diff --git a/files/galaxy/dynamic_job_rules/production/total_perspective_vortex/tools.yml b/files/galaxy/dynamic_job_rules/production/total_perspective_vortex/tools.yml
index 1b801c0e2..ca95db209 100644
--- a/files/galaxy/dynamic_job_rules/production/total_perspective_vortex/tools.yml
+++ b/files/galaxy/dynamic_job_rules/production/total_perspective_vortex/tools.yml
@@ -1,28 +1,4 @@
 tools:
-  ### Tools with resource updates being tested due to OOM errors ###
-  toolshed.g2.bx.psu.edu/repos/iuc/biom_convert/biom_convert/.*: # not enough jobs to tell whether this has fixed oom issue (19/10/23)
-    mem: 12
-  toolshed.g2.bx.psu.edu/repos/iuc/dada2_dada/dada2_dada/.*: # not enough jobs to tell whether this has fixed oom issue (19/10/23)
-    cores: 2
-    mem: 10
-  toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/.*: # not enough jobs to tell whether this has fixed oom issue (19/10/23)
-    mem: 12
-  toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/.*:
-    mem: 12
-  toolshed.g2.bx.psu.edu/repos/peterjc/seq_select_by_id/seq_select_by_id/.*:
-    mem: 12
-  toolshed.g2.bx.psu.edu/repos/artbio/cap3/cap3/.*:
-    mem: 8
-  toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/diffbind/.*:
-    mem: 8
-  toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS.*:
-    mem: 10
-  toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/.*:
-    mem: 8
-  toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/.*:
-    cores: 2
-    mem: 10
-  ### ###
   testtoolshed.g2.bx.psu.edu/repos/fubar/htseq_bams_to_count_matrix/htseqsams2mxlocal/.*:
     cores: 3
     mem: 11.5
@@ -40,6 +16,8 @@ tools:
   testtoolshed.g2.bx.psu.edu/repos/simon-gladman/phyloseq_ordination_plot/phyloseq_ordinate/.*:
     cores: 16
     mem: 61.4
+  toolshed.g2.bx.psu.edu/repos/artbio/cap3/cap3/.*:
+    mem: 8
   toolshed.g2.bx.psu.edu/repos/artbio/repenrich/repenrich/.*:
     cores: 8
     mem: 30.7
@@ -89,7 +67,7 @@ tools:
     mem: 61.4
     params:
       docker_enabled: true
-  toolshed.g2.bx.psu.edu/repos/bgruening/blobtoolkit/blobtoolkit/.*: #
+  toolshed.g2.bx.psu.edu/repos/bgruening/blobtoolkit/blobtoolkit/.*:
     params:
       singularity_enabled: true
   toolshed.g2.bx.psu.edu/repos/bgruening/canu/canu/.*:
@@ -99,9 +77,6 @@ tools:
       accept:
       - pulsar
       - pulsar-training-large
-  toolshed.g2.bx.psu.edu/repos/bgruening/cpat/cpat/.*:
-    params:
-      singularity_enabled: true
   toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_butina_clustering/.*:
     cores: 1
     mem: 3.8
@@ -125,6 +100,9 @@ tools:
   toolshed.g2.bx.psu.edu/repos/bgruening/circexplorer/circexplorer/.*:
     params:
       singularity_enabled: true
+  toolshed.g2.bx.psu.edu/repos/bgruening/cpat/cpat/.*:
+    params:
+      singularity_enabled: true
   toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/.*:
     cores: 8
     mem: 30.7
@@ -144,8 +122,8 @@ tools:
       - pulsar
       - pulsar-quick
   toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/.*:
-    cores: 10 
-    mem: 90 # TODO: delete this and get cores/mem from shared db if they are adjusted to 10c90g
+    cores: 10
+    mem: 90
     params:
       singularity_enabled: true
     scheduling:
@@ -174,6 +152,11 @@ tools:
   toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond_view/.*:
     params:
       singularity_enabled: true
+  toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/diffbind/.*:
+    mem: 8
+  toolshed.g2.bx.psu.edu/repos/bgruening/enumerate_charges/enumerate_charges/.*:
+    params:
+      singularity_enabled: true
   toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/.*:
     context:
       test_cores: 2
@@ -200,6 +183,8 @@ tools:
   toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicpca/hicexplorer_hicpca/.*:
     cores: 10
     mem: 38.3
+    params:
+      singularity_enabled: true
   toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/.*:
     cores: 120
     mem: 1922
@@ -258,26 +243,29 @@ tools:
     scheduling:
       accept:
       - pulsar
-  toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/.*:
-    params:
-      singularity_enabled: true
-    cores: 5
-    mem: 19.1
   toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/.*:
     cores: 4
     mem: 15.3
+    scheduling:
+      accept:
+      - pulsar
     rules:
     - id: sailfish_small_input_rule
       if: input_size < 0.2
       cores: 1
       mem: 3.8
-    scheduling:
-      accept:
-      - pulsar
+  toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/.*:
+    cores: 5
+    mem: 19.1
+    params:
+      singularity_enabled: true
+  toolshed.g2.bx.psu.edu/repos/bgruening/sdf_to_tab/sdf_to_tab/.*:
+    params:
+      singularity_enabled: true
   toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/.*:
     mem: 10
     params:
-      tmp_dir: true  
+      tmp_dir: true
   toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/.*:
     cores: 1
     mem: 3.8
@@ -337,6 +325,8 @@ tools:
       if: input_size >= 0.03
       fail: Too much data, Prokka is designed to annotate bacterial/virus genomes
         only. Prokka will not annotate eukaryotic genomes nor metagenomes.
+  toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/.*:
+    mem: 12
   toolshed.g2.bx.psu.edu/repos/csbl/repeatmodeler/repeatmodeler/.*:
     cores: 8
     mem: 30.7
@@ -470,13 +460,11 @@ tools:
     scheduling:
       accept:
       - pulsar
+  toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS.*:
+    mem: 10
   toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/.*:
     cores: 2
     mem: 7.6
-    # scheduling: # 9/9/23: removing from pulsar due to large output files compared to inputs
-    #   accept:
-    #   - pulsar
-    #   - pulsar-quick
   toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/.*:
     cores: 8
     mem: 30.7
@@ -520,8 +508,8 @@ tools:
     cores: 8
     mem: 30.7
     env:
-      _JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G
       SINGULARITYENV__JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G
+      _JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G
     scheduling:
       accept:
       - pulsar
@@ -671,8 +659,8 @@ tools:
     cores: 3
     mem: 11.5
     env:
-      _JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G
       SINGULARITYENV__JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G
+      _JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G
     scheduling:
       accept:
       - pulsar
@@ -688,10 +676,10 @@ tools:
       cores: 1
       mem: 3.8
   toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/.*:
-    params:
-      singularity_enabled: true
     cores: 3
     mem: 11.5
+    params:
+      singularity_enabled: true
   toolshed.g2.bx.psu.edu/repos/devteam/samtools.*:
     params:
       singularity_enabled: true
@@ -736,14 +724,30 @@ tools:
   toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy.*:
     params:
       singularity_enabled: true
+  toolshed.g2.bx.psu.edu/repos/ecology/pampa_communitymetrics/pampa_communitymetrics/.*:
+    params:
+      singularity_enabled: true
+  toolshed.g2.bx.psu.edu/repos/ecology/pampa_glmcomm/pampa_glmcomm/.*:
+    params:
+      singularity_enabled: true
+  toolshed.g2.bx.psu.edu/repos/ecology/pampa_glmsp/pampa_glmsp/.*:
+    params:
+      singularity_enabled: true
+  toolshed.g2.bx.psu.edu/repos/ecology/pampa_plotglm/pampa_plotglm/.*:
+    params:
+      singularity_enabled: true
+  toolshed.g2.bx.psu.edu/repos/ecology/pampa_presabs/pampa_presabs/.*:
+    params:
+      singularity_enabled: true
   toolshed.g2.bx.psu.edu/repos/galaxy-australia/alphafold2/alphafold/.*:
     gpus: 1
     cores: 8
     mem: 69
     params:
-      tmp_dir: true
       docker_enabled: true
-      docker_volumes: $job_directory:ro,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/data/alphafold_databases:/data:ro
+      docker_volumes: 
+        $job_directory:ro,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/data/alphafold_databases:/data:ro
+      tmp_dir: true
     rules:
     - if: |
         user and 'Alphafold' in [role.name for role in user.all_roles() if not role.deleted] and not (
@@ -772,24 +776,23 @@ tools:
         )])
       fail: |
         This tool is currently being beta-tested on GPUs and your account has not been given access. Contact help@genome.edu.au if you think this is in error.
-
   toolshed.g2.bx.psu.edu/repos/galaxy-australia/alphafold2/alphafold/2.1.*:
+    inherits: toolshed.g2.bx.psu.edu/repos/galaxy-australia/alphafold2/alphafold/.*
     params:
       docker_run_extra_arguments: --gpus all --env ALPHAFOLD_AA_LENGTH_MIN=16 --env
         ALPHAFOLD_AA_LENGTH_MAX=3000 --env ALPHAFOLD_DB=/data/v2.1
-    inherits: toolshed.g2.bx.psu.edu/repos/galaxy-australia/alphafold2/alphafold/.*
   toolshed.g2.bx.psu.edu/repos/galaxy-australia/alphafold2/alphafold/2.3.*:
+    inherits: toolshed.g2.bx.psu.edu/repos/galaxy-australia/alphafold2/alphafold/.*
     params:
       docker_run_extra_arguments: --gpus all --env ALPHAFOLD_AA_LENGTH_MIN=16 --env
         ALPHAFOLD_AA_LENGTH_MAX=3000 --env ALPHAFOLD_DB=/data/v2.3
     rules:
-      - if: |
-          min_version = '2.3.1+galaxy2'
-          helpers.tool_version_gte(tool, min_version)
-        params:
-          docker_run_extra_arguments: --gpus all --env ALPHAFOLD_AA_LENGTH_MIN=16 --env ALPHAFOLD_AA_LENGTH_MAX=3000 --env ALPHAFOLD_DB=/data
-    inherits: toolshed.g2.bx.psu.edu/repos/galaxy-australia/alphafold2/alphafold/.*
-
+    - if: |
+        min_version = '2.3.1+galaxy2'
+        helpers.tool_version_gte(tool, min_version)
+      params:
+        docker_run_extra_arguments: --gpus all --env ALPHAFOLD_AA_LENGTH_MIN=16 --env
+          ALPHAFOLD_AA_LENGTH_MAX=3000 --env ALPHAFOLD_DB=/data
   toolshed.g2.bx.psu.edu/repos/galaxy-australia/cactus_cactus/cactus_cactus/.*:
     context:
       test_cores: 10
@@ -918,6 +921,18 @@ tools:
     scheduling:
       accept:
       - pulsar
+  toolshed.g2.bx.psu.edu/repos/galaxyp/rawtools/rawtools/.*:
+    params:
+      singularity_enabled: true
+  toolshed.g2.bx.psu.edu/repos/genouest/braker3/braker3/.*:
+    cores: 6
+    mem: 4
+    params:
+      singularity_container_id_override: docker://teambraker/braker3:v.1.0.4
+      singularity_enabled: true
+    scheduling:
+      require:
+      - pulsar
   toolshed.g2.bx.psu.edu/repos/iracooke/protk_proteogenomics/.*:
     cores: 1
     mem: 3.8
@@ -950,7 +965,7 @@ tools:
       mem: 3.8
       scheduling:
         prefer:
-          - slurm
+        - slurm
     - id: abricate_medium_input_rule
       if: 0.005 <= input_size < 0.02
       cores: 4
@@ -1010,10 +1025,14 @@ tools:
       if: input_size < 0.5
       cores: 1
       mem: 3.8
+  toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/.*:
+    mem: 8
   toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/.*:
     scheduling:
       accept:
       - pulsar
+  toolshed.g2.bx.psu.edu/repos/iuc/biom_convert/biom_convert/.*:
+    mem: 12
   toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/3.*:
     cores: 2
     mem: 7.6
@@ -1106,6 +1125,14 @@ tools:
       if: 0.0002 <= input_size < 0.01
       cores: 2
       mem: 7.6
+  toolshed.g2.bx.psu.edu/repos/iuc/dada2_assigntaxonomyaddspecies/dada2_assignTaxonomyAddspecies/.*:
+    cores: 3
+    mem: 11.5
+    params:
+      singularity_enabled: true
+  toolshed.g2.bx.psu.edu/repos/iuc/dada2_dada/dada2_dada/.*:
+    cores: 2
+    mem: 10
   toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/.*:
     cores: 1
     mem: 3.8
@@ -1127,6 +1154,9 @@ tools:
     mem: 3.8
     params:
       singularity_enabled: true
+  toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/.*:
+    params:
+      singularity_enabled: true
   toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/.*:
     cores: 5
     mem: 19.1
@@ -1142,6 +1172,9 @@ tools:
     scheduling:
       accept:
       - pulsar
+  toolshed.g2.bx.psu.edu/repos/iuc/export2graphlan/export2graphlan/.*:
+    params:
+      singularity_enabled: true
   toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/.*:
     cores: 3
     mem: 11.5
@@ -1179,10 +1212,10 @@ tools:
     params:
       singularity_enabled: true
     scheduling:
-      prefer:
-        - pulsar
       require:
-        - gtdbtk_database
+      - gtdbtk_database
+      prefer:
+      - pulsar
   toolshed.g2.bx.psu.edu/repos/iuc/gtftobed12/gtftobed12/.*:
     params:
       singularity_enabled: true
@@ -1223,12 +1256,6 @@ tools:
   toolshed.g2.bx.psu.edu/repos/iuc/humann/humann/.*:
     cores: 32
     mem: 122.8
-    # scheduling:
-    #   accept:
-    #   - pulsar
-    #   reject:
-    #   - pulsar-mel2
-    #   - pulsar-QLD
     rules:
     - id: humann_small_input_rule
       if: input_size < 0.01
@@ -1301,6 +1328,9 @@ tools:
       accept:
       - pulsar
       - pulsar-quick
+  toolshed.g2.bx.psu.edu/repos/iuc/iwtomics_loadandplot/iwtomics_loadandplot/.*:
+    params:
+      singularity_enabled: true
   toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/.*:
     cores: 3
     mem: 11.5
@@ -1341,9 +1371,6 @@ tools:
       if: 0.1 <= input_size < 0.5
       cores: 16
       mem: 61.4
-  toolshed.g2.bx.psu.edu/repos/iuc/kraken_biom/kraken_biom/.*:
-    params:
-      singularity_enabled: true  
   toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/.*:
     cores: 16
     mem: 200
@@ -1363,6 +1390,9 @@ tools:
       execute: |
         from galaxy.jobs.mapper import JobNotReadyException
         raise JobNotReadyException()
+  toolshed.g2.bx.psu.edu/repos/iuc/kraken_biom/kraken_biom/.*:
+    params:
+      singularity_enabled: true
   toolshed.g2.bx.psu.edu/repos/iuc/krakentools_extract_kraken_reads/krakentools_extract_kraken_reads/.*:
     params:
       singularity_enabled: true
@@ -1370,10 +1400,13 @@ tools:
     params:
       singularity_enabled: true
   toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/.*:
-    params:
-      singularity_enabled: true
     cores: 7
     mem: 26.8
+    params:
+      singularity_enabled: true
+  toolshed.g2.bx.psu.edu/repos/iuc/links/links/.*:
+    cores: 4
+    mem: 15.3
   toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/.*:
     cores: 5
     mem: 19.1
@@ -1398,6 +1431,8 @@ tools:
       accept:
       - pulsar
       - pulsar-quick
+  toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/.*:
+    mem: 12
   toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgdiff/.*:
     scheduling:
       accept:
@@ -1518,7 +1553,8 @@ tools:
   toolshed.g2.bx.psu.edu/repos/iuc/mothur.*:
     params:
       docker_enabled: true
-      docker_run_extra_arguments: --pids-limit 10000 --ulimit fsize=1000000000 --env TERM=vt100
+      docker_run_extra_arguments: --pids-limit 10000 --ulimit fsize=1000000000 --env
+        TERM=vt100
   toolshed.g2.bx.psu.edu/repos/iuc/mothur_align_seqs/mothur_align_seqs/.*:
     cores: 7
     mem: 26.8
@@ -1733,6 +1769,9 @@ tools:
   toolshed.g2.bx.psu.edu/repos/iuc/mummer.*:
     params:
       singularity_enabled: true
+  toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/.*:
+    cores: 2
+    mem: 10
   toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/.*:
     cores: 5
     mem: 19.1
@@ -1768,54 +1807,54 @@ tools:
       if: 0.015 <= input_size < 1
       cores: 5
       mem: 19.1
-  toolshed.g2.bx.psu.edu/repos/iuc/picrust_categorize/picrust_categorize/.*:
+  toolshed.g2.bx.psu.edu/repos/iuc/phyml/phyml/.*:
+    cores: 120
+    mem: 1922
+    scheduling:
+      accept:
+      - pulsar
+      - pulsar-training-large
+  toolshed.g2.bx.psu.edu/repos/iuc/picrust2_add_descriptions/picrust2_add_descriptions/.*:
     params:
       singularity_enabled: true
-  toolshed.g2.bx.psu.edu/repos/iuc/picrust_compare_biom/picrust_compare_biom/.*:
+  toolshed.g2.bx.psu.edu/repos/iuc/picrust2_hsp/picrust2_hsp/.*:
     params:
       singularity_enabled: true
-  toolshed.g2.bx.psu.edu/repos/iuc/picrust_format_tree_and_trait_table/picrust_format_tree_and_trait_table/.*:
+  toolshed.g2.bx.psu.edu/repos/iuc/picrust2_metagenome_pipeline/picrust2_metagenome_pipeline/.*:
     params:
       singularity_enabled: true
-  toolshed.g2.bx.psu.edu/repos/iuc/picrust_metagenome_contributions/picrust_metagenome_contributions/.*:
+  toolshed.g2.bx.psu.edu/repos/iuc/picrust2_pathway_pipeline/picrust2_pathway_pipeline/.*:
     params:
       singularity_enabled: true
-  toolshed.g2.bx.psu.edu/repos/iuc/picrust_normalize_by_copy_number/picrust_normalize_by_copy_number/.*:
+  toolshed.g2.bx.psu.edu/repos/iuc/picrust2_pipeline/picrust2_pipeline/.*:
+    cores: 7
+    mem: 26.8
     params:
       singularity_enabled: true
-  toolshed.g2.bx.psu.edu/repos/iuc/picrust_predict_metagenomes/picrust_predict_metagenomes/.*:
+  toolshed.g2.bx.psu.edu/repos/iuc/picrust2_place_seqs/picrust2_place_seqs/.*:
     params:
       singularity_enabled: true
-  toolshed.g2.bx.psu.edu/repos/iuc/picrust2_add_descriptions/picrust2_add_descriptions/.*:
+  toolshed.g2.bx.psu.edu/repos/iuc/picrust2_shuffle_predictions/picrust2_shuffle_predictions/.*:
     params:
       singularity_enabled: true
-  toolshed.g2.bx.psu.edu/repos/iuc/picrust2_hsp/picrust2_hsp/.*:
+  toolshed.g2.bx.psu.edu/repos/iuc/picrust_categorize/picrust_categorize/.*:
     params:
       singularity_enabled: true
-  toolshed.g2.bx.psu.edu/repos/iuc/picrust2_metagenome_pipeline/picrust2_metagenome_pipeline/.*:
+  toolshed.g2.bx.psu.edu/repos/iuc/picrust_compare_biom/picrust_compare_biom/.*:
     params:
       singularity_enabled: true
-  toolshed.g2.bx.psu.edu/repos/iuc/picrust2_pathway_pipeline/picrust2_pathway_pipeline/.*:
+  toolshed.g2.bx.psu.edu/repos/iuc/picrust_format_tree_and_trait_table/picrust_format_tree_and_trait_table/.*:
     params:
       singularity_enabled: true
-  toolshed.g2.bx.psu.edu/repos/iuc/picrust2_pipeline/picrust2_pipeline/.*:
-    cores: 7
-    mem: 26.8
+  toolshed.g2.bx.psu.edu/repos/iuc/picrust_metagenome_contributions/picrust_metagenome_contributions/.*:
     params:
       singularity_enabled: true
-  toolshed.g2.bx.psu.edu/repos/iuc/picrust2_place_seqs/picrust2_place_seqs/.*:
+  toolshed.g2.bx.psu.edu/repos/iuc/picrust_normalize_by_copy_number/picrust_normalize_by_copy_number/.*:
     params:
       singularity_enabled: true
-  toolshed.g2.bx.psu.edu/repos/iuc/picrust2_shuffle_predictions/picrust2_shuffle_predictions/.*:
+  toolshed.g2.bx.psu.edu/repos/iuc/picrust_predict_metagenomes/picrust_predict_metagenomes/.*:
     params:
       singularity_enabled: true
-  toolshed.g2.bx.psu.edu/repos/iuc/phyml/phyml/.*:
-    cores: 120
-    mem: 1922
-    scheduling:
-      accept:
-      - pulsar
-      - pulsar-training-large
   toolshed.g2.bx.psu.edu/repos/iuc/pilon/pilon/.*:
     cores: 16
     mem: 61.4
@@ -1978,12 +2017,12 @@ tools:
     cores: 9
     mem: 34.5
   toolshed.g2.bx.psu.edu/repos/iuc/rnaspades/rnaspades/.*:
+    params:
+      singularity_enabled: true
     scheduling:
       accept:
       - pulsar
       - pulsar-training-large
-    params:
-      singularity_enabled: true
     rules:
     - id: rnaspades_small_input_rule
       if: input_size < 0.005
@@ -2058,6 +2097,18 @@ tools:
       if: 0.05 <= input_size < 0.5
       cores: 5
       mem: 19.1
+  toolshed.g2.bx.psu.edu/repos/iuc/scater_create_qcmetric_ready_sce/scater_create_qcmetric_ready_sce/.*:
+    params:
+      singularity_enabled: true
+  toolshed.g2.bx.psu.edu/repos/iuc/scater_filter/scater_filter/.*:
+    params:
+      singularity_enabled: true
+  toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_dist_scatter/scater_plot_dist_scatter/.*:
+    params:
+      singularity_enabled: true
+  toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_pca/scater_plot_pca/.*:
+    params:
+      singularity_enabled: true
   toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_seq/.*:
     cores: 20
     mem: 200
@@ -2585,6 +2636,8 @@ tools:
   toolshed.g2.bx.psu.edu/repos/peterjc/sample_seqs/sample_seqs/.*:
     params:
       singularity_enabled: true
+  toolshed.g2.bx.psu.edu/repos/peterjc/seq_select_by_id/seq_select_by_id/.*:
+    mem: 12
   toolshed.g2.bx.psu.edu/repos/pjbriggs/macs21/macs2_1_peakcalling/.*:
     cores: 9
     mem: 34.5
@@ -2592,8 +2645,8 @@ tools:
     cores: 3
     mem: 11.5
     env:
-      _JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G
       SINGULARITYENV__JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G
+      _JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G
     scheduling:
       accept:
       - pulsar
@@ -2618,6 +2671,9 @@ tools:
   toolshed.g2.bx.psu.edu/repos/recetox/.*:
     params:
       singularity_enabled: true
+  toolshed.g2.bx.psu.edu/repos/rnateam/chipseeker/chipseeker/.*:
+    params:
+      singularity_enabled: true
   toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/.*:
     cores: 8
     mem: 30.7
@@ -2668,11 +2724,6 @@ tools:
       if: input_size < 0.01
       cores: 1
       mem: 3.8
-  toolshed.g2.bx.psu.edu/repos/iuc/dada2_assigntaxonomyaddspecies/dada2_assignTaxonomyAddspecies/.*:
-    params:
-      singularity_enabled: true
-    cores: 3
-    mem: 11.5    
   .*bowtie2_index_builder_data_manager.*:
     cores: 16
     mem: 61.4
@@ -2765,6 +2816,26 @@ tools:
       require:
       - pulsar
       - pulsar-azure-gpu
+  cellranger:
+    cores: 6
+    mem: 20
+    params:
+      singularity_enabled: true
+    rules:
+    - if: |
+        not user or not 'cellranger' in [role.name for role in user.all_roles() if not role.deleted]
+      fail: Your account has not been given access to cellranger. Contact help@genome.edu.au
+        if you think this is in error.
+  fgenesh:
+    cores: 6
+    mem: 10
+    params:
+      singularity_enabled: true
+    rules:
+    - if: |
+        not user or not 'Fgenesh' in [role.name for role in user.all_roles() if not role.deleted]
+      fail: Your account has not been given access to fgenesh. Contact help@genome.edu.au
+        if you think this is in error.
   gtdbtk_classify_wf_test:
     cores: 16
     mem: 60
@@ -2811,35 +2882,4 @@ tools:
     mem: 19.1
     scheduling:
       accept:
-        - training-exempt # these jobs are exempt from training rules that would reduce allocated memory
-  cellranger:
-    cores: 6
-    mem: 20
-    params:
-      singularity_enabled: true
-    rules:
-      - if: |
-          not user or not 'cellranger' in [role.name for role in user.all_roles() if not role.deleted]
-        fail: Your account has not been given access to cellranger. Contact help@genome.edu.au if you think this is in error.
-  fgenesh:
-    cores: 6
-    mem: 10
-    params:
-      singularity_enabled: true
-    rules:
-      - if: |
-          not user or not 'Fgenesh' in [role.name for role in user.all_roles() if not role.deleted]
-        fail: Your account has not been given access to fgenesh. Contact help@genome.edu.au if you think this is in error.
-
-  toolshed.g2.bx.psu.edu/repos/genouest/braker3/braker3/.*:
-    mem: 4
-    cores: 6
-    params:
-      singularity_container_id_override: docker://teambraker/braker3:v.1.0.4
-      singularity_enabled: true
-    scheduling:
-      require:
-      - pulsar
-  toolshed.g2.bx.psu.edu/repos/iuc/links/links/.*:
-    cores: 4
-    mem: 15.3  
+      - training-exempt   # these jobs are exempt from training rules that would reduce allocated memory