enabled busco subworkflow

nf-core · Jan 11, 2024 · d8aad7d · d8aad7d
1 parent 1108d38
commit d8aad7d
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Showing 4 changed files with 17 additions and 11 deletions.
diff --git a/modules/local/busco_download.nf b/modules/local/busco_download.nf
@@ -11,8 +11,8 @@ process BUSCO_DOWNLOAD {
     val lineage
 
     output:
-    tuple val(meta), path("busco_downloads"), emit: download_dir
-    path "versions.yml"                     , emit: versions
+    path "busco_downloads", emit: download_dir
+    path "versions.yml"   , emit: versions
 
     when:
     task.ext.when == null || task.ext.when

diff --git a/modules/local/read2tree/main.nf b/modules/local/read2tree/main.nf
@@ -22,7 +22,7 @@ process READ2TREE {
     script:
     def args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"   
-    # If the process detects only 1 species
+    // If the process detects only 1 species
     if (fastq1.size() == 1) { 
         """
         read2tree \\
@@ -37,7 +37,7 @@ process READ2TREE {
         	read2tree: \$(echo \$(read2tree --version))
     	END_VERSIONS
         """   
-    # Otherwise, use multiple species mode
+    // Otherwise, use multiple species mode
     } else {
     	"""
     	# This creates the reference folder

diff --git a/subworkflows/local/busco_phylogeny.nf b/subworkflows/local/busco_phylogeny.nf
@@ -1,5 +1,6 @@
 include { BUSCO          } from '../../modules/nf-core/busco'
 include { BUSCO_DOWNLOAD } from '../../modules/local/busco_download'
+include { READ2TREE      } from '../../modules/local/read2tree'
 
 workflow BUSCO_PHYLOGENY {
 
@@ -15,7 +16,6 @@ workflow BUSCO_PHYLOGENY {
     // Only process Eukaryotic samples 
     input_filtered = input
         .filter { it[4] == "Eukaryota" }
-    input_filtered
 
     // Get all reference genomes in any group/sample
     unique_ref_fnas = input_filtered
@@ -28,11 +28,17 @@ workflow BUSCO_PHYLOGENY {
     BUSCO_DOWNLOAD ( Channel.from( "eukaryota_odb10" ) )
 
     // Extract BUSCO genes for all unique reference genomes used in any sample/group
-    BUSCO ( unique_ref_fnas, "genome", "eukaryota_odb", BUSCO_DOWNLOAD.out.download_dir, [] )
+    BUSCO (
+        unique_ref_fnas,
+        "genome",
+        "eukaryota_odb10",
+        BUSCO_DOWNLOAD.out.download_dir.first(), // .first() is needed to convert the queue channel to a value channel so it can be used multiple times.
+        [] )
 
     // Create Read2tree database
 
     // Run Read2tree
+    // READ2TREE ( )
 
 
     emit:

diff --git a/workflows/pathogensurveillance.nf b/workflows/pathogensurveillance.nf
@@ -163,11 +163,11 @@ workflow PATHOGENSURVEILLANCE {
         .combine(COARSE_SAMPLE_TAXONOMY.out.kingdom, by: 0) // val(meta), [file(fastq)], val(ref_meta), file(reference), val(group_meta), [val(ref_meta)], val(kingdom)
         .combine(COARSE_SAMPLE_TAXONOMY.out.depth, by:0) // val(meta), [file(fastq)], val(ref_meta), file(reference), val(group_meta), [val(ref_meta)], val(kingdom), val(depth)
         .map { it[0..1] + it[4..7] } // val(meta), [file(fastq)], val(group_meta), [val(ref_meta)], val(kingdom), val(depth)      
-    //BUSCO_PHYLOGENY (
-    //    busco_input,
-    //    DOWNLOAD_REFERENCES.out.sequence
-    //)
-    
+    BUSCO_PHYLOGENY (
+        busco_input,
+        DOWNLOAD_REFERENCES.out.sequence
+    )
+
     // Save version info
     CUSTOM_DUMPSOFTWAREVERSIONS (                                               
         ch_versions.unique().collectFile(name: 'collated_versions.yml')