53 lines
1.6 KiB
Plaintext
53 lines
1.6 KiB
Plaintext
#!/usr/bin/env nextflow
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nextflow.enable.dsl=2
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params.base_dir = '/omic/eureka/digital-patients'
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process REASSEMBLE {
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container 'harbor.cluster.omic.ai/omic/digital-patients/corto:latest'
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memory '8 GB'
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script:
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"""
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BASE="${params.base_dir}"
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echo "=== Listing _parts directories ==="
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find \$BASE -name "*_parts" -type d 2>/dev/null
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echo "=== Reassembling all chunked files ==="
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for parts_dir in \$(find \$BASE -name "*_parts" -type d 2>/dev/null); do
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# Derive the output filename by stripping _parts suffix
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out_file=\$(echo "\$parts_dir" | sed 's/_parts\$//')
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echo "Reassembling: \$parts_dir -> \$out_file"
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# Count parts
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n_parts=\$(ls \$parts_dir/part_* 2>/dev/null | wc -l)
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echo " Found \$n_parts parts"
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if [ "\$n_parts" -gt 0 ]; then
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cat \$parts_dir/part_* > "\$out_file"
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out_size=\$(du -h "\$out_file" | cut -f1)
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echo " Created: \$out_file (\$out_size)"
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else
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echo " WARNING: No parts found in \$parts_dir"
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fi
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done
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echo "=== Verification ==="
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echo "Imputed files:"
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ls -lh \$BASE/imputed/*.bgz 2>/dev/null || echo " None"
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echo "Healthy files:"
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ls -lh \$BASE/healthy/*.txt 2>/dev/null || echo " None"
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echo "Genome files:"
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ls -lh \$BASE/supporting-data/genome/hg38.* 2>/dev/null || echo " None"
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echo "Small files:"
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ls -lh \$BASE/MANE* \$BASE/regulon* \$BASE/LM22* \$BASE/ukbb* 2>/dev/null || echo " None"
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echo "=== REASSEMBLY COMPLETE ==="
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"""
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}
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workflow {
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REASSEMBLE()
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}
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