Merge pull request #107 from MartinPippel/update_busco

Update busco
NBISweden · Jan 15, 2024 · a84824e · a84824e
2 parents 3af6af1 + 9838f76
commit a84824e
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Showing 6 changed files with 39 additions and 16 deletions.
diff --git a/config/annotation_preprocessing_modules.config b/config/annotation_preprocessing_modules.config
@@ -19,7 +19,7 @@ process {
     withName: 'BUSCO' {
         time       = 2.d
         tag        = { "$lineage:$meta.id" }
-        ext.args   = '--mode genome --tar'
+        ext.args   = '--tar'
         publishDir = [
             path: "${params.outdir}/${publish_subdir}/busco", 
             mode: params.publishDir_mode,

diff --git a/modules.json b/modules.json
@@ -12,7 +12,7 @@
           },
           "busco": {
             "branch": "master",
-            "git_sha": "6d6552cb582f56b6101c452e16ee7c23073f91de",
+            "git_sha": "e3126f437c336c826f242842fe51769cfce0ec2d",
             "installed_by": ["modules"]
           },
           "fastp": {

diff --git a/modules/nf-core/busco/environment.yml b/modules/nf-core/busco/environment.yml
diff --git a/modules/nf-core/busco/main.nf b/modules/nf-core/busco/main.nf
diff --git a/modules/nf-core/busco/meta.yml b/modules/nf-core/busco/meta.yml
diff --git a/subworkflows/annotation_preprocessing/main.nf b/subworkflows/annotation_preprocessing/main.nf
@@ -17,13 +17,17 @@ workflow ANNOTATION_PREPROCESSING {
 
     ASSEMBLY_PURIFY( genome_assembly )
     ASSEMBLY_STATS( genome_assembly.mix( ASSEMBLY_PURIFY.out.fasta ) )
-    BUSCO( 
-        ASSEMBLY_PURIFY.out.fasta
-            .combine( ch_busco_lineage )
-            .multiMap { fasta, lineage ->
-                ch_fasta: [ [ id: fasta.baseName ], fasta ]
-                ch_busco: lineage
-            },
+
+    ch_busco_in = ASSEMBLY_PURIFY.out.fasta
+        .combine( ch_busco_lineage )
+        .multiMap { fasta, lineage ->
+            fasta: [ [ id: fasta.baseName ], fasta ]
+            lineage: lineage
+        }
+    BUSCO (
+        ch_busco_in.fasta,
+        "genome",
+        ch_busco_in.lineage,
         params.busco_lineages_path ? file( params.busco_lineages_path, checkIfExists: true ) : [],
         []
     )