fix: address requeste refactoring from amftools to maf

snakemake-workflows · Aug 19, 2024 · d38cced · d38cced
1 parent 080a9fc
commit d38cced
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Showing 4 changed files with 8 additions and 8 deletions.
diff --git a/.test/config-simple/config.yaml b/.test/config-simple/config.yaml
@@ -94,7 +94,7 @@ params:
 gene_coverage:
   min_avg_coverage: 0
 
-maftools:
+maf:
   activate: true
 
 report:

diff --git a/config/config.yaml b/config/config.yaml
@@ -74,9 +74,9 @@ report:
     # select a sample sheet column for stratification
     by-column: condition
 
-# standardized mutation overview plots with maftools:
+# standardized mutation overview plots with maf:
 # https://bioconductor.org/packages/release/bioc/vignettes/maftools/inst/doc/maftools.html
-maftools:
+maf:
   activate: false
 
 calling:

diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
@@ -162,10 +162,10 @@ def get_final_output(wildcards):
                 )
             )
 
-        if config["maftools"]["activate"]:
+        if config["maf"]["activate"]:
             final_output.extend(
                 expand(
-                    "results/maftools/{group}.{event}.{calling_type}.fdr-controlled.maf",
+                    "results/maf/{group}.{event}.{calling_type}.fdr-controlled.maf",
                     group=(
                         variants_groups
                         if calling_type == "variants"

diff --git a/workflow/rules/maftools.smk b/workflow/rules/maftools.smk
@@ -2,7 +2,7 @@ rule group_bcf_to_vcf:
     input:
         "results/final-calls/{group}.{event}.{calling_type}.fdr-controlled.bcf",
     output:
-        temp("results/maftools/{group}.{event}.{calling_type}.fdr-controlled.vcf"),
+        temp("results/maf/{group}.{event}.{calling_type}.fdr-controlled.vcf"),
     log:
         "logs/maftools/{group}.{event}.{calling_type}.fdr-controlled.log",
     wrapper:
@@ -11,10 +11,10 @@ rule group_bcf_to_vcf:
 
 rule group_vcf_to_maf:
     input:
-        vcf="results/maftools/{group}.{event}.{calling_type}.fdr-controlled.vcf",
+        vcf="results/maf/{group}.{event}.{calling_type}.fdr-controlled.vcf",
         ref=genome,
     output:
-        maf="results/maftools/{group}.{event}.{calling_type}.fdr-controlled.maf",
+        maf="results/maf/{group}.{event}.{calling_type}.fdr-controlled.maf",
     log:
         "logs/maftools/{group}.{event}.{calling_type}.fdr-controlled.log",
     conda: