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Simplified PVC debug script

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Olamide Isreal
2026-03-27 10:06:02 +01:00
parent de44607dc4
commit 83a79287b2
1 changed files with 9 additions and 32 deletions
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41
debug_pvc.nf
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@@ -1,45 +1,22 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl=2 nextflow.enable.dsl=2
process DEBUG {
params.outdir = '/omic/eureka/digital-patients' container 'harbor.cluster.omic.ai/omic/digital-patients/synthea:cudf'
process DEBUG_PVC {
container 'harbor.cluster.omic.ai/omic/digital-patients/corto:latest'
script: script:
""" """
echo "=== PVC mount check ===" echo "PWD: \$(pwd)"
echo "Current dir: \$(pwd)" echo "=== /omic/eureka/ ==="
echo "" ls /omic/eureka/ 2>&1 | head -20
echo "=== /omic/eureka contents ==="
ls -la /omic/eureka/ 2>&1 | head -20
echo ""
echo "=== /omic/eureka/digital-patients/ ===" echo "=== /omic/eureka/digital-patients/ ==="
ls -la /omic/eureka/digital-patients/ 2>&1 | head -30 ls -la /omic/eureka/digital-patients/ 2>&1 | head -30
echo ""
echo "=== /omic/eureka/digital-patients/imputed/ ===" echo "=== /omic/eureka/digital-patients/imputed/ ==="
ls -la /omic/eureka/digital-patients/imputed/ 2>&1 | head -20 ls -la /omic/eureka/digital-patients/imputed/ 2>&1 | head -20
echo ""
echo "=== /omic/eureka/digital-patients/healthy/ ===" echo "=== /omic/eureka/digital-patients/healthy/ ==="
ls -la /omic/eureka/digital-patients/healthy/ 2>&1 | head -20 ls -la /omic/eureka/digital-patients/healthy/ 2>&1 | head -20
echo ""
echo "=== /omic/eureka/digital-patients/supporting-data/ ===" echo "=== /omic/eureka/digital-patients/supporting-data/ ==="
ls -laR /omic/eureka/digital-patients/supporting-data/ 2>&1 | head -30 ls -laR /omic/eureka/digital-patients/supporting-data/ 2>&1 | head -30
echo "" echo "=== Test write ==="
echo "=== Check for assembled files ===" echo "test" > /omic/eureka/digital-patients/write_test.txt && echo "WRITE OK" || echo "WRITE FAILED"
ls -lh /omic/eureka/digital-patients/imputed/F5_SCHIZO* 2>&1 echo "DONE"
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() }
workflow {
DEBUG_PVC()
}