refactor: move convert sicer code to template file

modules/CCBR/custom/convertsicer/main.nf

@@ -20,43 +20,6 @@ process CONVERT_SICER {
         task.ext.when == null || task.ext.when
 
     script:
-    $/
-    #!/usr/bin/env python
-    import math
-    import platform
-    with open("${sicer_peaks}",'r') as f:
-        intxt = f.readlines()
-    # input columns if input-normalized: chrom, start, end, ChIP tag count, control tag count, p-value, fold-enrichment, q-value
-    # input columns if no input: chrom, start, end, score
-    outBroadPeak = [None] * len(intxt)
-    outBed = [None] * len(intxt)
-    for i in range(len(intxt)):
-        tmp = intxt[i].strip().split('\t')
-        if len(tmp) == 8:
-            # assuming that a p-value/q-value of 0 is super significant, -log10(1e-500)
-            if tmp[5] == "0.0":
-                pval="500"
-            else:
-                pval = str(-(math.log10(float(tmp[5]))))
-            if tmp[7] == "0.0":
-                qval="500"
-                qvalScore="5000"
-            else:
-                qval = str(-(math.log10(float(tmp[7]))))
-                qvalScore = str(int(-10*math.log10(float(tmp[7]))))
-            outBroadPeak[i] = "\t".join(tmp[0:3] + ["Peak"+str(i+1),tmp[3],".", tmp[6], pval, qval])
-            outBed[i] = "\t".join(tmp[0:3] + ["Peak"+str(i+1),qvalScore])
-        else:
-            score = str(int(float(tmp[3])))
-            outBed[i] = "\t".join(tmp[0:3] + ["Peak"+str(i+1),score])
-    # output broadPeak columns: chrom, start, end, name, ChIP tag count, strand, fold-enrichment, -log10 p-value, -log10 q-value
-    with open("${sicer_peaks.baseName}.converted.bed",'w') as g:
-        g.write( "\n".join(outBed) )
-    if outBroadPeak[0] != None:
-        with open("${sicer_peaks.baseName}.converted.broadPeak", 'w') as h:
-            h.write( "\n".join(outBroadPeak) )
-    with open("versions.yml", "w") as outfile:
-        outfile.write('"${task.process}":\\n')
-        outfile.write(f'  Python: "{platform.python_version()}"\\n')
-    /$
+    template 'convert-sicer.py'
+
 }

modules/CCBR/custom/convertsicer/templates/convert-sicer.py

@@ -0,0 +1,54 @@
+#!/usr/bin/env python
+import math
+import platform
+
+
+def main(infile, outbed, outpeak):
+    with open(infile, "r") as f:
+        intxt = f.readlines()
+    # input columns if input-normalized: chrom, start, end, ChIP tag count, control tag count, p-value, fold-enrichment, q-value
+    # input columns if no input: chrom, start, end, score
+    outBroadPeak = [None] * len(intxt)
+    outBed = [None] * len(intxt)
+    for i in range(len(intxt)):
+        tmp = intxt[i].strip().split("\t")
+        if len(tmp) == 8:
+            # assuming that a p-value/q-value of 0 is super significant, -log10(1e-500)
+            if tmp[5] == "0.0":
+                pval = "500"
+            else:
+                pval = str(-(math.log10(float(tmp[5]))))
+            if tmp[7] == "0.0":
+                qval = "500"
+                qvalScore = "5000"
+            else:
+                qval = str(-(math.log10(float(tmp[7]))))
+                qvalScore = str(int(-10 * math.log10(float(tmp[7]))))
+            outBroadPeak[i] = "\t".join(
+                tmp[0:3] + ["Peak" + str(i + 1), tmp[3], ".", tmp[6], pval, qval]
+            )
+            outBed[i] = "\t".join(tmp[0:3] + ["Peak" + str(i + 1), qvalScore])
+        else:
+            score = str(int(float(tmp[3])))
+            outBed[i] = "\t".join(tmp[0:3] + ["Peak" + str(i + 1), score])
+    # output broadPeak columns: chrom, start, end, name, ChIP tag count, strand, fold-enrichment, -log10 p-value, -log10 q-value
+    with open(outbed, "w") as g:
+        g.write("\n".join(outBed))
+    if outBroadPeak[0] != None:
+        with open(outpeak, "w") as h:
+            h.write("\n".join(outBroadPeak))
+
+
+def write_versions():
+    with open("versions.yml", "w") as outfile:
+        outfile.write('"${task.process}":\\n')
+        outfile.write(f'  Python: "{platform.python_version()}"\\n')
+
+
+if __name__ == "__main__":
+    write_versions()
+    main(
+        "${sicer_peaks}",
+        "${sicer_peaks.baseName}.converted.bed",
+        "${sicer_peaks.baseName}.converted.broadPeak",
+    )