Merge branch 'update/metafusion' of github.com:mskcc/forte into updat…

…e/metafusion
mskcc · Sep 23, 2024 · aeac5f0 · aeac5f0
2 parents bf4e6be + 0bb2044
commit aeac5f0
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/conf/igenomes.config b/conf/igenomes.config
@@ -50,7 +50,7 @@ params {
             cdna           = "http://ftp.ensemblgenomes.org/pub/viruses/fasta/sars_cov_2/cdna/Sars_cov_2.ASM985889v3.cdna.all.fa.gz"
             metafusion_blocklist = "https://raw.githubusercontent.com/anoronh4/forte-references/main/GRCh37_test/blocklist_breakpoints.bedpe"
             ensembl_version = 75
-            clinicalgenes = "${projectDir}/assets/clinical_whitelist.txt"
+            clinicalgenes = "${projectDir}/assets/clinical_allowlist_hg19.txt"
             transcripts     = "https://ftp.ensembl.org/pub/release-75/mysql/homo_sapiens_core_75_37/transcript.txt.gz"
         }
 /*

diff --git a/subworkflows/local/fusion.nf b/subworkflows/local/fusion.nf
@@ -142,7 +142,7 @@ workflow FUSION {
             ADD_FLAG.out.unfiltered_cff
                 .join(ONCOKB_FUSIONANNOTATOR.out.oncokb_fusions, by:0)
                 .join(AGFUSION_BATCH.out.fusion_transcripts_tsv, by:0),
-            transcipts
+            transcripts
         )
     } else {
         CFF_FINALIZE(