cutandrun
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nf-core
Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.
Version `2.14.1` of [nf-core/tools](https://github.com/nf-core/tools) has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline. Please make sure to...
**Issue** * There is an open `` tag in the last working section (`### 4.3`), but no closing tag. * Then section 5 starts. Then, right after `###6.5` starts, there...
### Description of the bug I'm using the nextflow cut&run pipeline which I used last year for cut&run analysis. I'm now getting an error from the mark duplicates step citing...
### Description of feature Hello, I would like to propose a module to plot consensus peak set. I find myself generating DeepTools heatmaps of the consensus peak set from nf-core/cutandrun...
Error with kernel swap limit/ cgroup while executing NFCORE_CUTANDRUN:CUTANDRUN:SAMTOOLS_CUSTOMVIEW
### Description of the bug Hi, thank you for developing this pipeline. It has exactly all the steps I am interested in. I am receiving the following error related to...
Dev
## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested,...
### Description of feature I experienced a problem where the pipeline fails first with PRESEQ_LCEXTRAP and then with NFCORE_CUTANDRUN:CUTANDRUN:MACS2_CALLPEAK_NOIGG or PREPARE_PEAKCALLING:UCSC_BEDGRAPHTOBIGWIG depending on configuration. This was caused by empty bam...
### Description of feature With the release of MACS version 3 could you implement the new version? Thank you in advance!
### Description of feature See above
Hello, I had [a long stare](https://github.com/nf-core/cutandrun/issues/197) at the cut'n'run result files and now came up my own little downstream workflow to finally have some gene lists and FASTA files. This...
