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Fix stage_data.nf: use ubuntu container with apt-get, create dirs on PVC

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Olamide Isreal
2026-04-01 09:30:00 +01:00
parent d1c471fa2a
commit 4b9152cf3c
1 changed files with 44 additions and 47 deletions
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91
stage_data.nf
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@@ -1,74 +1,69 @@
nextflow.enable.dsl=2
process STAGE_DATA {
container 'harbor.cluster.omic.ai/omic/digital-patients/synthea:cudf'
memory '2 GB'
container 'ubuntu:22.04'
memory '4 GB'
cpus 2
script:
"""
BASE="/omic/eureka/digital-patients"
echo "=== Installing dependencies ==="
apt-get update -qq && apt-get install -y -qq openssh-client sshpass curl > /dev/null 2>&1
echo "=== Cleaning up old _parts directories ==="
find \$BASE -name "*_parts" -type d -exec rm -rf {} + 2>/dev/null || true
echo "Cleanup done"
echo "=== Creating directory structure ==="
mkdir -p \$BASE/imputed \$BASE/healthy \$BASE/supporting-data/vcf \$BASE/supporting-data/ucsc-liftover \$BASE/supporting-data/genome \$BASE/output
echo "=== Current state of PVC ==="
ls -la \$BASE/ 2>/dev/null || echo "Base dir missing"
ls -la \$BASE/imputed/ 2>/dev/null || echo "imputed dir empty/missing"
ls -la \$BASE/healthy/ 2>/dev/null || echo "healthy dir empty/missing"
ls -la \$BASE/supporting-data/genome/ 2>/dev/null || echo "genome dir empty/missing"
ls -la \$BASE/ 2>/dev/null
echo "=== Downloading files from alien server ==="
apt-get update -qq && apt-get install -y -qq sshpass > /dev/null 2>&1 || true
# Function to download via sshpass+scp
download() {
local remote="\$1"
local local_path="\$2"
mkdir -p \$(dirname "\$local_path")
if [ -f "\$local_path" ]; then
echo "SKIP (exists): \$local_path"
ls -lh "\$local_path"
return
fi
echo "Downloading: \$remote -> \$local_path"
sshpass -p 'bl3rg3r5' scp -o StrictHostKeyChecking=no -P 9100 "omic@nucleus.omic.ai:\$remote" "\$local_path"
sshpass -p 'bl3rg3r5' scp -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null -P 9100 "omic@nucleus.omic.ai:\$remote" "\$local_path"
ls -lh "\$local_path"
}
# Imputed files (schizophrenia)
if [ ! -f "\$BASE/imputed/F5_SCHIZO.gwas.imputed_v3.both_sexes.tsv.bgz" ]; then
download "/mnt/Avatar/imputed/ukbb/imputed/F5_SCHIZO.gwas.imputed_v3.both_sexes.tsv.bgz" "\$BASE/imputed/F5_SCHIZO.gwas.imputed_v3.both_sexes.tsv.bgz"
else
echo "SKIP: F5_SCHIZO both_sexes already present"
fi
echo "=== Downloading imputed files ==="
download "/mnt/Avatar/imputed/ukbb/imputed/F5_SCHIZO.gwas.imputed_v3.both_sexes.tsv.bgz" "\$BASE/imputed/F5_SCHIZO.gwas.imputed_v3.both_sexes.tsv.bgz"
download "/mnt/Avatar/imputed/ukbb/imputed/F5_SCHIZO.gwas.imputed_v3.female.tsv.bgz" "\$BASE/imputed/F5_SCHIZO.gwas.imputed_v3.female.tsv.bgz"
download "/mnt/Avatar/imputed/ukbb/imputed/F5_SCHIZO.gwas.imputed_v3.male.tsv.bgz" "\$BASE/imputed/F5_SCHIZO.gwas.imputed_v3.male.tsv.bgz"
if [ ! -f "\$BASE/imputed/F5_SCHIZO.gwas.imputed_v3.female.tsv.bgz" ]; then
download "/mnt/Avatar/imputed/ukbb/imputed/F5_SCHIZO.gwas.imputed_v3.female.tsv.bgz" "\$BASE/imputed/F5_SCHIZO.gwas.imputed_v3.female.tsv.bgz"
else
echo "SKIP: F5_SCHIZO female already present"
fi
echo "=== Downloading gnomad files ==="
download "/mnt/Avatar/digital_patient/gnomad.genomes.v4.1.sites.female.txt" "\$BASE/healthy/gnomad.genomes.v4.1.sites.female.txt"
download "/mnt/Avatar/digital_patient/gnomad.genomes.v4.1.sites.male.txt" "\$BASE/healthy/gnomad.genomes.v4.1.sites.male.txt"
if [ ! -f "\$BASE/imputed/F5_SCHIZO.gwas.imputed_v3.male.tsv.bgz" ]; then
download "/mnt/Avatar/imputed/ukbb/imputed/F5_SCHIZO.gwas.imputed_v3.male.tsv.bgz" "\$BASE/imputed/F5_SCHIZO.gwas.imputed_v3.male.tsv.bgz"
else
echo "SKIP: F5_SCHIZO male already present"
fi
echo "=== Downloading supporting-data files ==="
download "/mnt/Avatar/dd/synthea/supporting-data/genome/hg38.fa" "\$BASE/supporting-data/genome/hg38.fa"
download "/mnt/Avatar/dd/synthea/supporting-data/genome/hg38.dict" "\$BASE/supporting-data/genome/hg38.dict"
download "/mnt/Avatar/dd/synthea/supporting-data/ucsc-liftover/hg19ToHg38.over.chain.gz" "\$BASE/supporting-data/ucsc-liftover/hg19ToHg38.over.chain.gz"
download "/mnt/Avatar/dd/synthea/supporting-data/vcf/vcf_template.vcf" "\$BASE/supporting-data/vcf/vcf_template.vcf"
# Gnomad files
if [ ! -f "\$BASE/healthy/gnomad.genomes.v4.1.sites.female.txt" ]; then
download "/mnt/Avatar/digital_patient/gnomad.genomes.v4.1.sites.female.txt" "\$BASE/healthy/gnomad.genomes.v4.1.sites.female.txt"
else
echo "SKIP: gnomad female already present"
fi
echo "=== Downloading phenotype file ==="
download "/mnt/Avatar/imputed/ukbb/metadata/ukbb_phenotypes.csv" "\$BASE/ukbb_phenotypes_filtered.csv"
if [ ! -f "\$BASE/healthy/gnomad.genomes.v4.1.sites.male.txt" ]; then
download "/mnt/Avatar/digital_patient/gnomad.genomes.v4.1.sites.male.txt" "\$BASE/healthy/gnomad.genomes.v4.1.sites.male.txt"
else
echo "SKIP: gnomad male already present"
fi
# hg38.fa (3.3GB)
if [ ! -f "\$BASE/supporting-data/genome/hg38.fa" ]; then
download "/mnt/Avatar/dd/synthea/supporting-data/genome/hg38.fa" "\$BASE/supporting-data/genome/hg38.fa"
else
echo "SKIP: hg38.fa already present"
fi
echo "=== Copying small files from DRS (already on PVC via DRS upload) ==="
# These were uploaded via DRS and should already be on PVC
# If not, they're in the git repo that WES cloned
for f in MANE.GRCh38.v1.3.update.tsv regulon.rda LM22_sourceGEP_ensg.txt; do
if [ ! -f "\$BASE/\$f" ]; then
echo "Small file missing on PVC, checking if available from WES workdir..."
# WES clones the repo, so the file might be in the current workdir's repo
else
echo "SKIP (exists): \$BASE/\$f"
fi
done
echo "=== Final verification ==="
echo "Imputed:"
@@ -76,7 +71,9 @@ process STAGE_DATA {
echo "Healthy:"
ls -lh \$BASE/healthy/*.txt 2>/dev/null || echo " NONE"
echo "Genome:"
ls -lh \$BASE/supporting-data/genome/hg38.* 2>/dev/null || echo " NONE"
ls -lh \$BASE/supporting-data/genome/* 2>/dev/null || echo " NONE"
echo "Supporting-data:"
ls -lh \$BASE/supporting-data/vcf/* \$BASE/supporting-data/ucsc-liftover/* 2>/dev/null || echo " NONE"
echo "Small files:"
ls -lh \$BASE/MANE* \$BASE/regulon* \$BASE/LM22* \$BASE/ukbb* 2>/dev/null || echo " NONE"