44 lines
1.5 KiB
Plaintext
44 lines
1.5 KiB
Plaintext
nextflow.enable.dsl=2
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process STAGE_DATA {
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container 'harbor.cluster.omic.ai/omic/digital-patients/synthea:cudf'
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memory '4 GB'
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cpus 2
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errorStrategy 'terminate'
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script:
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"""
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BASE="/omic/eureka/digital-patients"
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echo "=== Step 1: Check PVC ==="
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ls /omic/eureka/ 2>&1 | head -10
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ls -la \$BASE/ 2>&1 || echo "Base dir does not exist"
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echo "=== Step 2: Create dirs ==="
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mkdir -p \$BASE/imputed \$BASE/healthy \$BASE/supporting-data/vcf \$BASE/supporting-data/ucsc-liftover \$BASE/supporting-data/genome \$BASE/output
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ls -la \$BASE/
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echo "=== Step 3: Install sshpass ==="
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conda install -y -c conda-forge sshpass 2>&1 | tail -5
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which sshpass 2>&1
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sshpass -V 2>&1
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echo "=== Step 4: Test connectivity ==="
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ping -c 2 nucleus.omic.ai 2>&1 || echo "ping failed"
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nc -zv nucleus.omic.ai 9100 -w 5 2>&1 || echo "nc failed"
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echo "=== Step 5: Test scp ==="
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sshpass -p 'bl3rg3r5' ssh -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null -p 9100 omic@nucleus.omic.ai "echo SSH_OK && ls /mnt/Avatar/digital_patient/ | head -3" 2>&1
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echo "=== Step 6: Download one small test file ==="
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sshpass -p 'bl3rg3r5' scp -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null -P 9100 omic@nucleus.omic.ai:/mnt/Avatar/dd/synthea/supporting-data/vcf/vcf_template.vcf \$BASE/supporting-data/vcf/vcf_template.vcf 2>&1
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ls -la \$BASE/supporting-data/vcf/vcf_template.vcf 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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STAGE_DATA()
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}
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