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Add debug_pvc.nf to inspect PVC contents

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Olamide Isreal
2026-03-26 19:27:11 +01:00
parent bb11c598a0
commit 983a2c3246
1 changed files with 45 additions and 0 deletions
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debug_pvc.nf Normal file
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#!/usr/bin/env nextflow
nextflow.enable.dsl=2
params.outdir = '/omic/eureka/digital-patients'
process DEBUG_PVC {
container 'harbor.cluster.omic.ai/omic/digital-patients/corto:latest'
script:
"""
echo "=== PVC mount check ==="
echo "Current dir: \$(pwd)"
echo ""
echo "=== /omic/eureka contents ==="
ls -la /omic/eureka/ 2>&1 | head -20
echo ""
echo "=== /omic/eureka/digital-patients/ ==="
ls -la /omic/eureka/digital-patients/ 2>&1 | head -30
echo ""
echo "=== /omic/eureka/digital-patients/imputed/ ==="
ls -la /omic/eureka/digital-patients/imputed/ 2>&1 | head -20
echo ""
echo "=== /omic/eureka/digital-patients/healthy/ ==="
ls -la /omic/eureka/digital-patients/healthy/ 2>&1 | head -20
echo ""
echo "=== /omic/eureka/digital-patients/supporting-data/ ==="
ls -laR /omic/eureka/digital-patients/supporting-data/ 2>&1 | head -30
echo ""
echo "=== Check for assembled files ==="
ls -lh /omic/eureka/digital-patients/imputed/F5_SCHIZO* 2>&1
ls -lh /omic/eureka/digital-patients/healthy/gnomad* 2>&1
ls -lh /omic/eureka/digital-patients/supporting-data/genome/hg38* 2>&1
echo ""
echo "=== Small files check ==="
ls -lh /omic/eureka/digital-patients/MANE* 2>&1
ls -lh /omic/eureka/digital-patients/regulon* 2>&1
ls -lh /omic/eureka/digital-patients/LM22* 2>&1
ls -lh /omic/eureka/digital-patients/ukbb* 2>&1
echo "=== DEBUG COMPLETE ==="
"""
}
workflow {
DEBUG_PVC()
}