Merge pull request #233 from mskcc-omics-workflows/develop

Create neoantigen head branch

Author: nikhil

modules/msk/generatemutfasta/1.2/resources/usr/bin/generateMutFasta.py

@@ -118,22 +118,9 @@ def main():
                 n_missing_tx_id += 1
 
             if len(mut.mt_altered_aa) > 5:
-                id_string = (
-                    str(mut.maf_row["Transcript_ID"])
-                    + " Variant "
-                    + str(mut.maf_row["Chromosome"])
-                    + ":"
-                    + str(mut.maf_row["Start_Position"])
-                    + "-"
-                    + str(mut.maf_row["End_Position"])
-                    + " Ref:"
-                    + str(mut.maf_row["Reference_Allele"])
-                    + " Alt:"
-                    + str(mut.maf_row["Tumor_Seq_Allele2"])
-                )
-                out_fa.write(">" + id_string + "\n")
+                out_fa.write(">" + mut.identifier_key + "_M\n")
                 out_fa.write(mut.mt_altered_aa + "\n")
-                out_WT_fa.write(">" + id_string + "\n")
+                out_WT_fa.write(">" + mut.identifier_key + "_W\n")
                 out_WT_fa.write(mut.wt_altered_aa + "\n")
 
                 ### write out WT/MT CDS + AA for debugging purposes

modules/msk/generatemutfasta/1.2/tests/main.nf.test.snap

@@ -10,7 +10,7 @@
                         "id": "test",
                         "single_end": false
                     },
-                    "test.MUT.sequences.fa:md5,dff338ec438ac75aa674b64ea8e26544"
+                    "test.MUT.sequences.fa:md5,3d2ff66590a4329f9a24e03bdf84e0ab"
                 ]
             ],
             [
@@ -19,16 +19,16 @@
                         "id": "test",
                         "single_end": false
                     },
-                    "test.WT.sequences.fa:md5,51415a40a725a16eaa8f5c51fa43799e"
+                    "test.WT.sequences.fa:md5,4bfcfc4d29d01ddc4108f39350936228"
                 ]
             ],
             "test_generate_mut_fasta.log"
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.10.2"
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2026-01-28T15:30:02.572804474"
+        "timestamp": "2026-02-09T15:03:37.884362"
     },
     "generatemutfasta_1.2 - maf - fasta - stub": {
         "content": [
@@ -96,9 +96,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
         },
-        "timestamp": "2025-12-18T16:08:27.448965"
+        "timestamp": "2026-02-09T15:03:51.569621"
     }
 }