Hide the CSV from the rest of the pipeline

sanger-tol · May 20, 2024 · 0e6fa8e · 0e6fa8e
1 parent efa7b1e
commit 0e6fa8e
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Showing 3 changed files with 38 additions and 23 deletions.
diff --git a/subworkflows/local/busco_diamond_blastp.nf b/subworkflows/local/busco_diamond_blastp.nf
@@ -11,7 +11,7 @@ include { RESTRUCTUREBUSCODIR       } from '../../modules/local/restructurebusco
 workflow BUSCO_DIAMOND {
     take:
     fasta        // channel: [ val(meta), path(fasta) ]
-    csv          // channel: [ val(meta), path(csv) ]
+    busco_lin    // channel: val([busco_lineages])
     busco_db     // channel: path(busco_db)
     blastp       // channel: path(blastp_db)
 
@@ -20,30 +20,14 @@ workflow BUSCO_DIAMOND {
     ch_versions = Channel.empty()
 
 
-    //
-    // Get NCBI species ID
-    //
-    csv
-    | map { meta, csv -> csv }
-    | splitCsv(header: ['key', 'value'])
-    | filter { it.key == "taxon_id" }
-    | map { it.value }
-    | set { ch_taxid }
-
-
     //
     // Prepare the BUSCO linages
     //
     // 0. Initialise sone variables
     basal_lineages = [ "eukaryota_odb10", "bacteria_odb10", "archaea_odb10" ]
     def lineage_position = 0
-    // 1. Parse the NCBI_GET_ODB_TAXON output
-    csv
-    | map { meta, csv -> csv }
-    | splitCsv(header: ['key', 'value'])
-    | filter { it.key == "busco_lineage" }
-    | map { it.value }
-    | collect
+    // 1. Start from the taxon's lineages
+    busco_lin
     // 2. Add the (missing) basal lineages
     | map { lineages -> (lineages + basal_lineages).unique() }
     | flatten ()
@@ -139,7 +123,6 @@ workflow BUSCO_DIAMOND {
     first_table = ch_first_table          // channel: [ val(meta), path(full_table) ]
     all_tables  = ch_indexed_buscos       // channel: [ val(meta), path(full_tables) ]
     blastp_txt  = DIAMOND_BLASTP.out.txt  // channel: [ val(meta), path(txt) ]
-    taxon_id    = ch_taxid                // channel: taxon_id
     multiqc                               // channel: [ meta, summary ]
     versions    = ch_versions             // channel: [ versions.yml ]
 }
diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf
@@ -70,6 +70,37 @@ workflow INPUT_CHECK {
     ch_versions = ch_versions.mix(GENERATE_CONFIG.out.versions.first())
 
 
+    //
+    // Parse the CSV file
+    //
+    GENERATE_CONFIG.out.csv
+    | map { meta, csv -> csv }
+    | splitCsv(header: ['key', 'value'])
+    | branch {
+        taxon_id: it.key == "taxon_id"
+                    return it.value
+        busco_lineage: it.key == "busco_lineage"
+                    return it.value
+    }
+    | set { ch_parsed_csv }
+
+
+    //
+    // Get NCBI species ID
+    //
+    ch_parsed_csv.taxon_id
+    | first
+    | set { ch_taxon_id }
+
+
+    //
+    // Get the BUSCO linages
+    //
+    ch_parsed_csv.busco_lineage
+    | collect
+    | set { ch_busco_lineages }
+
+
     if ( params.accession ) {
         read_files
         | map { meta, data -> meta.id.split("_")[0..-2].join("_") }
@@ -89,7 +120,8 @@ workflow INPUT_CHECK {
     emit:
     reads                                   // channel: [ val(meta), path(datafile) ]
     config = ch_config                      // channel: [ val(meta), path(yaml) ]
-    csv_params = GENERATE_CONFIG.out.csv    // channel: [ val(meta), path(csv) ]
+    taxon_id = ch_taxon_id                  // channel: val(taxon_id)
+    busco_lineages = ch_busco_lineages      // channel: val([busco_lin])
     versions = ch_versions                  // channel: [ versions.yml ]
 }
 

diff --git a/workflows/blobtoolkit.nf b/workflows/blobtoolkit.nf
@@ -138,7 +138,7 @@ workflow BLOBTOOLKIT {
     //
     BUSCO_DIAMOND (
         PREPARE_GENOME.out.genome,
-        INPUT_CHECK.out.csv_params,
+        INPUT_CHECK.out.busco_lineages,
         ch_busco_db,
         ch_blastp,
     )
@@ -162,7 +162,7 @@ workflow BLOBTOOLKIT {
         RUN_BLASTX.out.blastx_out,
         PREPARE_GENOME.out.genome,
         ch_blastn,
-        BUSCO_DIAMOND.out.taxon_id
+        INPUT_CHECK.out.taxon_id
     )
 
     //