fixed busco dataset in a tuple

Ensembl · Jun 27, 2024 · 74cc47d · 74cc47d
1 parent a992df4
commit 74cc47d
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Showing 6 changed files with 16 additions and 16 deletions.
diff --git a/pipelines/nextflow/modules/busco/busco_dataset.nf b/pipelines/nextflow/modules/busco/busco_dataset.nf
@@ -25,8 +25,8 @@ process BUSCO_DATASET {
     tuple val(gca), val(taxon_id), val(dbname)
 
     output:
-    stdout emit: dataset
-    tuple val(gca), val(dbname)
+    //stdout emit: dataset
+    tuple val(gca), val(dbname), stdout
 
     script:
     """

diff --git a/pipelines/nextflow/modules/busco/busco_genome_lineage.nf b/pipelines/nextflow/modules/busco/busco_genome_lineage.nf
@@ -25,11 +25,11 @@ process BUSCO_GENOME_LINEAGE {
     maxForks 10
 
     input:
-    val(busco_dataset)
-    tuple val(gca), val(dbname), path(genome_file)
+    //val(busco_dataset)
+    tuple val(gca), val(dbname), path(genome_file), val(busco_dataset)
 
     output:
-    tuple val(gca), val(dbname), path("genome_output/*.txt") 
+    tuple val(gca), val(dbname), path("genome_output/*.txt")
 
     script:
     def buscoDataset = params.busco_dataset ? params.busco_dataset.trim() : busco_dataset.trim()

diff --git a/pipelines/nextflow/modules/busco/busco_protein_lineage.nf b/pipelines/nextflow/modules/busco/busco_protein_lineage.nf
@@ -23,8 +23,8 @@ process BUSCO_PROTEIN_LINEAGE {
     maxForks 10
 
     input:
-    val(busco_dataset)
-    tuple val(gca), val(dbname), path(translation_file)
+    //val(busco_dataset)
+    tuple val(gca), val(dbname), path(translation_file), val(busco_dataset)
 
     output:
     tuple val(gca), val(dbname), path("protein_output/*.txt")

diff --git a/pipelines/nextflow/modules/fetch_genome.nf b/pipelines/nextflow/modules/fetch_genome.nf
@@ -24,10 +24,10 @@ process FETCH_GENOME {
   afterScript "sleep $params.files_latency"  // Needed because of file system latency
   maxForks 10
   input:
-  tuple val(gca), val(dbname)
+  tuple val(gca), val(dbname), val(busco_dataset)
 
   output:
-  tuple val(gca), val(dbname), path("*.fna")
+  tuple val(gca), val(dbname), path("*.fna"), val(busco_dataset)
 
   script:
   """

diff --git a/pipelines/nextflow/modules/fetch_proteins.nf b/pipelines/nextflow/modules/fetch_proteins.nf
@@ -26,10 +26,10 @@ process FETCH_PROTEINS {
     maxForks 20
 
     input:
-    tuple val(gca), val(dbname)
+    tuple val(gca), val(dbname), val(busco_dataset)
 
     output:
-    tuple val(gca), val(dbname), path("*_translations.fa")
+    tuple val(gca), val(dbname), path("*_translations.fa"),val(busco_dataset) 
 
     script:
     scientific_name = getMetaValue(dbname, "species.production_name")[0].meta_value.toString().toLowerCase()

diff --git a/pipelines/nextflow/subworkflows/run_busco.nf b/pipelines/nextflow/subworkflows/run_busco.nf
@@ -55,12 +55,12 @@ workflow RUN_BUSCO{
     def db_meta1=db_meta
     db_meta1.flatten().view { d -> "GCA: ${d.gca}, Taxon ID: ${d.taxon_id}, Core name: ${d.core}"}
 
-    def (dataset, db) = BUSCO_DATASET(db_meta.flatten()) 
+    def (dataset_db) = BUSCO_DATASET(db_meta.flatten()) 
     // Run Busco in genome mode
     if (busco_mode.contains('genome')) {
         def output_typeG = "genome"
-        def genomeData = FETCH_GENOME(db)
-        def buscoGenomeOutput = BUSCO_GENOME_LINEAGE(dataset, genomeData)
+        def genomeData = FETCH_GENOME(dataset_db)
+        def buscoGenomeOutput = BUSCO_GENOME_LINEAGE(genomeData)
         def buscoGenomeSummaryOutput = BUSCO_GENOME_OUTPUT(output_typeG,buscoGenomeOutput)
         if (params.copyToFtp) {
             COPY_GENOME_OUTPUT(buscoGenomeSummaryOutput)
@@ -70,8 +70,8 @@ workflow RUN_BUSCO{
     // Run Busco in protein mode
     if (busco_mode.contains('protein')) {
         def output_typeP = "protein"
-        def proteinData = FETCH_PROTEINS (db)
-        def buscoProteinOutput = BUSCO_PROTEIN_LINEAGE(dataset,proteinData)
+        def proteinData = FETCH_PROTEINS (dataset_db)
+        def buscoProteinOutput = BUSCO_PROTEIN_LINEAGE(proteinData)
         def (buscoProteinSummaryOutput) = BUSCO_PROTEIN_OUTPUT(output_typeP, buscoProteinOutput)
         if (copyToFtp) {
             COPY_PROTEIN_OUTPUT(buscoProteinSummaryOutput)