Skip to content
This repository was archived by the owner on Jan 27, 2020. It is now read-only.
This repository was archived by the owner on Jan 27, 2020. It is now read-only.

RunHaplotypecaller fails on scratch #471

@szilvajuhos

Description

@szilvajuhos

When running on scratch, the bed files are missing. It works when NFX_WORK is on a local directory:

export NXF_TEMP=/scratch
export NXF_LAUNCHBASE=/scratch
export NXF_WORK=/scratch
export NXF_HOME=/castor/project/proj_nobackup/nextflow
nextflow run /castor/project/proj_nobackup/CAW/default/main.nf --step skipPreprocessing --tools HaplotypeCaller --sample Preprocessing/Recalibrated/recalibrated.tsv
...
  ##### ERROR
  ##### ERROR MESSAGE: Could not read file chr14_16133336-16140527.bed because The interval file does not exist.
  ##### ERROR ------------------------------------------------------------------------------------------

changing NXF_WORK to `pwd`/work fixes the issue.

Metadata

Metadata

Labels

Type

No type

Projects

No projects

Relationships

None yet

Development

No branches or pull requests

Issue actions