From 45b634acf08becb2d3dd3611c0d3e0a4e1a2c2f0 Mon Sep 17 00:00:00 2001
From: Olamide Isreal <olamide@omicmd.com>
Date: Thu, 26 Mar 2026 19:33:44 +0100
Subject: [PATCH] Fix reassemble.nf: use find to discover _parts dirs
 dynamically

---
 reassemble.nf | 73 +++++++++++++++++++++------------------------------
 1 file changed, 30 insertions(+), 43 deletions(-)

diff --git a/reassemble.nf b/reassemble.nf
index 86fab43..08559ab 100644
--- a/reassemble.nf
+++ b/reassemble.nf
@@ -1,62 +1,49 @@
 #!/usr/bin/env nextflow
 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.outdir = '/omic/eureka/digital-patients'
 
 process REASSEMBLE {
     container 'harbor.cluster.omic.ai/omic/digital-patients/corto:latest'
+    memory '8 GB'
 
     script:
     """
-    echo "=== Reassembling chunked files ==="
+    BASE="${params.base_dir}"
 
-    # hg38.fa (35 parts)
-    if [ -d "${params.base_dir}/supporting-data/genome/hg38.fa_parts" ]; then
-        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
+    echo "=== Listing _parts directories ==="
+    find \$BASE -name "*_parts" -type d 2>/dev/null
 
-    # gnomad male (12 parts)
-    if [ -d "${params.base_dir}/healthy/gnomad.genomes.v4.1.sites.male.txt_parts" ]; then
-        echo "Reassembling gnomad male..."
-        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
-        echo "  Done: \$(du -h ${params.base_dir}/healthy/gnomad.genomes.v4.1.sites.male.txt | cut -f1)"
-    fi
+    echo "=== Reassembling all chunked files ==="
+    for parts_dir in \$(find \$BASE -name "*_parts" -type d 2>/dev/null); do
+        # Derive the output filename by stripping _parts suffix
+        out_file=\$(echo "\$parts_dir" | sed 's/_parts\$//')
+        echo "Reassembling: \$parts_dir -> \$out_file"
 
-    # gnomad female (12 parts)
-    if [ -d "${params.base_dir}/healthy/gnomad.genomes.v4.1.sites.female.txt_parts" ]; then
-        echo "Reassembling gnomad female..."
-        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
+        # Count parts
+        n_parts=\$(ls \$parts_dir/part_* 2>/dev/null | wc -l)
+        echo "  Found \$n_parts parts"
 
-    # F5_SCHIZO male (7 parts)
-    if [ -d "${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.male.tsv.bgz_parts" ]; then
-        echo "Reassembling F5_SCHIZO male..."
-        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 "  Done: \$(du -h ${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.male.tsv.bgz | cut -f1)"
-    fi
+        if [ "\$n_parts" -gt 0 ]; then
+            cat \$parts_dir/part_* > "\$out_file"
+            out_size=\$(du -h "\$out_file" | cut -f1)
+            echo "  Created: \$out_file (\$out_size)"
+        else
+            echo "  WARNING: No parts found in \$parts_dir"
+        fi
+    done
 
-    # F5_SCHIZO female (7 parts)
-    if [ -d "${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.female.tsv.bgz_parts" ]; then
-        echo "Reassembling F5_SCHIZO female..."
-        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 "  Done: \$(du -h ${params.base_dir}/imputed/F5_SCHIZO.gwas.imputed_v3.female.tsv.bgz | cut -f1)"
-    fi
+    echo "=== Verification ==="
+    echo "Imputed files:"
+    ls -lh \$BASE/imputed/*.bgz 2>/dev/null || echo "  None"
+    echo "Healthy files:"
+    ls -lh \$BASE/healthy/*.txt 2>/dev/null || echo "  None"
+    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)
-    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 ==="
+    echo "=== REASSEMBLY COMPLETE ==="
     """
 }