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Configure pipeline for WES execution on k8s cluster

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- Add main.nf as WES entry point with PVC-based paths
- Update nextflow.config with k8s/k8s_gpu profiles (eureka-pvc)
- Update params.json defaults to /omic/eureka/digital-patients/ paths
- Remove stageInMode 'copy' from corto and vcf2prot for k8s compat
- Add reassemble.nf for one-time chunk reassembly on PVC
This commit is contained in:
Olamide Isreal
2026-03-26 17:58:28 +01:00
parent 9e6a16c19b
commit 88627edc25
6 changed files with 371 additions and 325 deletions
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reassemble.nf Normal file
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#!/usr/bin/env nextflow
nextflow.enable.dsl=2
// One-time script to reassemble chunked files on the PVC
// Run once, then delete. Not part of the main pipeline.
params.base_dir = '/omic/eureka/digital-patients'
params.outdir = '/omic/eureka/digital-patients'
process REASSEMBLE {
container 'alpine:latest'
executor 'local'
script:
"""
echo "=== Reassembling chunked files ==="
# hg38.fa (35 parts)
if [ -d "${params.base_dir}/supporting-data/genome/hg38.fa_parts" ]; then
echo "Reassembling hg38.fa..."
cat ${params.base_dir}/supporting-data/genome/hg38.fa_parts/part_* > ${params.base_dir}/supporting-data/genome/hg38.fa
echo " Done: \$(du -h ${params.base_dir}/supporting-data/genome/hg38.fa | cut -f1)"
fi
# gnomad male (12 parts)
if [ -d "${params.base_dir}/healthy/gnomad.genomes.v4.1.sites.male.txt_parts" ]; then
echo "Reassembling gnomad male..."
cat ${params.base_dir}/healthy/gnomad.genomes.v4.1.sites.male.txt_parts/part_* > ${params.base_dir}/healthy/gnomad.genomes.v4.1.sites.male.txt
echo " Done: \$(du -h ${params.base_dir}/healthy/gnomad.genomes.v4.1.sites.male.txt | cut -f1)"
fi
# gnomad female (12 parts)
if [ -d "${params.base_dir}/healthy/gnomad.genomes.v4.1.sites.female.txt_parts" ]; then
echo "Reassembling gnomad female..."
cat ${params.base_dir}/healthy/gnomad.genomes.v4.1.sites.female.txt_parts/part_* > ${params.base_dir}/healthy/gnomad.genomes.v4.1.sites.female.txt
echo " Done: \$(du -h ${params.base_dir}/healthy/gnomad.genomes.v4.1.sites.female.txt | cut -f1)"
fi
# F5_SCHIZO male (7 parts)
if [ -d "${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.male.tsv.bgz_parts" ]; then
echo "Reassembling F5_SCHIZO male..."
cat ${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.male.tsv.bgz_parts/part_* > ${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.male.tsv.bgz
echo " Done: \$(du -h ${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.male.tsv.bgz | cut -f1)"
fi
# F5_SCHIZO female (7 parts)
if [ -d "${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.female.tsv.bgz_parts" ]; then
echo "Reassembling F5_SCHIZO female..."
cat ${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.female.tsv.bgz_parts/part_* > ${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.female.tsv.bgz
echo " Done: \$(du -h ${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.female.tsv.bgz | cut -f1)"
fi
# F5_SCHIZO both_sexes (7 parts)
if [ -d "${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.both_sexes.tsv.bgz_parts" ]; then
echo "Reassembling F5_SCHIZO both_sexes..."
cat ${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.both_sexes.tsv.bgz_parts/part_* > ${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.both_sexes.tsv.bgz
echo " Done: \$(du -h ${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.both_sexes.tsv.bgz | cut -f1)"
fi
echo "=== All reassembly complete ==="
"""
}
workflow {
REASSEMBLE()
}