Fix sample name detection

ahmig · ahmig · commit d47ffe5abf3b · 2025-09-05T14:38:59.000+02:00
diff --git a/workflow/scripts/compile_variants.R b/workflow/scripts/compile_variants.R
@@ -14,7 +14,7 @@ tables <- lapply(
     snakemake@input,
     function(path) {
         read_tsv(path) %>%
-            mutate(SAMPLE = sub('\\.tsv$', '', path))
+            mutate(SAMPLE = sub('\\.masked.filtered.tsv$', '', basename(path)))
     }
 )
 

Original file line number	Diff line number	Diff line change
`@@ -14,7 +14,7 @@ tables <- lapply(`
`14`	`14`	`snakemake@input,`
`15`	`15`	`function(path) {`
`16`	`16`	`read_tsv(path) %>%`
`17`		`- mutate(SAMPLE = sub('\\.tsv$', '', path))`
	`17`	`+ mutate(SAMPLE = sub('\\.masked.filtered.tsv$', '', basename(path)))`
`18`	`18`	`}`
`19`	`19`	`)`
`20`	`20`