Add --auto-lineage option and remove single_end

Co-authored-by: Jill V. Hagey, PhD <jvhagey@gmail.com>

modules/busco/main.nf

@@ -9,7 +9,7 @@ process BUSCO {
 
     input:
     tuple val(meta), path('tmp_input/*')
-    each lineage                          // Required:    lineage to check against
+    each lineage                          // Required:    lineage to check against, "auto" enables --auto-lineage instead
     path busco_lineages_path              // Recommended: path to busco lineages - downloads if not set
     path config_file                      // Optional:    busco configuration file
 
@@ -27,6 +27,7 @@ process BUSCO {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}-${lineage}"
     def busco_config = config_file ? "--config $config_file" : ''
+    def busco_lineage = lineage.equals('auto') ? '--auto-lineage' : "--lineage_dataset ${lineage}"
     def busco_lineage_dir = busco_lineages_path ? "--offline --download_path ${busco_lineages_path}" : ''
     """
     # Nextflow changes the container --entrypoint to /bin/bash (container default entrypoint: /usr/local/env-execute)
@@ -63,7 +64,7 @@ process BUSCO {
         --cpu $task.cpus \\
         --in "\$INPUT_SEQS" \\
         --out ${prefix}-busco \\
-        --lineage_dataset $lineage \\
+        $busco_lineage \\
         $busco_lineage_dir \\
         $busco_config \\
         $args

tests/modules/busco/main.nf

@@ -4,28 +4,59 @@ nextflow.enable.dsl = 2
 
 include { BUSCO } from '../../../modules/busco/main.nf'
 
-// This tests genome decompression, empty input channels and data download
 workflow test_busco_genome_single_fasta {
 
     input = [
-        [ id:'test', single_end:false ], // meta map
+        [ id:'test' ], // meta map
         file( params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
     ]
 
     BUSCO (
         input,
-        ['bacteria_odb10', 'bacteroidetes_odb10'],
+        ['auto','bacteria_odb10', 'bacteroidetes_odb10'],  // Launch with auto to use --auto-lineage, and specified lineages
         [], // Download busco lineage
         [], // No config
     )
 
     /* Output tree:
-    /tmp/tmpisa3ktco/busco/
+    /tmp/tmp846crjv2/busco/
-    ├── short_summary.specific.bacteria_odb10.genome.fna.json -> /tmp/tmpm91x0mn2/8a/ff5c15baba0942cca15a8d53e98009/short_summary.specific.bacteria_odb10.genome.fna.json
+    ├── short_summary.generic.bacteria_odb10.genome.fna.json -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/short_summary.generic.bacteria_odb10.genome.fna.json
-    ├── short_summary.specific.bacteria_odb10.genome.fna.txt -> /tmp/tmpm91x0mn2/8a/ff5c15baba0942cca15a8d53e98009/short_summary.specific.bacteria_odb10.genome.fna.txt
+    ├── short_summary.generic.bacteria_odb10.genome.fna.txt -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/short_summary.generic.bacteria_odb10.genome.fna.txt
-    ├── short_summary.specific.bacteroidetes_odb10.genome.fna.json -> /tmp/tmpm91x0mn2/91/3abf602561d35fcd917711402977a3/short_summary.specific.bacteroidetes_odb10.genome.fna.json
+    ├── short_summary.specific.bacteria_odb10.genome.fna.json -> /tmp/tmpi6af66j1/45/107812e983a8e695c380ebc215e7d9/short_summary.specific.bacteria_odb10.genome.fna.json
-    ├── short_summary.specific.bacteroidetes_odb10.genome.fna.txt -> /tmp/tmpm91x0mn2/91/3abf602561d35fcd917711402977a3/short_summary.specific.bacteroidetes_odb10.genome.fna.txt
+    ├── short_summary.specific.bacteria_odb10.genome.fna.txt -> /tmp/tmpi6af66j1/45/107812e983a8e695c380ebc215e7d9/short_summary.specific.bacteria_odb10.genome.fna.txt
-    ├── test-bacteria_odb10-busco -> /tmp/tmpm91x0mn2/8a/ff5c15baba0942cca15a8d53e98009/test-bacteria_odb10-busco/
+    ├── short_summary.specific.bacteroidales_odb10.genome.fna.json -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/short_summary.specific.bacteroidales_odb10.genome.fna.json
+    ├── short_summary.specific.bacteroidales_odb10.genome.fna.txt -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/short_summary.specific.bacteroidales_odb10.genome.fna.txt
+    ├── short_summary.specific.bacteroidetes_odb10.genome.fna.json -> /tmp/tmpi6af66j1/a2/eb4a34894f3ac5554759ad6c9f652b/short_summary.specific.bacteroidetes_odb10.genome.fna.json
+    ├── short_summary.specific.bacteroidetes_odb10.genome.fna.txt -> /tmp/tmpi6af66j1/a2/eb4a34894f3ac5554759ad6c9f652b/short_summary.specific.bacteroidetes_odb10.genome.fna.txt
+    ├── test-auto-busco -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/test-auto-busco/
+    │   ├── genome.fna/
+    │   │   ├── auto_lineage/
+    │   │   │   ├── run_archaea_odb10/
+    │   │   │   ├── run_bacteria_odb10/
+    │   │   │   └── run_eukaryota_odb10/
+    │   │   ├── logs/
+    │   │   │   ├── hmmsearch_err.log
+    │   │   │   ├── hmmsearch_out.log
+    │   │   │   ├── metaeuk_err.log
+    │   │   │   ├── metaeuk_out.log
+    │   │   │   ├── prodigal_err.log
+    │   │   │   ├── prodigal_out.log
+    │   │   │   ├── sepp_err.log
+    │   │   │   └── sepp_out.log
+    │   │   ├── prodigal_output/
+    │   │   │   └── predicted_genes/
+    │   │   ├── run_bacteria_odb10 -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/test-auto-busco/genome.fna/auto_lineage/run_bacteria_odb10/  [recursive, not followed]
+    │   │   └── run_bacteroidales_odb10/
+    │   │       ├── busco_sequences/
+    │   │       ├── full_table.tsv
+    │   │       ├── hmmer_output/
+    │   │       ├── missing_busco_list.tsv
+    │   │       ├── short_summary.json
+    │   │       └── short_summary.txt
+    │   └── logs/
+    │       └── busco.log
+    ├── test-auto-busco.batch_summary.txt -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/test-auto-busco.batch_summary.txt
+    ├── test-bacteria_odb10-busco -> /tmp/tmpi6af66j1/45/107812e983a8e695c380ebc215e7d9/test-bacteria_odb10-busco/
     │   ├── genome.fna/
     │   │   ├── logs/
     │   │   │   ├── hmmsearch_err.log
@@ -43,8 +74,8 @@ workflow test_busco_genome_single_fasta {
     │   │       └── short_summary.txt
     │   └── logs/
     │       └── busco.log
-    ├── test-bacteria_odb10-busco.batch_summary.txt -> /tmp/tmpm91x0mn2/8a/ff5c15baba0942cca15a8d53e98009/test-bacteria_odb10-busco.batch_summary.txt
+    ├── test-bacteria_odb10-busco.batch_summary.txt -> /tmp/tmpi6af66j1/45/107812e983a8e695c380ebc215e7d9/test-bacteria_odb10-busco.batch_summary.txt
-    ├── test-bacteroidetes_odb10-busco -> /tmp/tmpm91x0mn2/91/3abf602561d35fcd917711402977a3/test-bacteroidetes_odb10-busco/
+    ├── test-bacteroidetes_odb10-busco -> /tmp/tmpi6af66j1/a2/eb4a34894f3ac5554759ad6c9f652b/test-bacteroidetes_odb10-busco/
     │   ├── genome.fna/
     │   │   ├── logs/
     │   │   │   ├── hmmsearch_err.log
@@ -62,8 +93,8 @@ workflow test_busco_genome_single_fasta {
     │   │       └── short_summary.txt
     │   └── logs/
     │       └── busco.log
-    ├── test-bacteroidetes_odb10-busco.batch_summary.txt -> /tmp/tmpm91x0mn2/91/3abf602561d35fcd917711402977a3/test-bacteroidetes_odb10-busco.batch_summary.txt
+    ├── test-bacteroidetes_odb10-busco.batch_summary.txt -> /tmp/tmpi6af66j1/a2/eb4a34894f3ac5554759ad6c9f652b/test-bacteroidetes_odb10-busco.batch_summary.txt
-    └── versions.yml -> /tmp/tmpm91x0mn2/91/3abf602561d35fcd917711402977a3/versions.yml
+    └── versions.yml -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/versions.yml
     */
 
 }
@@ -71,7 +102,7 @@ workflow test_busco_genome_single_fasta {
 workflow test_busco_genome_multi_fasta {
 
     input = [
-        [ id:'test', single_end:false ], // meta map
+        [ id:'test' ], // meta map
         [
             file( params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true),
             file( params.test_data['candidatus_portiera_aleyrodidarum']['genome']['genome_fasta'], checkIfExists: true)
@@ -133,7 +164,7 @@ workflow test_busco_genome_multi_fasta {
 workflow test_busco_eukaryote_metaeuk {
 
     input = [
-        [ id:'test', single_end:false ], // meta map
+        [ id:'test' ], // meta map
         file( params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
     ]
 
@@ -174,7 +205,7 @@ workflow test_busco_eukaryote_metaeuk {
 workflow test_busco_eukaryote_augustus {
 
     input = [
-        [ id:'test', single_end:false ], // meta map
+        [ id:'test' ], // meta map
         file( params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
     ]
 
@@ -218,7 +249,7 @@ workflow test_busco_eukaryote_augustus {
 workflow test_busco_protein {
 
     input = [
-        [ id:'test', single_end:false ], // meta map
+        [ id:'test' ], // meta map
         file( params.test_data['candidatus_portiera_aleyrodidarum']['genome']['proteome_fasta'], checkIfExists: true)
     ]
 
@@ -254,7 +285,7 @@ workflow test_busco_protein {
 workflow test_busco_transcriptome {
 
     input = [
-        [ id:'test', single_end:false ], // meta map
+        [ id:'test' ], // meta map
         file( params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true)
     ]
 

tests/modules/busco/test.yml

@@ -3,6 +3,20 @@
   tags:
     - busco
   files:
+    - path: output/busco/short_summary.generic.bacteria_odb10.genome.fna.json
+      contains:
+        - "one_line_summary"
+        - "input_file"
+        - "mode"
+        - "dataset"
+    - path: output/busco/short_summary.generic.bacteria_odb10.genome.fna.txt
+      contains:
+        - "BUSCO version"
+        - "The lineage dataset is"
+        - "BUSCO was run in mode"
+        - "Complete BUSCOs"
+        - "Missing BUSCOs"
+        - "Dependencies and versions"
     - path: output/busco/short_summary.specific.bacteria_odb10.genome.fna.json
       contains:
         - "one_line_summary"
@@ -17,6 +31,20 @@
         - "Complete BUSCOs"
         - "Missing BUSCOs"
         - "Dependencies and versions"
+    - path: output/busco/short_summary.specific.bacteroidales_odb10.genome.fna.json
+      contains:
+        - "one_line_summary"
+        - "input_file"
+        - "mode"
+        - "dataset"
+    - path: output/busco/short_summary.specific.bacteroidales_odb10.genome.fna.txt
+      contains:
+        - "BUSCO version"
+        - "The lineage dataset is"
+        - "BUSCO was run in mode"
+        - "Complete BUSCOs"
+        - "Missing BUSCOs"
+        - "Dependencies and versions"
     - path: output/busco/short_summary.specific.bacteroidetes_odb10.genome.fna.json
       contains:
         - "one_line_summary"
@@ -31,6 +59,8 @@
         - "Complete BUSCOs"
         - "Missing BUSCOs"
         - "Dependencies and versions"
+    - path: output/busco/test-auto-busco.batch_summary.txt
+      md5sum: 32f7765c310f33555c31c7a3e64c990e
     - path: output/busco/test-bacteria_odb10-busco.batch_summary.txt
       md5sum: e50690742e9ae6abdd2bf99334ff9e12
     - path: output/busco/test-bacteroidetes_odb10-busco.batch_summary.txt