83 lines
3.5 KiB
Plaintext
83 lines
3.5 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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script:
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"""
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set +e
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BASE="/omic/eureka/digital-patients"
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echo "=== Cleaning up old _parts directories ==="
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find \$BASE -name "*_parts" -type d -exec rm -rf {} + 2>/dev/null
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echo "Cleanup done"
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echo "=== Creating directory structure ==="
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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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echo "Dirs created"
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echo "=== Current PVC state ==="
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ls -la \$BASE/ 2>/dev/null || echo "Base dir issue"
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echo "=== Installing sshpass ==="
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conda install -y -c conda-forge sshpass 2>&1 | tail -3
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which sshpass && echo "sshpass OK" || echo "sshpass NOT FOUND"
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download() {
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remote="\$1"
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local_path="\$2"
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if [ -f "\$local_path" ]; then
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echo "SKIP (exists): \$local_path"
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return 0
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fi
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echo "Downloading: \$remote -> \$local_path"
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sshpass -p 'bl3rg3r5' scp -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null -P 9100 "omic@nucleus.omic.ai:\$remote" "\$local_path" 2>&1
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if [ -f "\$local_path" ]; then
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ls -lh "\$local_path"
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return 0
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else
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echo "FAILED: \$local_path"
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return 1
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fi
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}
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echo "=== Downloading imputed files ==="
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download "/mnt/Avatar/imputed/ukbb/imputed/F5_SCHIZO.gwas.imputed_v3.both_sexes.tsv.bgz" "\$BASE/imputed/F5_SCHIZO.gwas.imputed_v3.both_sexes.tsv.bgz"
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download "/mnt/Avatar/imputed/ukbb/imputed/F5_SCHIZO.gwas.imputed_v3.female.tsv.bgz" "\$BASE/imputed/F5_SCHIZO.gwas.imputed_v3.female.tsv.bgz"
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download "/mnt/Avatar/imputed/ukbb/imputed/F5_SCHIZO.gwas.imputed_v3.male.tsv.bgz" "\$BASE/imputed/F5_SCHIZO.gwas.imputed_v3.male.tsv.bgz"
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echo "=== Downloading gnomad files ==="
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download "/mnt/Avatar/digital_patient/gnomad.genomes.v4.1.sites.female.txt" "\$BASE/healthy/gnomad.genomes.v4.1.sites.female.txt"
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download "/mnt/Avatar/digital_patient/gnomad.genomes.v4.1.sites.male.txt" "\$BASE/healthy/gnomad.genomes.v4.1.sites.male.txt"
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echo "=== Downloading supporting-data files ==="
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download "/mnt/Avatar/dd/synthea/supporting-data/genome/hg38.fa" "\$BASE/supporting-data/genome/hg38.fa"
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download "/mnt/Avatar/dd/synthea/supporting-data/genome/hg38.dict" "\$BASE/supporting-data/genome/hg38.dict"
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download "/mnt/Avatar/dd/synthea/supporting-data/ucsc-liftover/hg19ToHg38.over.chain.gz" "\$BASE/supporting-data/ucsc-liftover/hg19ToHg38.over.chain.gz"
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download "/mnt/Avatar/dd/synthea/supporting-data/vcf/vcf_template.vcf" "\$BASE/supporting-data/vcf/vcf_template.vcf"
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echo "=== Downloading phenotype file ==="
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download "/mnt/Avatar/imputed/ukbb/metadata/ukbb_phenotypes.csv" "\$BASE/ukbb_phenotypes_filtered.csv"
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echo "=== Final verification ==="
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echo "Imputed:"
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ls -lh \$BASE/imputed/*.bgz 2>/dev/null || echo " NONE"
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echo "Healthy:"
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ls -lh \$BASE/healthy/*.txt 2>/dev/null || echo " NONE"
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echo "Genome:"
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ls -lh \$BASE/supporting-data/genome/* 2>/dev/null || echo " NONE"
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echo "Support:"
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ls -lh \$BASE/supporting-data/vcf/* \$BASE/supporting-data/ucsc-liftover/* 2>/dev/null || echo " NONE"
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echo "Small:"
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ls -lh \$BASE/MANE* \$BASE/regulon* \$BASE/LM22* \$BASE/ukbb* 2>/dev/null || echo " NONE"
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echo "=== STAGING 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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