Olamide Isreal
88627edc25
- 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
67 lines
3.0 KiB
Plaintext
67 lines
3.0 KiB
Plaintext
#!/usr/bin/env nextflow
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nextflow.enable.dsl=2
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// One-time script to reassemble chunked files on the PVC
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// Run once, then delete. Not part of the main pipeline.
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params.base_dir = '/omic/eureka/digital-patients'
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params.outdir = '/omic/eureka/digital-patients'
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process REASSEMBLE {
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container 'alpine:latest'
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executor 'local'
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script:
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"""
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echo "=== Reassembling chunked files ==="
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# hg38.fa (35 parts)
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if [ -d "${params.base_dir}/supporting-data/genome/hg38.fa_parts" ]; then
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echo "Reassembling hg38.fa..."
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cat ${params.base_dir}/supporting-data/genome/hg38.fa_parts/part_* > ${params.base_dir}/supporting-data/genome/hg38.fa
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echo " Done: \$(du -h ${params.base_dir}/supporting-data/genome/hg38.fa | cut -f1)"
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fi
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# gnomad male (12 parts)
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if [ -d "${params.base_dir}/healthy/gnomad.genomes.v4.1.sites.male.txt_parts" ]; then
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echo "Reassembling gnomad male..."
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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
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echo " Done: \$(du -h ${params.base_dir}/healthy/gnomad.genomes.v4.1.sites.male.txt | cut -f1)"
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fi
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# gnomad female (12 parts)
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if [ -d "${params.base_dir}/healthy/gnomad.genomes.v4.1.sites.female.txt_parts" ]; then
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echo "Reassembling gnomad female..."
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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
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echo " Done: \$(du -h ${params.base_dir}/healthy/gnomad.genomes.v4.1.sites.female.txt | cut -f1)"
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fi
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# F5_SCHIZO male (7 parts)
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if [ -d "${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.male.tsv.bgz_parts" ]; then
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echo "Reassembling F5_SCHIZO male..."
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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
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echo " Done: \$(du -h ${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.male.tsv.bgz | cut -f1)"
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fi
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# F5_SCHIZO female (7 parts)
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if [ -d "${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.female.tsv.bgz_parts" ]; then
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echo "Reassembling F5_SCHIZO female..."
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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
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echo " Done: \$(du -h ${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.female.tsv.bgz | cut -f1)"
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fi
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# F5_SCHIZO both_sexes (7 parts)
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if [ -d "${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.both_sexes.tsv.bgz_parts" ]; then
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echo "Reassembling F5_SCHIZO both_sexes..."
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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
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echo " Done: \$(du -h ${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.both_sexes.tsv.bgz | cut -f1)"
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fi
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echo "=== All reassembly complete ==="
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"""
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}
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workflow {
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REASSEMBLE()
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}
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