Skip to content

Issues: maxplanck-ie/snakepipes

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

30 Open 404 Closed
30 Open 404 Closed
Author
Filter by author
Label
Filter by label
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Milestones
Filter by milestone
Assignee
Filter by who’s assigned
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Issues list

allow user to specify mincount for filtering windows for DB with CSAW ATAC-seq ChIP-Seq External Tool An update/modification of an external tool is needed
#1014 opened Apr 23, 2024 by katsikora
[Request] looping inputs for multiple ChIP-seq comparisons
#1013 opened Apr 21, 2024 by sunta3iouxos
1
plotFinger fails due to insaficient wall time
#1011 opened Apr 16, 2024 by sunta3iouxos
6
mRNA-seq: sambamba markdup fails because "too many open files"
#1010 opened Apr 15, 2024 by caballero
Error in mRNA-seq allelic-mapping when using custom genome allelic bug RNA-seq
#1009 opened Apr 15, 2024 by caballero
update the snakePipes installed from the github documentation question
#1007 opened Apr 12, 2024 by sunta3iouxos
add support for custom model formula to mRNAseq and other workflows ATAC-seq ChIP-Seq enhancement RNA-seq WGBS
#988 opened Feb 20, 2024 by katsikora
1 of 6 tasks
2
mamba vs conda conda
#983 opened Feb 15, 2024 by WardDeb
1
move from setup.py to pytoml enhancement help wanted
#975 opened Jan 26, 2024 by katsikora
test boa for building snakePipes enhancement
#974 opened Jan 26, 2024 by katsikora
fix --predictChIPDict for cutNX bug ChIP-Seq External Tool An update/modification of an external tool is needed
#973 opened Jan 26, 2024 by katsikora
TO-DO before upcoming release
#969 opened Jan 23, 2024 by katsikora
5 tasks
ruamel.yaml vs pyyaml enhancement
#967 opened Jan 20, 2024 by WardDeb
make splitSampleSheet more flexible and include any column between name and condition enhancement RNA-seq
#955 opened Nov 10, 2023 by katsikora
continuation from #924, warnings.warn("fragmentSize.metric.tsv is empty, this sets bug ChIP-Seq
#926 opened Aug 21, 2023 by sunta3iouxos
12
no spikeIn chromosomes found with extention _spikein createIndices
#924 opened Aug 18, 2023 by sunta3iouxos
12
difference in conda env hashes between snakePipes and snakemake conda
#914 opened Aug 9, 2023 by katsikora
1
ATAC example miss /bamCoverage/*.filtered.seq_depth_norm.bw files ATAC-seq test_data
#910 opened Jul 27, 2023 by HamletShaoE
5
conda envs get re-created by another user of the same group conda
#903 opened Jun 6, 2023 by katsikora
2 tasks
1
CI dag test CICD
#901 opened Jun 5, 2023 by WardDeb
1
update snakemake and implement native slurm support enhancement help wanted
#888 opened Mar 16, 2023 by katsikora
DNA-mapping pipeline gets stuck at origFASTQ rule when using a custom cluster config yaml bug
#887 opened Mar 6, 2023 by TobiasHohl
4
update and reformat documentation documentation
#878 opened Jan 20, 2023 by katsikora
6 tasks
filter bam rule in umi_tools.snakefile doesn't include bwa
#871 opened Jan 5, 2023 by jeffhsu3
Error during DNA-Mapping workflow: bowtie2.index.err: No output file specified DNA-mapping
#861 opened Oct 28, 2022 by jurummel
2
ProTip! Mix and match filters to narrow down what you’re looking for.