Adjusted Augustus Config Path settings. Suggested by @mahesh-panchal

modules/busco/main.nf

@@ -9,6 +9,7 @@ process BUSCO {
 
     input:
     tuple val(meta), path(fasta)
+    val(mode)
     path(augustus_config)
     val(lineage)
 
@@ -24,15 +25,26 @@ process BUSCO {
     """
     # Ensure the input is uncompressed
     gzip -cdf $fasta > __UNCOMPRESSED_FASTA_FILE__
+    
+    # Nextflow changes the container --entrypoint to /bin/bash (container default entrypoint: /usr/local/env-execute)
+    # Check for container variable initialisation script and source it.
+    if [ -f "/usr/local/env-activate.sh" ]; then
+        # . "/usr/local/env-activate.sh"  # Errors out because of various unbound variables
+        export PATH='/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin'
+        export CONDA_PREFIX='/usr/local'
+        export CONDA_SHLVL='1'
+        export CONDA_DEFAULT_ENV='/usr/local'
+        export CONDA_PROMPT_MODIFIER=''
+        . "/usr/local/etc/conda/activate.d/activate-r-base.sh"
+        . "/usr/local/etc/conda/activate.d/augustus.sh"
+        . "/usr/local/etc/conda/activate.d/openjdk_activate.sh"
+    fi
+    
     # Copy the image's AUGUSTUS config directory if it was not provided to the module
     [ ! -e augustus_config ] && cp -a /usr/local/config augustus_config
-    AUGUSTUS_CONFIG_PATH=augustus_config \\
-    busco \\
-        $args \\
-        --augustus \\
-        --cpu $task.cpus \\
-        --in __UNCOMPRESSED_FASTA_FILE__ \\
-        --out $meta.id
+    
+    # Busco command
+    AUGUSTUS_CONFIG_PATH=augustus_config busco $args --augustus --mode $mode --cpu $task.cpus --in __UNCOMPRESSED_FASTA_FILE__ --out $meta.id
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/busco/meta.yml

@@ -24,6 +24,9 @@ input:
       type: file
       description: Nucleic or amino acid sequence file in FASTA format
       pattern: "*.{fasta}"
+  - mode:
+      type: value
+      description: Sets the assessment MODE – genome, proteins, transcriptome
   - augustus_config:
       type: directory
       description: AUGUSTUS config directory

tests/modules/busco/main.nf

@@ -3,24 +3,13 @@
 nextflow.enable.dsl = 2
 
 include { BUSCO as BUSCO_BACTE } from '../../../modules/busco/main.nf'
-include { BUSCO as BUSCO_CHR22 } from '../../../modules/busco/main.nf'
-include { UNTAR                } from '../../../modules/untar/main.nf'
 
 // This tests genome decompression, empty input channels and data download
-workflow test_busco_bacteroidales {
+workflow test_busco {
    input = [ [ id:'test' ], file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true) ]    
    BUSCO_BACTE ( input,
+                 "genome",
                  [],
                  [] )
 }
 
-// This tests uncompressed genome, BUSCO lineage file provided via input channel, and offline mode
-workflow test_busco_chr22 {
-    input = [ [ id:'test' ],  file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
-    lineage_dataset = [ file(params.test_data['homo_sapiens']['genome']['chr22_odb10_tar_gz'], checkIfExists: true) ]
-    UNTAR(lineage_dataset)
-    BUSCO_CHR22 ( input,
-                  [],
-                  UNTAR.out.untar )
-}
-

tests/modules/busco/test.yml

@@ -1,5 +1,5 @@
-- name: busco test_busco_bacteroidales
-  command: nextflow run ./tests/modules/busco -entry test_busco_bacteroidales -c ./tests/config/nextflow.config -c ./tests/modules/busco/nextflow.config
+- name: busco test_busco
+  command: nextflow run ./tests/modules/busco -entry test_busco -c ./tests/config/nextflow.config -c ./tests/modules/busco/nextflow.config
   tags:
     - busco
   files:
@@ -8,13 +8,3 @@
     - path: output/busco/test/run_bacteroidales_odb10/short_summary.txt
       contains: ['Complete BUSCOs (C)']
 
-- name: busco test_busco_chr22
-  command: nextflow run ./tests/modules/busco -entry test_busco_chr22 -c ./tests/config/nextflow.config -c ./tests/modules/busco/nextflow.config
-  tags:
-    - busco
-  files:
-    - path: output/busco/test/run_chr22_odb10/full_table.tsv
-      md5sum: 83f20e8996c591338ada73b6ab0eb269
-    - path: output/busco/test/run_chr22_odb10/short_summary.txt
-      contains: ['Complete BUSCOs (C)']
-