fix: revert base.config and fix micromono

Author: chasemc

conf/base.config

@@ -29,30 +29,30 @@ process {
 
     withLabel:process_single {
         cpus   = { check_max( 1                    , 'cpus'    ) }
-        memory = { check_max( 5.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 10.h  * task.attempt  , 'time'    ) }
+        memory = { check_max( 500.MB * task.attempt, 'memory'  ) }
+        time   = { check_max( 2.h  * task.attempt  , 'time'    ) }
     }
     withLabel:process_low {
         cpus   = { check_max( 1     * task.attempt, 'cpus'    ) }
         memory = { check_max( 2.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 40.h   * task.attempt, 'time'    ) }
+        time   = { check_max( 4.h   * task.attempt, 'time'    ) }
     }
     withLabel:process_medium {
-        cpus   = { check_max( 5     * task.attempt, 'cpus'    ) }
+        cpus   = { check_max( 4     * task.attempt, 'cpus'    ) }
         memory = { check_max( 20.GB * task.attempt, 'memory'  ) }
         time   = { check_max( 80.h   * task.attempt, 'time'    ) }
     }
     withLabel:process_high {
-        cpus   = { check_max( 24    * task.attempt, 'cpus'    ) }
-        memory = { check_max( 100.GB * task.attempt, 'memory'  ) }
+        cpus   = { check_max( 16    * task.attempt, 'cpus'    ) }
+        memory = { check_max( 60.GB * task.attempt, 'memory'  ) }
         time   = { check_max( 16.h  * task.attempt, 'time'    ) }
     }
     withLabel:process_long {
         time   = { check_max( 24.h  * task.attempt, 'time'    ) }
     }
     withLabel:process_high_memory {
-        memory = { check_max( 2000.GB * task.attempt, 'memory' ) }
-    }   
+        memory = { check_max( 60.GB * task.attempt, 'memory' ) }
+    }
     withLabel:error_ignore {
         errorStrategy = 'ignore'
     }

conf/examples/input_examples/by_taxa/micromonospora.config

@@ -13,7 +13,7 @@ Use as follows:
 params {
     config_profile_name          = 'Annotate all RefSeq Micromonospora'
     config_profile_description   = 'Minimal test dataset to check pipeline function'
-    ncbi_datasets_command        ='genome taxon "micromonospora chokorienses" --assembly-source refseq --exclude-atypical'
+    ncbi_datasets_command        ='genome taxon "micromonospora" --assembly-source refseq --exclude-atypical'
 
     /*
     ///////////////////////////////////
@@ -37,22 +37,45 @@ params {
         // want to set fasta_splits to a higher number to allow checkpointing. Howevever, setting
         // fasta_splits too high will result in diminishing returns due to overhead and possibly
         // too-few proteins per file (would probably keep <1000 for any size of dataset)
-        fasta_splits                = 24
-        max_cpus                    = 24
-        max_memory                  = '100.GB'
-        max_time                    = 48.h
+        max_cpus                    = 96
+        max_memory                  = '800.GB'
+        max_time                    = 500.h
+        slurm_queue_size            = 48
 
 }
 
 process {
 
-    withName:'ANTISMASH'{
-        ext.args   = "--skip-zip-file --allow-long-headers --skip-sanitisation --minimal --enable-genefunctions --enable-lanthipeptides --enable-lassopeptides --enable-nrps-pks --enable-sactipeptides --enable-t2pks --enable-thiopeptides --enable-tta"
-        ext.args2   = "--hmmdetection-strictness 'loose'"
+withName:HMMER_HMMSEARCH {
+        cpus   = { check_max (2     * task.attempt, 'cpus'   ) }
+        memory = { check_max (2.GB * task.attempt, 'memory' ) }
+        time   = { check_max (24.h  * task.attempt, 'time'   ) }
     }
-
-    withName:'MMSEQS2_CLUSTER'{
-        // https://github.com/soedinglab/mmseqs2/wiki#how-to-set-the-right-alignment-coverage-to-cluster
-        ext.args2 = '-c 0.7 --cov-mode 0'
+    withLabel:process_single {
+        cpus   = { check_max( 1                    , 'cpus'    ) }
+        memory = { check_max( 5.GB * task.attempt, 'memory'  ) }
+        time   = { check_max( 10.h  * task.attempt  , 'time'    ) }
+    }
+    withLabel:process_low {
+        cpus   = { check_max( 1     * task.attempt, 'cpus'    ) }
+        memory = { check_max( 2.GB * task.attempt, 'memory'  ) }
+        time   = { check_max( 40.h   * task.attempt, 'time'    ) }
+    }
+    withLabel:process_medium {
+        cpus   = { check_max( 5     * task.attempt, 'cpus'    ) }
+        memory = { check_max( 20.GB * task.attempt, 'memory'  ) }
+        time   = { check_max( 80.h   * task.attempt, 'time'    ) }
+    }
+    withLabel:process_high {
+        cpus   = { check_max( 24    * task.attempt, 'cpus'    ) }
+        memory = { check_max( 100.GB * task.attempt, 'memory'  ) }
+        time   = { check_max( 16.h  * task.attempt, 'time'    ) }
+    }
+    withLabel:process_long {
+        time   = { check_max( 24.h  * task.attempt, 'time'    ) }
     }
+    withLabel:process_high_memory {
+        memory = { check_max( 400.GB * task.attempt, 'memory' ) }
+    }   
+    
 }