BUG NFCORE_RNAVAR:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY
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bug
- Dominant language
- Nextflow
- Stars
- 61
- Forks
- 47
- Avg merge
- 1d 1h
- Merged PRs (30d)
- 1
Description
Description of the bug
There is BUG in NFCORE_RNAVAR:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY, it gets stuck. With the use of iGenome configuration and also with local files. It cannot be skipped as it hard-coded rule.
However, its tied to profile singularity, it works with docker.
Command used and terminal output
nextflow run nf-core/rnavar -r 1.2.3 --input ./sample-sheet_BAM.csv --outdir ./OUT_fromBAM \
-c cpu_config_BAM.config \
-profile conda,singularity \
--genome GRCh38 \
--dbsnp dbsnp151_common.hg38.vcf.gz --dbsnp_tbi dbsnp151_common.hg38.vcf.gz.tbi \
--no_intervals true
Relevant files
System information
No response
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Reproduce the issue with the provided nf-core/rnavar command using the conda,singularity profile and inspect nextflow.log, focusing on NFCORE_RNAVAR:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY. Compare the behavior with the docker profile and determine why this process remains stuck; done means the pipeline completes this step under Singularity.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100