atacseq

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CONTROL description needs clarifications

1

### Description of feature The "CONTROL" option description in the "[samplesheet input](https://nf-co.re/atacseq/2.1.2/docs/usage#samplesheet-input)" section needs to be improved. 1. What exactly the control option does? From the description, it appears "CONTROL"...

mdozmorov

### Description of feature I had success when running atacseq (-r 2.1.2) for samples with small genome. When I tried to run other samples with big genome and one of...

BianyunY-ACRD

### Description of the bug When running the atac-seq pipeline on our SLURM cluster, it keeps failing at seemingly arbitrary points, with an error message saying that the process was...

hdbeukel

### Description of the bug @lindenb reported a bug with `/LAB-DATA/BiRD/shares/ITX/ITX_GLICID/commun/PF/NTS-333_NGS_Rimbert_ATAC-Seq/fastq/P1_S1_B1_S1` as a sample id, that created files in this position, because this id was used as prefix... I do...

maxulysse

Adding peak-calling with Genrich (fix #108) and multi-mapping read analysis

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**This PR:** -------- 1. Addresses issue #108: This version of the pipeline keeps the current pipeline structure the same but adds a separate "branch" for peak-calling with [Genrich](https://github.com/jsh58/Genrich) and its...

samuelruizperez

Hi @drpatelh not sure if notifications work for "closed" issue threads. sorry if they do. I was hoping I could re-open this issue as I am still experiencing it with...

hcliedtke

Error executing process > 'NFCORE_ATACSEQ:ATACSEQ:CUSTOM_DUMPSOFTWAREVERSIONS (1)'

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### Description of the bug Hi everyone! I was running the atacseq pipeline v 2.0 using Slurm as the executor. However, towards the end, it raised an error as following:...

anijudy

CSI bam index not working

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### Description of the bug With large genomes, the .bai index file format is insufficient so .csi file format is specified by "ext.args='-c'" in SAMTOOLS_INDEX. The pipeline first fails with...

heathfuqua

Add GRCm39 option to config

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### Description of feature Hi, I'd like to request that GRCm39 be added as an option for running the pipeline. Would this change require anything more involved than updating the...

laurenhsu1

Reduce available memory for Picard Mark Duplicates

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Right now, the pipeline fails for me with the following error: ``` Error executing process > 'NFCORE_ATACSEQ:ATACSEQ:MERGED_LIBRARY_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (DMSO_REP4)' Caused by: Process `NFCORE_ATACSEQ:ATACSEQ:MERGED_LIBRARY_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (DMSO_REP4)` terminated with an error exit status (1)...

ryan-moreno