Merge pull request #275 from LCR-BCCRC/module/fishhook/1.0

Module/fishhook/1.0
LCR-BCCRC · Aug 15, 2023 · 51e4ad4 · 51e4ad4
2 parents 4ebe1be + 2082626
commit 51e4ad4
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Showing 3 changed files with 7 additions and 10 deletions.
diff --git a/modules/fishhook/1.0/config/default.yaml b/modules/fishhook/1.0/config/default.yaml
@@ -15,8 +15,8 @@ lcr-modules:
         options:
             include_silent_mutation: False #Include silent mutations in maf file
             tiles_size: 1000 #This is the size of tiles you want to split the genome into, leave blank if you want to use a gene list as hypothese
-            gene_list: "" #If you do not provide a tile size, please provide a gene list in gtf format (e.g GENCODE v19 genes for GRCH37: gencode.v19.genes.gtf) for Fishhook to do a gene-centric analysis
-            gene_list_only_protein_coding: True #Only include protein coding genes in gene list
+            target_gene_list: "" #If you do not provide a tile size, please provide a gene list in gtf format (e.g GENCODE v19 genes for GRCH37: gencode.v19.genes.gtf) for Fishhook to do a gene-centric analysis
+            target_gene_list_only_protein_coding: True #Only include protein coding genes in gene list
             covariates: "" #please supply a coveriate file in bed format, leave it blank if you want to run FishHook without covariates
 
         conda_envs:

diff --git a/modules/fishhook/1.0/fishhook.smk b/modules/fishhook/1.0/fishhook.smk
@@ -126,7 +126,7 @@ rule _run_fishhook:
         fishhook = ancient(str(CFG["dirs"]["inputs"] + "fishhook_installed.success")),
         maf = str(rules._fishhook_prepare_maf.output.maf)
     output:
-        tsv = CFG["dirs"]["fishhook"] + "{sample_set}/fishhook.output.maf"
+        tsv = CFG["dirs"]["fishhook"] + "{sample_set}/fishhook.output.tsv"
     conda:
         CFG["conda_envs"]["fishhook"]
     threads:
@@ -137,8 +137,8 @@ rule _run_fishhook:
         tiles_size = CFG["options"]["tiles_size"],
         coveriate = CFG["options"]["covariates"],
         include_silent = CFG["options"]["include_silent_mutation"],
-        gene_list = CFG["options"]["gene_list"],
-        gene_list_only_protein_coding = CFG["options"]["gene_list_only_protein_coding"]
+        target_gene_list = CFG["options"]["target_gene_list"],
+        target_gene_list_only_protein_coding = CFG["options"]["target_gene_list_only_protein_coding"]
     script:
         "scr/R/run_fishhook.R"
 

diff --git a/modules/fishhook/1.0/scr/R/run_fishhook.R b/modules/fishhook/1.0/scr/R/run_fishhook.R
@@ -36,10 +36,8 @@ if(is.null(snakemake@params[[1]])){
     message("Subsetting Gene List for Protein Coding Gene Only...")
     genes = genes %Q% (gene_type == 'protein_coding') 
   }
-
   fish = Fish(hypotheses = genes, 
-                    events = events, 
-                    eligible = eligible, 
+                    events = events,
                     idcol = 'Tumor_Sample_Barcode',
                     use_local_mut_density=TRUE)
 }else{
@@ -48,8 +46,7 @@ if(is.null(snakemake@params[[1]])){
   tiles = gr.tile(seqinfo(maf), snakemake@params[[1]])
 
   fish = Fish(hypotheses = tiles, 
-                    events = events, 
-                    eligible = eligible, 
+                    events = events,
                     idcol = 'Tumor_Sample_Barcode',
                     use_local_mut_density=TRUE)
 }