Move CI to use miniprot (#160)

* Move CI to use miniprot

* use metaeuk for non-test runs

* Removed extra whitespace

* Removed comment that applied to metaeuk

* Removed extra whitespace

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Co-authored-by: Matthieu Muffato <[email protected]>

Author: tkchafin

conf/modules.config

@@ -86,10 +86,8 @@ process {
         // Obey "use_work_dir_as_temp", except for large genomes
         scratch = { !params.use_work_dir_as_temp || (meta.genome_size < 2000000000) }
         ext.args = { 'test' in workflow.profile.tokenize(',') || 'test_raw' in workflow.profile.tokenize(',') || 'test_nobusco' in workflow.profile.tokenize(',') ?
-                        // Additional configuration to speed processes up during testing.
-                        // Note: BUSCO *must* see the double-quotes around the parameters
-                        '--force --metaeuk --metaeuk_parameters \'"-s=2"\' --metaeuk_rerun_parameters \'"-s=2"\''
-                    : '--force --metaeuk'  }
+                        '--force'  // Runs with miniprot
+                    : '--force --metaeuk' }
     }
 
     withName: "RESTRUCTUREBUSCODIR" {