atacseq
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nf-core
ATAC-seq peak-calling and QC analysis pipeline
### Description of feature It has been almost an year since the last release. There seem to be many changes on the dev branch that could be useful. For example,...
### Description of feature Hi all, I've been asked to run diffbind on our ATACseq data; Unless I'm wrong **diffbind** requires a samplesheet with each replicate and, for each replicate...
### Description of the bug some of the docker containers used in the pipeline are in old deprecated docker formats, and docker doesn't want to pull them: ### Command used...
Made changes to ATACSeqQC.R to handle hg38 and handle errors if it is a custom reference. ## PR checklist - [ ] This comment contains a description of changes (with...
### Description of feature The parameters used by `chromap` are the ones suggested for ATAC-seq in their documentation, see [here](https://github.com/haowenz/chromap#map-atac-seqscatac-seq-short-reads). This includes the `--Tn5-shift`; thus, the shift is applied by...
### Description of feature I have a bulk ATAC-seq dataset that used a spike-in Drosophila DNA control. Info about the kit used can be found [here](https://www.activemotif.com/documents/2278.pdf). It would be great...
### Description of the bug Hello, Can you help with this error. It repeats when I try to run this command: `nextflow run nf-core/atacseq -profile conda --input ./ATAC_samples.csv --outdir ./results...
### Description of the bug An error "No space left on device" occurred by process `NFCORE_ATACSEQ:ATACSEQ:MERGED_LIBRARY_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (E145I_REP1)`. Possible reason "--TMP_DIR" arguments are hardcoded in modules.config (example https://github.com/nf-core/atacseq/blob/1a1dbe52ffbd82256c941a032b0e22abbd925b8a/conf/modules.config#L358). Caused by: Process...
### Description of the bug Hi, I want to perform NF-core ATAC-seq but I have issues with the trimming for only one sample.. I don't understand what the issue is.....
