nf-core atacseq issues - Githubissues

nf-core / atacseq

ATAC-seq peak-calling and QC analysis pipeline

https://nf-co.re/atacseq

MIT License

179 stars 116 forks source link

issues

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Newest Most commented Recently updated Oldest Least commented Least recently updated

Picard "--TMP_DIR" arguments are hardcoded

#378 vondoRishi opened 3 weeks ago
0
ERROR ~ Error executing process > 'NFCORE_ATACSEQ:ATACSEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE

#377 Kermaa opened 3 weeks ago
0
AttributeError: module 'matplotlib.cm' has no attribute 'register_cmap'

#376 kasiabla opened 1 month ago
2
Review of PR 301 to Discuss fixes of #164 #168 #169

#375 lpantano opened 1 month ago
5
Update bedtools_genomecov image to use gnu sort

#374 JoseEspinosa closed 1 month ago
4
New release please?

#373 siddharthab opened 2 months ago
1
Remove empty path components from output paths

#372 siddharthab closed 2 months ago
2
Check for sample IDs characters in samplesheet and report line numbers when erroring

#371 JoseEspinosa closed 2 months ago
2
Add line number when reporting errors in check_samplesheet.py

#370 JoseEspinosa closed 2 months ago
1
Increase memory and use sort in `bedtool_genomecov` process when dealing with merged replicates

#369 JoseEspinosa closed 2 months ago
3
Fix save_unaligned parameter description in schema

#368 JoseEspinosa closed 2 months ago
1
Feature Request: call peaks for each replicate (diffbind), not only the merged data

#367 lindenb opened 2 months ago
3
Merge template v2.14.1

#366 JoseEspinosa closed 2 months ago
1
Important! Template update for nf-core/tools v2.14.1

#365 nf-core-bot closed 2 months ago
0
Unable to join Slack channel

#364 JessicaHacheney closed 2 months ago
4
Important! Template update for nf-core/tools v2.14.0

#363 nf-core-bot closed 4 months ago
1
Synchronize example samplesheets with the usage.md

#362 bjlang closed 2 months ago
1
deprecated container formats

#361 LinearParadox opened 5 months ago
1
Merge template 2.13.1

#360 JoseEspinosa closed 4 months ago
1
Improve website on parameters section Alignment Options for argument --save_unaligned

#359 aghr closed 2 months ago
1
Wip clarification usage

#358 VErconi closed 4 months ago
4
Get rid of lib to merge tools v2.13.1

#357 JoseEspinosa closed 5 months ago
2
Get template v2.13.1 (get rid of lib)

#356 JoseEspinosa closed 2 months ago
1
Fix double slash in directory urls

#355 bjlang closed 5 months ago
2
Please pin the version of the nf-validation plugin!

#354 mirpedrol closed 2 months ago
1
Remove lib library

#353 JoseEspinosa closed 2 months ago
1
Important! Template update for nf-core/tools v2.13.1

#352 nf-core-bot closed 4 months ago
0
URGENT: pin nf-validation version

#351 nvnieuwk closed 6 months ago
2
Important! Template update for nf-core/tools v2.13

#350 nf-core-bot closed 6 months ago
0
question for constructing samplesheet

#349 pseudacriscrucifer closed 2 months ago
2
Merging template 2.12

#348 JoseEspinosa closed 7 months ago
2
Important! Template update for nf-core/tools v2.12

#347 nf-core-bot closed 7 months ago
0
suggestion: use samtools view --uncompressed before piping in bamtools_filter

#346 lindenb opened 7 months ago
0
Feature Request: summary table for each sample

#345 lindenb opened 7 months ago
0
Increase memory allocation for BEDTOOLS_GENOMECOV

#344 SPPearce closed 2 months ago
7
bam_csi_index parameter for ATACSeq

#343 BianyunY-ACRD opened 8 months ago
0
Important! Template update for nf-core/tools v2.11.1

#342 nf-core-bot closed 7 months ago
1
Important! Template update for nf-core/tools v2.11

#341 nf-core-bot closed 8 months ago
1
implement the bam_csi_index parameter in atacseq pipeline

#340 BianyunY-ACRD opened 10 months ago
0
Process terminated for an unknown reason (SLURM)

#339 hdbeukel opened 10 months ago
1
the sample field from the samplesheet is too lenient

#338 maxulysse opened 11 months ago
0
CONTROL description needs clarifications

#337 mdozmorov closed 4 months ago
2
Merge template v2.10

#336 JoseEspinosa closed 11 months ago
1
Important! Template update for nf-core/tools v2.10

#335 nf-core-bot closed 11 months ago
0
MAKE_GENE_BED making 0kb .bed files

#334 hcliedtke opened 1 year ago
0
Revert "DO NOT MERGE yet: Discuss fixes of #164 #168 #169 "

#333 bjlang closed 1 year ago
1
Fix double slash in directory urls

#332 jhanifen closed 5 months ago
2
Adding peak-calling with Genrich (fix #108) and multi-mapping read analysis

#331 samuelruizperez opened 1 year ago
2
Error executing process > 'NFCORE_ATACSEQ:ATACSEQ:CUSTOM_DUMPSOFTWAREVERSIONS (1)'

#330 anijudy closed 2 months ago
2
Create samplesheet_with_control.csv

#329 bjlang closed 1 year ago
1