Merge pull request #180 from erikrikarddaniel/fix-eukulele-field-name

Fix prefix for eukulele columns in summary
nf-core · Sep 13, 2023 · ca5de38 · ca5de38
2 parents d57e1db + 44ae6ef
commit ca5de38
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Showing 2 changed files with 19 additions and 16 deletions.
diff --git a/modules/local/sum_taxonomy.nf b/modules/local/sum_taxonomy.nf
@@ -9,8 +9,8 @@ process SUM_TAXONOMY {
 
     input:
 
-    tuple val(meta), path(taxonomy)
-    path(fcs)
+    tuple val(meta), val(db), path(taxonomy)
+    path feature_counts
 
     output:
 
@@ -29,21 +29,17 @@ process SUM_TAXONOMY {
 
     library(tidyverse)
 
-    TYPE_ORDER = c('sample', 'database', 'field', 'value')
-    # call the tables into variables
-    taxonomy <- read_tsv("${prefix}.taxonomy_classification.tsv.gz", show_col_types = FALSE )
+    # Read the taxonomy and counts tables
+    taxonomy <- read_tsv("${taxonomy}", show_col_types = FALSE )
 
-    counts <- list.files(pattern = "*.counts.tsv.gz") %>%
-        map_df(~read_tsv(.,  show_col_types  = FALSE)) %>%
+    counts <- read_tsv("${feature_counts}", show_col_types = FALSE) %>%
         mutate(sample = as.character(sample))
 
+    # Join the two and count the number of ORFs with assigned taxonomy
     counts %>%
-        right_join(taxonomy, by = 'orf') %>%
-        group_by(sample) %>%
-        drop_na() %>%
-        count(orf) %>%
-        summarise( value = sum(n), .groups = 'drop') %>%
-        add_column(database = "${prefix}", field = "n_orfs") %>%
+        inner_join(taxonomy, by = 'orf') %>%
+        count(sample, name = 'value') %>%
+        mutate(database = "${db}", field = "eukulele_n_orfs") %>%
         relocate(value, .after = last_col()) %>%
         write_tsv('${prefix}_summary.tsv.gz')
 

diff --git a/subworkflows/local/eukulele.nf b/subworkflows/local/eukulele.nf
@@ -11,12 +11,13 @@ workflow SUB_EUKULELE {
 
     take:
         eukulele // Channel: val(meta), path(fasta), val(database), path(directory) 
-        collect_fcs
+        feature_counts
 
     main:
         ch_versions = Channel.empty()
 
-        EUKULELE_DOWNLOAD ( eukulele.filter{ it[2] }.map { [ it[2], it[3] ] } )
+
+        EUKULELE_DOWNLOAD ( eukulele.filter { it[2] }.map { [ it[2], it[3] ] } )
         ch_download = EUKULELE_DOWNLOAD.out.db
 
         Channel.empty()
@@ -28,7 +29,13 @@ workflow SUB_EUKULELE {
         EUKULELE_SEARCH( ch_eukulele )
 
         FORMAT_TAX( EUKULELE_SEARCH.out.taxonomy_estimation.map { [ it[0], it[1] ] } )
-        SUM_TAXONOMY( FORMAT_TAX.out.tax, collect_fcs )
+
+        FORMAT_TAX.out.tax
+            .join(ch_eukulele)
+            .map { [ it[0], it[3], it[1] ] }
+            .set { ch_sum_taxonomy }
+
+        SUM_TAXONOMY ( ch_sum_taxonomy, feature_counts )
 
     emit:
         taxonomy_summary    = SUM_TAXONOMY.out.taxonomy_summary