diff --git a/modules/msk/generatemutfasta/1.2/resources/usr/bin/generateMutFasta.py b/modules/msk/generatemutfasta/1.2/resources/usr/bin/generateMutFasta.py index ed576e38..1afc95ce 100755 --- a/modules/msk/generatemutfasta/1.2/resources/usr/bin/generateMutFasta.py +++ b/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 diff --git a/modules/msk/generatemutfasta/1.2/tests/main.nf.test.snap b/modules/msk/generatemutfasta/1.2/tests/main.nf.test.snap index 60c19112..cc9060bc 100644 --- a/modules/msk/generatemutfasta/1.2/tests/main.nf.test.snap +++ b/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" } } \ No newline at end of file