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innf-core/atacseq (press backspace or delete to remove)Description of feature
Hi,
I ve been helping my coworker run this pipeline, but we hit an error with SAMTOOLS_INDEX, which I see isn t that
uncommon. Using ext.args, we were able to resolve the error, ...
enhancement
emilytrybulec
- Opened yesterday
- #414
Description of the bug
As discussed in this issue, the calculation for actual number of cores used by Trimgalore is convoluted. The current
calculation is present in this code. But, the actual core usage ...
bug
PramodRaoB
- Opened 10 days ago
- #413
Can you explain how does ataqv compute the TSS Enrichmentscore ? It seems to be different than what ENCODE recommends
arugula2388
- 1
- Opened 25 days ago
- #411
Description of the bug
Dear Authors,
Thank you for developing and maintaining this pipeline.
There is a potential issue with the merged replicates, as it is not clear why Task 6.7 is defined as Count ...
bug
SuhasSrinivasan
- Opened on Feb 1
- #410
Description of the bug
Hello,
I am using the nf-core/atacseq pipeline and need to specify the --read_length parameter for my FASTQ files, which have a
read length of 76 bp. However, the pipeline currently ...
bug
MikeKazz
- Opened on Jan 24
- #408
Description of feature
Despite specifying 32 cores through Slurm and Nextflow config, FastQC uses only 10 threads/cores, that is 1 thread per
FASTQ file, even though there are more than 10 FASTQ files ...
enhancement
- Opened on Jan 15
- #404
Description of feature
It would be very helpful if the default mode is changed to narrow peak, as most ATAC-seq analysis is centered around
finding TFs and regulatory elements.
enhancement
- Opened on Jan 12
- #403
Description of the bug
The pipeline completed in default broad peak mode, and only required rerunning the MACS2 task in narrow peak mode. But
the process resumes from BWA alignment task which is unexpected ...
bug
- 1
- Opened on Jan 12
- #402
Description of the bug
When input fastq files in the sample sheet are not found, the pipeline does not display this error in the
console/terminal. The other initial steps like genome indexing still continue, ...
bug
- Opened on Jan 11
- #401
Description of the bug
When using the nextflow log command, there is no duration and status for a running pipeline.
Command used and terminal output
$ nextflow log
TIMESTAMP DURATION RUN NAME ...
bug
- Opened on Jan 11
- #400
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