Merge pull request #213 from erikrikarddaniel/reorder-prokka-cols

Reorder & rename prokka cols, save output to better named file
nf-core · Nov 28, 2023 · 601a673 · 601a673
2 parents f7a3c45 + 2f5726e
commit 601a673
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Showing 2 changed files with 6 additions and 3 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -234,7 +234,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/summary_tables" },
             mode: 'copy',
-            pattern: "*.annotations.tsv.gz"
+            pattern: "*.prokka-annotations.tsv.gz"
         ]
     }
 

diff --git a/modules/local/prokkagff2tsv.nf b/modules/local/prokkagff2tsv.nf
@@ -11,7 +11,7 @@ process PROKKAGFF2TSV {
     tuple val(meta), path(gff)
 
     output:
-    tuple val(meta), path("*.annotations.tsv.gz"), emit: tsv
+    tuple val(meta), path("*.prokka-annotations.tsv.gz"), emit: tsv
     path "versions.yml"                          , emit: versions
 
     when:
@@ -29,6 +29,7 @@ process PROKKAGFF2TSV {
     library(dplyr)
     library(tidyr)
     library(readr)
+    library(stringr)
 
     fread(
         cmd = "zgrep -P '\\t' $gff",
@@ -39,9 +40,11 @@ process PROKKAGFF2TSV {
         pivot_wider(names_from = k, values_from = v) %>%
         select(-a, -b) %>%
         rename(orf = ID) %>%
+        rename_all(str_to_lower) %>%
+        relocate(sort(colnames(.)[8:ncol(.)]), .after = 7) %>%
         relocate(orf) %>%
         as.data.table() %>%
-        write_tsv("${prefix}.annotations.tsv.gz")
+        write_tsv("${prefix}.prokka-annotations.tsv.gz")
 
     writeLines(
         c(