 opened Sep 10, 2024 by sunta3iouxos
snakePipes 3.0.0 logging
#1051 opened Sep 6, 2024 by katsikora
5
Add ChIPQC ChIP-Seq enhancement
#1048 opened Sep 5, 2024 by katsikora
1
error while running the DNA-mapping
#1045 opened Sep 3, 2024 by sunta3iouxos
3
dependency issues wgbs
#1044 opened Sep 3, 2024 by sunta3iouxos
3
predictChIPDict for samples without input bug ChIP-Seq
#1024 opened Jul 30, 2024 by LeilyR
1
error in samtools sort
#1021 opened Jul 22, 2024 by sunta3iouxos
3
ProTip! What’s not been updated in a month: updated:<2024-12-14.