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nf-core
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atacseq
ATAC-seq peak-calling and QC analysis pipeline
https://nf-co.re/atacseq
MIT License
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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
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