chore: migrate embedded script

docker/bedtools/2.31.1/Dockerfile

@@ -1,6 +1,7 @@
 FROM quay.io/biocontainers/bedtools:2.31.1--hf5e1c6e_2 AS bedtools
-FROM python:3.9.19
+FROM python:3.13.0
 
 COPY --from=bedtools /usr/local/bin/ /usr/local/bin/
+COPY --from=scripts --chmod=777 hic/filter_hic.py /usr/local/bin/filter_hic.py
 
 ENTRYPOINT [ "bash" ]

scripts/hic/filter_hic.py

@@ -0,0 +1,45 @@
+
+from collections import defaultdict
+import argparse
+
+def get_args():
+    parser = argparse.ArgumentParser(
+        description="Filter Hi-C data.")
+    parser.add_argument(
+        "--prefix", type=str, help="Prefix for output file.")
+    parser.add_argument(
+        "--all_valid_pairs", type=str, help="All valid pairs file.")
+    parser.add_argument(
+        "--filter_pairs", type=str, help="Filter pairs file.")
+
+    args = parser.parse_args()
+    return args
+
+if __name__ == "__main__":
+    args = get_args()
+
+    f=open(args.filter_pairs)
+    blackID=defaultdict(int)
+    while True:
+        line=f.readline()
+        if not line:
+            break
+        cols=line.strip().split("\t")
+        ID=cols[0]
+        blackID[ID]=1
+
+    f2=open(args.all_valid_pairs)
+    outfile1=args.prefix + ".allValidPairs.filtered"
+    outfile2=args.prefix + ".allValidPairs.removed"
+    of1=open(outfile1,'w')
+    of2=open(outfile2,'w')
+    while True:
+        line=f2.readline()
+        if not line:
+            break
+        cols=line.strip().split("\t")
+        id=cols[0]
+        if id in blackID:
+            of2.write(line)
+        else:
+            of1.write(line)

tools/hilow.wdl

@@ -311,34 +311,10 @@ task filter {
 
         cat <(cut -f 4 left.bed) <(cut -f 4 right.bed)|sort -u > filter.pair
 
-        python <<CODE
-            from collections import defaultdict
-            f=open("filter.pair")
-            blackID=defaultdict(int)
-            while True:
-                line=f.readline()
-                if not line:
-                    break
-                cols=line.strip().split("\t")
-                ID=cols[0]
-                blackID[ID]=1
-
-            f2=open("~{all_valid_pairs}")
-            outfile1="~{prefix}.allValidPairs.filtered"
-            outfile2="~{prefix}.allValidPairs.removed"
-            of1=open(outfile1,'w')
-            of2=open(outfile2,'w')
-            while True:
-                line=f2.readline()
-                if not line:
-                    break
-                cols=line.strip().split("\t")
-                id=cols[0]
-                if id in blackID:
-                    of2.write(line)
-                else:
-                    of1.write(line)
-        CODE
+        python /usr/local/bin/filter_hic.py \
+            --all_valid_pairs ~{all_valid_pairs} \
+            --filter_pair filter.pair \
+            --prefix ~{prefix}
 
         all=$(wc -l ~{all_valid_pairs} |cut -d " " -f 1)
         filtered=$(wc -l ~{prefix}.allValidPairs.removed | cut -d " " -f 1)