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Fix reassemble.nf: use find to discover _parts dirs dynamically

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Olamide Isreal
2026-03-26 19:33:44 +01:00
parent 983a2c3246
commit 45b634acf0
1 changed files with 30 additions and 43 deletions
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73
reassemble.nf
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@@ -1,62 +1,49 @@
#!/usr/bin/env nextflow #!/usr/bin/env nextflow
nextflow.enable.dsl=2 nextflow.enable.dsl=2
// One-time script to reassemble chunked files on the PVC
// Run once, then delete. Not part of the main pipeline.
params.base_dir = '/omic/eureka/digital-patients' params.base_dir = '/omic/eureka/digital-patients'
params.outdir = '/omic/eureka/digital-patients'
process REASSEMBLE { process REASSEMBLE {
container 'harbor.cluster.omic.ai/omic/digital-patients/corto:latest' container 'harbor.cluster.omic.ai/omic/digital-patients/corto:latest'
memory '8 GB'
script: script:
""" """
echo "=== Reassembling chunked files ===" BASE="${params.base_dir}"
# hg38.fa (35 parts) echo "=== Listing _parts directories ==="
if [ -d "${params.base_dir}/supporting-data/genome/hg38.fa_parts" ]; then find \$BASE -name "*_parts" -type d 2>/dev/null
echo "Reassembling hg38.fa..."
cat ${params.base_dir}/supporting-data/genome/hg38.fa_parts/part_* > ${params.base_dir}/supporting-data/genome/hg38.fa
echo " Done: \$(du -h ${params.base_dir}/supporting-data/genome/hg38.fa | cut -f1)"
fi
# gnomad male (12 parts) echo "=== Reassembling all chunked files ==="
if [ -d "${params.base_dir}/healthy/gnomad.genomes.v4.1.sites.male.txt_parts" ]; then for parts_dir in \$(find \$BASE -name "*_parts" -type d 2>/dev/null); do
echo "Reassembling gnomad male..." # Derive the output filename by stripping _parts suffix
cat ${params.base_dir}/healthy/gnomad.genomes.v4.1.sites.male.txt_parts/part_* > ${params.base_dir}/healthy/gnomad.genomes.v4.1.sites.male.txt out_file=\$(echo "\$parts_dir" | sed 's/_parts\$//')
echo " Done: \$(du -h ${params.base_dir}/healthy/gnomad.genomes.v4.1.sites.male.txt | cut -f1)" echo "Reassembling: \$parts_dir -> \$out_file"
fi
# gnomad female (12 parts) # Count parts
if [ -d "${params.base_dir}/healthy/gnomad.genomes.v4.1.sites.female.txt_parts" ]; then n_parts=\$(ls \$parts_dir/part_* 2>/dev/null | wc -l)
echo "Reassembling gnomad female..." echo " Found \$n_parts parts"
cat ${params.base_dir}/healthy/gnomad.genomes.v4.1.sites.female.txt_parts/part_* > ${params.base_dir}/healthy/gnomad.genomes.v4.1.sites.female.txt
echo " Done: \$(du -h ${params.base_dir}/healthy/gnomad.genomes.v4.1.sites.female.txt | cut -f1)"
fi
# F5_SCHIZO male (7 parts) if [ "\$n_parts" -gt 0 ]; then
if [ -d "${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.male.tsv.bgz_parts" ]; then cat \$parts_dir/part_* > "\$out_file"
echo "Reassembling F5_SCHIZO male..." out_size=\$(du -h "\$out_file" | cut -f1)
cat ${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.male.tsv.bgz_parts/part_* > ${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.male.tsv.bgz echo " Created: \$out_file (\$out_size)"
echo " Done: \$(du -h ${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.male.tsv.bgz | cut -f1)" else
fi echo " WARNING: No parts found in \$parts_dir"
fi
done
# F5_SCHIZO female (7 parts) echo "=== Verification ==="
if [ -d "${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.female.tsv.bgz_parts" ]; then echo "Imputed files:"
echo "Reassembling F5_SCHIZO female..." ls -lh \$BASE/imputed/*.bgz 2>/dev/null || echo " None"
cat ${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.female.tsv.bgz_parts/part_* > ${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.female.tsv.bgz echo "Healthy files:"
echo " Done: \$(du -h ${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.female.tsv.bgz | cut -f1)" ls -lh \$BASE/healthy/*.txt 2>/dev/null || echo " None"
fi echo "Genome files:"
ls -lh \$BASE/supporting-data/genome/hg38.* 2>/dev/null || echo " None"
echo "Small files:"
ls -lh \$BASE/MANE* \$BASE/regulon* \$BASE/LM22* \$BASE/ukbb* 2>/dev/null || echo " None"
# F5_SCHIZO both_sexes (7 parts) echo "=== REASSEMBLY COMPLETE ==="
if [ -d "${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.both_sexes.tsv.bgz_parts" ]; then
echo "Reassembling F5_SCHIZO both_sexes..."
cat ${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.both_sexes.tsv.bgz_parts/part_* > ${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.both_sexes.tsv.bgz
echo " Done: \$(du -h ${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.both_sexes.tsv.bgz | cut -f1)"
fi
echo "=== All reassembly complete ==="
""" """
} }