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icbi-lab / nextNEOpi

nextNEOpi: a comprehensive pipeline for computational neoantigen prediction
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work folder #47

Closed amoschoomy closed 1 year ago

amoschoomy commented 1 year ago

Hi, I'm running into disk quota error in my hpc while running the pipeline. I checked in my HPC, turns out while the pipeline is running, nextNEOpi is writing data into the folder named work that is enormously large. How do I prevent this from using up my disk quota? I've already set up $TMPDIR (there's a default tmp directory created by our HPC everytime a batch script is submitted) as shown below but the work folder still gets written in my HPC.

export JAVA_CMD=/home/uqachoo1/mambaforge/envs/env/bin/java
export NXF_OPTS='-Xms1g -Xmx4g'

nextflow run nextNEOpi.nf \
    --batchFile /home/uqachoo1/nextNEOpi-1.4.0/wesmRNA_batchFile_fastq.csv \
    -config conf/params.config \
    --outputDir /QRISdata/Q6373/results/test_results \
    --trim_adapters true \
    --trim_adapters_RNAseq true \
    --use_NetChop false \
    --tmpDir $TMPDIR \
    -profile singularity,cluster \
    --accept_license \
    --MIXCR_lic /home/uqachoo1/nextNEOpi-1.4.0/mi.license  \

Much thanks!

riederd commented 1 year ago

Hi,

the option --tmpDir does not set the nextflow work directory. You may want to use the nextflow -work-dir command line option to specify a custom workdir. See also: https://www.nextflow.io/docs/latest/cli.html?highlight=work-dir#run