nf-core cutandrun issues

nf-core / cutandrun

Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.

https://nf-co.re/cutandrun

MIT License

79 stars 45 forks source link

issues

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Suggestion to implement "greenlist normalization"

#257 GeroKn opened 1 week ago
0
Is the default binsize really 1 when using `CPM` normalization?

#256 nvictus opened 1 week ago
1
Process `NFCORE_CUTANDRUN:CUTANDRUN:MULTIQC` input file name collision

#255 AprilJack opened 2 weeks ago
0
NFCORE_CUTANDRUN:CUTANDRUN:DEEPTOOLS_PLOTHEATMAP_PEAKS terminated with an error exit status (137)

#254 monovich opened 3 weeks ago
1
ERROR ~ ERROR: Please check input samplesheet -> Read 1 FastQ file does not exist!

#253 avanthikav opened 1 month ago
1
ERROR ~ Error executing process > 'NFCORE_CUTANDRUN:CUTANDRUN:CUSTOM_DUMPSOFTWAREVERSIONS (1)'

#252 cutleraging opened 1 month ago
4
Error executing process > 'NFCORE_CUTANDRUN:CUTANDRUN:DEEPTOOLS_QC:DEEPTOOLS_MULTIBAMSUMMARY (all_target_bams)': AttributeError: module 'matplotlib.cm' has no attribute 'register_cmap'

#251 haipinghao opened 1 month ago
2
The AWS Access Key Id you provided does not exist in our records

#250 cutleraging opened 1 month ago
1
Fixed issue #248

#249 Alessandro201 opened 1 month ago
1
PLOT_CONSENSUS_PEAKS worflow does not produce the upset plot

#248 Alessandro201 opened 1 month ago
2
Provide relative paths to resources in IGV session file

#247 siddharthab opened 1 month ago
2
Question: How are multiple replicates of control condition used?

#246 ChristophH closed 1 month ago
2
test error with conda

#245 lecook closed 3 months ago
1
How to set sample sheet without IgG control?

#244 yxralba088 opened 3 months ago
2
test error with singularity: Error executing process > 'NFCORE_CUTANDRUN:CUTANDRUN:CUSTOM_DUMPSOFTWAREVERSIONS (1)'

#243 mglgc closed 2 months ago
8
Important! Template update for nf-core/tools v2.14.1

#242 nf-core-bot opened 4 months ago
0
Important! Template update for nf-core/tools v2.14.0

#241 nf-core-bot closed 4 months ago
1
picard mark duplicates error command exit status 140

#240 natpeckett opened 4 months ago
1
Generate a heatmap for consensus peaks

#239 ftabaro opened 4 months ago
0
Dev

#238 ahepperla opened 5 months ago
3
Update nextflow.config to load custom pipeline configs

#237 ahepperla closed 5 months ago
2
Error with kernel swap limit/ cgroup while executing NFCORE_CUTANDRUN:CUTANDRUN:SAMTOOLS_CUSTOMVIEW

#236 Prathyusha-konda opened 5 months ago
2
Run cannot start due to "Unknown option"

#235 mpiersonsmela closed 4 months ago
3
Error on the test run

#234 elissonnog closed 4 months ago
3
Important! Template update for nf-core/tools v2.13.1

#233 nf-core-bot closed 4 months ago
1
Fix for hidden output docs

#232 jpcartailler opened 6 months ago
6
Important! Template update for nf-core/tools v2.13

#231 nf-core-bot closed 6 months ago
0
3.2.2 Release Candidiate

#230 chris-cheshire closed 7 months ago
1
Important! Template update for nf-core/tools v2.12

#229 nf-core-bot closed 6 months ago
1
Update MACS to v3

#228 alexpmagalhaes opened 7 months ago
1
Align spike-in with less stringent params based on the left over from primary alignment

#227 chris-cheshire opened 7 months ago
0
don't want to skip FRiP score calculation

#226 jdanaK closed 7 months ago
1
Missing GTF path in genome config for UCSC yeast assembly `sacCer3`

#225 mniederhuber closed 8 months ago
1
Error executing process CUTANDRUN:CUSTOM_DUMPSOFTWAREVERSIONS

#224 ycedenocedeno closed 4 months ago
1
ERROR ~ ERROR: Please check input samplesheet

#223 martinezvbs closed 8 months ago
2
Important! Template update for nf-core/tools v2.11.1

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

#221 nf-core-bot closed 8 months ago
1
Errors with deeptools computeMatrix

#220 xxiann closed 5 months ago
1
Improve error handling after error in PREPARE_GENOME:BLACKLIST_BEDTOOLS_INTERSECT

#219 H-Bell opened 9 months ago
0
Restricting or sorting deeptools plotprofile and heatmap by genes/gene expression

#218 KinseyFisher closed 8 months ago
1
Updates

#217 chris-cheshire closed 7 months ago
1
close issue

#216 dhusmann closed 10 months ago
0
Updates

#215 chris-cheshire closed 10 months ago
2
3.2.1 Release Candidiate

#214 chris-cheshire closed 10 months ago
1
error with import imp

#213 fanying2015 closed 10 months ago
1
Important! Template update for nf-core/tools v2.10

#212 nf-core-bot closed 10 months ago
0
Version 3.2 does not run, fails in frag histogram step

#211 skilpinen opened 11 months ago
10
Update version

#210 chris-cheshire closed 10 months ago
1
Updates

#209 chris-cheshire closed 1 year ago
2
Update genome blacklists to actual CUT&RUN data

#208 chris-cheshire closed 1 year ago
0