Minimize the metadata of VCF at the beginning of the workflow

bin/minimize_vcf.py

@@ -0,0 +1,31 @@
+#!/usr/bin/env python3.8
+
+import pandas as pd
+import sys
+
+def main():
+    df = pd.read_csv(sys.stdin, sep="\t", comment="#", header=None)
+    df = df[df.columns[0:8]]
+    df.columns = ["#CHROM", "POS", "ID", "REF", "ALT", "QUAL", "FILTER", "INFO"]
+    df = df[df.FILTER == "PASS"]
+    df = df.copy()
+    df["INFO"] = "."
+    vcfbody = df.to_csv(sep="\t", index=False)
+
+    vcfcontigheader = "\n".join(f"##contig=<ID={chr},length={gdf.POS.max()}>" for (chr, gdf) in df.groupby("#CHROM"))
+
+    vcfheader = f"""
+##fileformat=VCFv4.2
+{vcfcontigheader}
+    """.strip()
+
+    vcfcontent = f"""
+{vcfheader}
+{vcfbody}
+    """.strip()
+
+    print(vcfcontent)
+
+
+if __name__ == "__main__":
+    main()

main.nf

@@ -78,11 +78,11 @@ validateInputParams()
 // Process to handle the VCF file
 process NORMALIZE_VCF {
     input:
-    path vcf
+    path vcf, stageAs: "input.vcf.unk"
 
     output:
-    path "input.vcf.gz", emit: vcf
-    path "input.vcf.gz.tbi", emit: tbi
+    path "input.mini.vcf.gz", emit: vcf
+    path "input.mini.vcf.gz.tbi", emit: tbi
 
     script:
     """
@@ -94,22 +94,25 @@ process NORMALIZE_VCF {
         INPUT_VCF_TYPE="\$(file -b \${SYM_LINK})"
     fi
 
- 
+
     if echo "\${INPUT_VCF_TYPE}" | grep -q 'BGZF'; then
         echo "The file is in BGZF format, ready for tabix."
-        cp $vcf input.vcf.gz
+        bgzip -d $vcf > input.vcf
     elif echo "\${INPUT_VCF_TYPE}" | grep -q 'gzip compressed data'; then
         echo "GZIP format detected, converting to BGZF."
-        gunzip -c $vcf | bgzip > input.vcf.gz
+        gunzip -c $vcf > input.vcf
     elif echo "\${INPUT_VCF_TYPE}" | grep -q 'ASCII text'; then
         echo "Plain VCF file detected, compressing and indexing."
-        bgzip -c $vcf > input.vcf.gz
+        cp $vcf input.vcf
     else
         echo "The file $vcf does not exist or is not a recognized format."
         exit 1
     fi
 
-    tabix -p vcf input.vcf.gz
+    minimize_vcf.py < input.vcf > input.mini.vcf
+    bgzip -c input.mini.vcf > input.mini.vcf.gz
+
+    tabix -p vcf input.mini.vcf.gz
     """
 }