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Fix stage_data.nf: use synthea:cudf container, Python-based downloads with sshpass/expect fallback

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Olamide Isreal
2026-04-01 10:03:56 +01:00
parent 4b9152cf3c
commit c3c073e964
1 changed files with 92 additions and 71 deletions
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163
stage_data.nf
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@@ -1,83 +1,104 @@
nextflow.enable.dsl=2 nextflow.enable.dsl=2
process STAGE_DATA { process STAGE_DATA {
container 'ubuntu:22.04' container 'harbor.cluster.omic.ai/omic/digital-patients/synthea:cudf'
memory '4 GB' memory '4 GB'
cpus 2 cpus 2
script: script:
""" """
BASE="/omic/eureka/digital-patients" #!/opt/conda/envs/synthea/bin/python3
import subprocess, os, sys
BASE = "/omic/eureka/digital-patients"
def run(cmd):
print(f"RUN: {cmd}", flush=True)
r = subprocess.run(cmd, shell=True, capture_output=True, text=True)
if r.stdout: print(r.stdout, flush=True)
if r.stderr: print(r.stderr, flush=True)
return r.returncode
print("=== Cleaning up old _parts directories ===", flush=True)
run(f"find {BASE} -name '*_parts' -type d -exec rm -rf {{}} + 2>/dev/null || true")
print("=== Creating directory structure ===", flush=True)
for d in ["imputed", "healthy", "supporting-data/vcf", "supporting-data/ucsc-liftover", "supporting-data/genome", "output"]:
os.makedirs(f"{BASE}/{d}", exist_ok=True)
print("=== Current PVC state ===", flush=True)
run(f"ls -la {BASE}/")
print("=== Installing sshpass ===", flush=True)
# Try conda first, then apt
rc = run("conda install -y -c conda-forge sshpass 2>/dev/null || apt-get update -qq && apt-get install -y -qq sshpass 2>/dev/null || pip install sshpass 2>/dev/null")
# Check if sshpass is available
rc = run("which sshpass || echo 'sshpass not found, trying expect'")
echo "=== Installing dependencies ===" # If sshpass not available, use expect or python paramiko
apt-get update -qq && apt-get install -y -qq openssh-client sshpass curl > /dev/null 2>&1 has_sshpass = subprocess.run("which sshpass", shell=True, capture_output=True).returncode == 0
echo "=== Cleaning up old _parts directories ===" def download(remote, local_path):
find \$BASE -name "*_parts" -type d -exec rm -rf {} + 2>/dev/null || true if os.path.isfile(local_path):
echo "Cleanup done" size = os.path.getsize(local_path)
print(f"SKIP (exists, {size} bytes): {local_path}", flush=True)
echo "=== Creating directory structure ===" return True
mkdir -p \$BASE/imputed \$BASE/healthy \$BASE/supporting-data/vcf \$BASE/supporting-data/ucsc-liftover \$BASE/supporting-data/genome \$BASE/output print(f"Downloading: {remote} -> {local_path}", flush=True)
if has_sshpass:
echo "=== Current state of PVC ===" cmd = f"sshpass -p 'bl3rg3r5' scp -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null -P 9100 'omic@nucleus.omic.ai:{remote}' '{local_path}'"
ls -la \$BASE/ 2>/dev/null else:
# Fallback: use expect
download() { cmd = f'''expect -c "
local remote="\$1" set timeout 3600
local local_path="\$2" spawn scp -o StrictHostKeyChecking=no -P 9100 omic@nucleus.omic.ai:{remote} {local_path}
if [ -f "\$local_path" ]; then expect \\"password:\\"
echo "SKIP (exists): \$local_path" send \\"bl3rg3r5\\r\\"
ls -lh "\$local_path" expect eof
return "'''
fi rc = run(cmd)
echo "Downloading: \$remote -> \$local_path" if rc == 0 and os.path.isfile(local_path):
sshpass -p 'bl3rg3r5' scp -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null -P 9100 "omic@nucleus.omic.ai:\$remote" "\$local_path" size = os.path.getsize(local_path)
ls -lh "\$local_path" print(f" OK: {size} bytes", flush=True)
} return True
else:
echo "=== Downloading imputed files ===" print(f" FAILED (rc={rc})", flush=True)
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" return False
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" files = [
("/mnt/Avatar/imputed/ukbb/imputed/F5_SCHIZO.gwas.imputed_v3.both_sexes.tsv.bgz", f"{BASE}/imputed/F5_SCHIZO.gwas.imputed_v3.both_sexes.tsv.bgz"),
echo "=== Downloading gnomad files ===" ("/mnt/Avatar/imputed/ukbb/imputed/F5_SCHIZO.gwas.imputed_v3.female.tsv.bgz", f"{BASE}/imputed/F5_SCHIZO.gwas.imputed_v3.female.tsv.bgz"),
download "/mnt/Avatar/digital_patient/gnomad.genomes.v4.1.sites.female.txt" "\$BASE/healthy/gnomad.genomes.v4.1.sites.female.txt" ("/mnt/Avatar/imputed/ukbb/imputed/F5_SCHIZO.gwas.imputed_v3.male.tsv.bgz", f"{BASE}/imputed/F5_SCHIZO.gwas.imputed_v3.male.tsv.bgz"),
download "/mnt/Avatar/digital_patient/gnomad.genomes.v4.1.sites.male.txt" "\$BASE/healthy/gnomad.genomes.v4.1.sites.male.txt" ("/mnt/Avatar/digital_patient/gnomad.genomes.v4.1.sites.female.txt", f"{BASE}/healthy/gnomad.genomes.v4.1.sites.female.txt"),
("/mnt/Avatar/digital_patient/gnomad.genomes.v4.1.sites.male.txt", f"{BASE}/healthy/gnomad.genomes.v4.1.sites.male.txt"),
echo "=== Downloading supporting-data files ===" ("/mnt/Avatar/dd/synthea/supporting-data/genome/hg38.fa", f"{BASE}/supporting-data/genome/hg38.fa"),
download "/mnt/Avatar/dd/synthea/supporting-data/genome/hg38.fa" "\$BASE/supporting-data/genome/hg38.fa" ("/mnt/Avatar/dd/synthea/supporting-data/genome/hg38.dict", f"{BASE}/supporting-data/genome/hg38.dict"),
download "/mnt/Avatar/dd/synthea/supporting-data/genome/hg38.dict" "\$BASE/supporting-data/genome/hg38.dict" ("/mnt/Avatar/dd/synthea/supporting-data/ucsc-liftover/hg19ToHg38.over.chain.gz", f"{BASE}/supporting-data/ucsc-liftover/hg19ToHg38.over.chain.gz"),
download "/mnt/Avatar/dd/synthea/supporting-data/ucsc-liftover/hg19ToHg38.over.chain.gz" "\$BASE/supporting-data/ucsc-liftover/hg19ToHg38.over.chain.gz" ("/mnt/Avatar/dd/synthea/supporting-data/vcf/vcf_template.vcf", f"{BASE}/supporting-data/vcf/vcf_template.vcf"),
download "/mnt/Avatar/dd/synthea/supporting-data/vcf/vcf_template.vcf" "\$BASE/supporting-data/vcf/vcf_template.vcf" ("/mnt/Avatar/imputed/ukbb/metadata/ukbb_phenotypes.csv", f"{BASE}/ukbb_phenotypes_filtered.csv"),
]
echo "=== Downloading phenotype file ==="
download "/mnt/Avatar/imputed/ukbb/metadata/ukbb_phenotypes.csv" "\$BASE/ukbb_phenotypes_filtered.csv" print("=== Downloading files ===", flush=True)
ok = 0
echo "=== Copying small files from DRS (already on PVC via DRS upload) ===" fail = 0
# These were uploaded via DRS and should already be on PVC for remote, local in files:
# If not, they're in the git repo that WES cloned if download(remote, local):
for f in MANE.GRCh38.v1.3.update.tsv regulon.rda LM22_sourceGEP_ensg.txt; do ok += 1
if [ ! -f "\$BASE/\$f" ]; then else:
echo "Small file missing on PVC, checking if available from WES workdir..." fail += 1
# WES clones the repo, so the file might be in the current workdir's repo
else print(f"\\n=== Download results: {ok} ok, {fail} failed ===", flush=True)
echo "SKIP (exists): \$BASE/\$f"
fi print("\\n=== Final verification ===", flush=True)
done run(f"echo 'Imputed:' && ls -lh {BASE}/imputed/*.bgz 2>/dev/null || echo ' NONE'")
run(f"echo 'Healthy:' && ls -lh {BASE}/healthy/*.txt 2>/dev/null || echo ' NONE'")
echo "=== Final verification ===" run(f"echo 'Genome:' && ls -lh {BASE}/supporting-data/genome/* 2>/dev/null || echo ' NONE'")
echo "Imputed:" run(f"echo 'Support:' && ls -lh {BASE}/supporting-data/vcf/* {BASE}/supporting-data/ucsc-liftover/* 2>/dev/null || echo ' NONE'")
ls -lh \$BASE/imputed/*.bgz 2>/dev/null || echo " NONE" run(f"echo 'Small:' && ls -lh {BASE}/MANE* {BASE}/regulon* {BASE}/LM22* {BASE}/ukbb* 2>/dev/null || echo ' NONE'")
echo "Healthy:"
ls -lh \$BASE/healthy/*.txt 2>/dev/null || echo " NONE" if fail > 0:
echo "Genome:" print("STAGING FAILED - some files missing", flush=True)
ls -lh \$BASE/supporting-data/genome/* 2>/dev/null || echo " NONE" sys.exit(1)
echo "Supporting-data:" print("=== STAGING COMPLETE ===", flush=True)
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"
echo "=== STAGING COMPLETE ==="
""" """
} }