diff --git a/debug_pvc.nf b/debug_pvc.nf index 979a751..a2adbdd 100644 --- a/debug_pvc.nf +++ b/debug_pvc.nf @@ -1,45 +1,22 @@ -#!/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' - +process DEBUG { + container 'harbor.cluster.omic.ai/omic/digital-patients/synthea:cudf' script: """ - echo "=== PVC mount check ===" - echo "Current dir: \$(pwd)" - echo "" - echo "=== /omic/eureka contents ===" - ls -la /omic/eureka/ 2>&1 | head -20 - echo "" + echo "PWD: \$(pwd)" + echo "=== /omic/eureka/ ===" + ls /omic/eureka/ 2>&1 | head -20 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 ===" + echo "=== Test write ===" + echo "test" > /omic/eureka/digital-patients/write_test.txt && echo "WRITE OK" || echo "WRITE FAILED" + echo "DONE" """ } - -workflow { - DEBUG_PVC() -} +workflow { DEBUG() }