Updated config files

mskcc · Mar 6, 2025 · aee5695 · aee5695
1 parent d3dd8a5
commit aee5695
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Showing 3 changed files with 12 additions and 1 deletion.
diff --git a/conf/modules.config b/conf/modules.config
@@ -32,4 +32,7 @@ process {
     withName: 'NEOANTIGENUTILS_NEOANTIGENINPUT' {
         ext.args = "--kD_cutoff ${params.kd_cutoff}"
     }
-}
+
+    withName: 'NEOANTIGENEDITING_COMPUTEFITNESS' {
+        ext.args = "--a_param ${params.compute_fitness_a} --k_param ${params.compute_fitness_k} --w_param ${params.compute_fitness_w}"
+    }
diff --git a/conf/prod.config b/conf/prod.config
@@ -37,8 +37,12 @@ params {
     phylo_mcmc_samples = 2500
     phylo_num_chains = 15
     kd_cutoff = 500
+    compute_fitness_a = 22.897590714815188
+    compute_fitness_k = 1
+    compute_fitness_w = 0.22402192838740312
 
     iedbfasta = 'https://raw.githubusercontent.com/mskcc/NeoantigenEditing/refs/heads/main/data/iedb.fasta'
     cds = 'https://github.com/mskcc-omics-workflows/test-datasets/raw/neoantigen/neoantigen/Homo_sapiens.GRCh37.75.cds.all.fa.gz'
     cdna = 'https://github.com/mskcc-omics-workflows/test-datasets/raw/neoantigen/neoantigen/Homo_sapiens.GRCh37.75.cdna.all.fa.gz'
+    gtf = 'https://github.com/mskcc-omics-workflows/test-datasets/raw/neoantigen/neoantigen/Homo_sapiens.GRCh37.75.gtf.gz'
 }
diff --git a/conf/test.config b/conf/test.config
@@ -33,8 +33,12 @@ params {
     phylo_num_chains = 2
     netmhc3 = true
     kd_cutoff = 500
+    compute_fitness_a = 22.897590714815188
+    compute_fitness_k = 1
+    compute_fitness_w = 0.22402192838740312
 
     iedbfasta = 'https://raw.githubusercontent.com/mskcc-omics-workflows/test-datasets/neoantigen/neoantigen/neoantigenEditing/data/iedb.fasta'
     cds = 'https://github.com/mskcc-omics-workflows/test-datasets/raw/neoantigen/neoantigen/Homo_sapiens.GRCh37.75.cds.all.fa.gz'
     cdna = 'https://github.com/mskcc-omics-workflows/test-datasets/raw/neoantigen/neoantigen/Homo_sapiens.GRCh37.75.cdna.all.fa.gz'
+    gtf = 'https://github.com/mskcc-omics-workflows/test-datasets/raw/neoantigen/neoantigen/Homo_sapiens.GRCh37.75.gtf.gz'
 }