Report all BUSCOs and in the right order

sanger-tol · Jan 15, 2024 · b99101b · b99101b
1 parent 7527e7a
commit b99101b
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Showing 4 changed files with 28 additions and 16 deletions.
diff --git a/modules/local/blobtoolkit/createblobdir.nf b/modules/local/blobtoolkit/createblobdir.nf
@@ -9,7 +9,7 @@ process BLOBTOOLKIT_CREATEBLOBDIR {
 
     input:
     tuple val(meta), path(window, stageAs: 'windowstats/*')
-    tuple val(meta1), path(busco)
+    tuple val(meta1), path(busco, stageAs: 'lineage??/*')
     tuple val(meta2), path(blastp)
     tuple val(meta3), path(yaml)
     path(taxdump)
@@ -24,14 +24,15 @@ process BLOBTOOLKIT_CREATEBLOBDIR {
     script:
     def args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
+    def busco_args = busco.collect { "--busco " + it } .join(' ')
     def hits_blastp = blastp ? "--hits ${blastp}" : ""
     """
     blobtools replace \\
         --bedtsvdir windowstats \\
         --meta ${yaml} \\
         --taxdump ${taxdump} \\
         --taxrule buscogenes \\
-        --busco ${busco} \\
+        ${busco_args} \\
         ${hits_blastp} \\
         --threads ${task.cpus} \\
         $args \\

diff --git a/subworkflows/local/busco_diamond_blastp.nf b/subworkflows/local/busco_diamond_blastp.nf
@@ -51,7 +51,7 @@ workflow BUSCO_DIAMOND {
 
 
     // Add the basal lineages to the list (excluding duplicates)
-    basal_lineages = [ "archaea_odb10", "bacteria_odb10", "eukaryota_odb10" ]
+    basal_lineages = [ "eukaryota_odb10", "bacteria_odb10", "archaea_odb10" ]
     ch_ancestral_lineages
     | map { lineages -> (lineages + basal_lineages).unique() }
     | flatten ()
@@ -86,11 +86,26 @@ workflow BUSCO_DIAMOND {
     ch_versions = ch_versions.mix ( DIAMOND_BLASTP.out.versions.first() )
 
 
-    // Select BUSCO results for taxonomically closest database
+    // Index the lineages in the taxonomic order
+    def lineage_index = 0
+    ch_lineages
+    | map { lineage -> [lineage, lineage_index++] }
+    | set { ch_ordered_lineages }
+
+
+    // Order BUSCO results accoring to ch_lineages
     BUSCO.out.full_table
-    | combine ( ch_lineages.toList().map { it[0] } )
-    | filter { meta, table, lineage -> table =~ /$lineage/ }
-    | map { meta, table, lineage -> [ meta, table ] }
+    | map { meta, table -> [table.parent.baseName.minus("run_"), meta, table] }
+    | join ( ch_ordered_lineages )
+    | map { lineage, meta, table, index -> [meta, table, index] }
+    | groupTuple()
+    | map { meta, tables, indexes -> [ meta, tables.withIndex().sort { a, b -> indexes[a[1]] <=> indexes[b[1]] } . collect { table, i -> table } ] }
+    | set { ch_indexed_buscos }
+
+
+    // Select BUSCO results for taxonomically closest database
+    ch_indexed_buscos
+    | map { meta, tables -> [meta, tables[0]] }
     | set { ch_first_table }
 
 
@@ -102,7 +117,7 @@ workflow BUSCO_DIAMOND {
 
     emit:
     first_table = ch_first_table          // channel: [ val(meta), path(full_table) ] 
-    full_table  = BUSCO.out.full_table    // channel: [ val(meta), path(full_tables) ]
+    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 ]

diff --git a/subworkflows/local/collate_stats.nf b/subworkflows/local/collate_stats.nf
@@ -9,7 +9,7 @@ include { BLOBTOOLKIT_WINDOWSTATS } from '../../modules/local/blobtoolkit/window
 
 workflow COLLATE_STATS {
     take: 
-    busco_table // channel: [ val(meta), path(full_table) ]
+    busco       // channel: [ val(meta), path(full_table) ]
     bed         // channel: [ val(meta), path(bed) ]
     freq        // channel: [ val(meta), path(freq) ]
     mononuc     // channel: [ val(meta), path(mononuc) ]
@@ -20,11 +20,7 @@ workflow COLLATE_STATS {
 
 
     // Count BUSCO genes in a region
-    busco_table
-    | groupTuple()
-    | set { ch_busco }
-
-    BLOBTOOLKIT_COUNTBUSCOS ( ch_busco, bed )
+    BLOBTOOLKIT_COUNTBUSCOS ( busco, bed )
     ch_versions = ch_versions.mix ( BLOBTOOLKIT_COUNTBUSCOS.out.versions.first() )
 
 

diff --git a/workflows/blobtoolkit.nf b/workflows/blobtoolkit.nf
@@ -172,7 +172,7 @@ workflow BLOBTOOLKIT {
     // SUBWORKFLOW: Collate genome statistics by various window sizes
     //
     COLLATE_STATS ( 
-        BUSCO_DIAMOND.out.full_table, 
+        BUSCO_DIAMOND.out.all_tables,
         COVERAGE_STATS.out.bed, 
         COVERAGE_STATS.out.freq, 
         COVERAGE_STATS.out.mononuc, 
@@ -186,7 +186,7 @@ workflow BLOBTOOLKIT {
     BLOBTOOLS ( 
         INPUT_CHECK.out.config,
         COLLATE_STATS.out.window_tsv,
-        BUSCO_DIAMOND.out.first_table,
+        BUSCO_DIAMOND.out.all_tables,
         BUSCO_DIAMOND.out.blastp_txt.ifEmpty([[],[]]),
         RUN_BLASTX.out.blastx_out.ifEmpty([[],[]]),
         RUN_BLASTN.out.blastn_out.ifEmpty([[],[]]),