46 lines
1.5 KiB
Plaintext
46 lines
1.5 KiB
Plaintext
#!/usr/bin/env nextflow
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nextflow.enable.dsl=2
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params.outdir = '/omic/eureka/digital-patients'
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process DEBUG_PVC {
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container 'harbor.cluster.omic.ai/omic/digital-patients/corto:latest'
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script:
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"""
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echo "=== PVC mount check ==="
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echo "Current dir: \$(pwd)"
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echo ""
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echo "=== /omic/eureka contents ==="
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ls -la /omic/eureka/ 2>&1 | head -20
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echo ""
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echo "=== /omic/eureka/digital-patients/ ==="
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ls -la /omic/eureka/digital-patients/ 2>&1 | head -30
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echo ""
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echo "=== /omic/eureka/digital-patients/imputed/ ==="
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ls -la /omic/eureka/digital-patients/imputed/ 2>&1 | head -20
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echo ""
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echo "=== /omic/eureka/digital-patients/healthy/ ==="
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ls -la /omic/eureka/digital-patients/healthy/ 2>&1 | head -20
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echo ""
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echo "=== /omic/eureka/digital-patients/supporting-data/ ==="
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ls -laR /omic/eureka/digital-patients/supporting-data/ 2>&1 | head -30
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echo ""
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echo "=== Check for assembled files ==="
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ls -lh /omic/eureka/digital-patients/imputed/F5_SCHIZO* 2>&1
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ls -lh /omic/eureka/digital-patients/healthy/gnomad* 2>&1
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ls -lh /omic/eureka/digital-patients/supporting-data/genome/hg38* 2>&1
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echo ""
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echo "=== Small files check ==="
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ls -lh /omic/eureka/digital-patients/MANE* 2>&1
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ls -lh /omic/eureka/digital-patients/regulon* 2>&1
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ls -lh /omic/eureka/digital-patients/LM22* 2>&1
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ls -lh /omic/eureka/digital-patients/ukbb* 2>&1
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echo "=== DEBUG COMPLETE ==="
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"""
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}
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workflow {
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DEBUG_PVC()
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}
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