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Sydney-Informatics-Hub / Germline-StructuralV-nf

Germline structural variant calling pipeline for short read WGS datasets
GNU General Public License v3.0
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Fixed *.config & queue in PBS_gadi_runpipeline.sh #67

Closed chlu0571 closed 11 months ago

chlu0571 commented 11 months ago
  1. Replaced the exact .sif of singularity cache in nextflow.config and there were no more pulling Docker .img from online. Nextflow only applied the *.sif we provide in singularity cache.
  2. Replaced the copyq queue in PBS_gadi_runpipeline.sh
  3. chmod 777 pullContainers.sh if you unhashed the beforeScript in gadi.config

The whole pipeline worked well if I hashed the beforeScript in gadi.config and ran separately. The problem seems to be that while pulling containers was still going on or not finished, the nextflow already started the follwoing process.