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.
### Description of the bug Same arguments as with version 3.1 and that works, but the 3.2 fails with following error: frag_hist["group"] = group_short NameError: name 'group_short' is not defined...
### Description of the bug The "SAMTOOLS_CUSTOMVIEW" process fails on some files due to a segmentation fault, with a core dump, suggesting a memory issue. On my most recent run...
### Description of the bug Cannot download iGenomes because of Access ID Key invalid Downloading plugin [email protected] ERROR ~ The AWS Access Key Id you provided does not exist in...
## 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 the bug Hello, The workflow `NFCORE_CUTANDRUN:CUTANDRUN:PEAK_QC:PLOT_CONSENSUS_PEAKS` is run with 0 exit code, however, while the folder `${params.outdir}/04_reporting/consensus_upset_plots` is created, the upset plots are not produced. Here is...
### Description of the bug Currently, the IGV reporting directory tries to keep all the resource files within it to make the directory self-contained. It does so through the `includeInputs`...
hi, i meet the same error. Could you please tell me how to solve it? thanks, alba _Originally posted by @yxralba088 in https://github.com/nf-core/cutandrun/issues/134#issuecomment-2121577307_
I have updated the code, added flows, and beautified the code. Needs a review ## PR checklist - [ ] This comment contains a description of changes (with reason). -...
### Description of the bug Possible discrepancy with what the docs say in the [table](https://github.com/nf-core/cutandrun/blob/6e1125d4fee4ea7c8b70ed836bb0e92a89e3305f/docs/usage.md#read-normalisation) and the code, where the default value appears to be 50: https://github.com/nf-core/cutandrun/blob/6e1125d4fee4ea7c8b70ed836bb0e92a89e3305f/nextflow.config#L66 ### Command used...
