From 5dd78846ed7c9f73e64cebdc51fb15fd6f00c340 Mon Sep 17 00:00:00 2001
From: cat-bro <cathjb@gmail.com>
Date: Fri, 23 May 2025 13:21:59 +1000
Subject: [PATCH 1/2] prepend existing rule ids with 'tpvdb_'
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Make rule IDs to start with “tpvdb_” to provide better insight into their provenance.

This could break some logic for anyone already overriding these rules by ID downstream, but it seems like a sensible change while there are not many rules in the tpvdb.
---
 tools.yml | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/tools.yml b/tools.yml
index d33e176..f0da3fd 100644
--- a/tools.yml
+++ b/tools.yml
@@ -217,7 +217,7 @@ tools:
     cores: 20
     mem: 120
     rules:
-    - id: hifiasm_small_input_rule
+    - id: tpvdb_hifiasm_small_input_rule
       if: input_size <= 0.2
       cores: 6
       mem: 40
@@ -235,7 +235,7 @@ tools:
     cores: 8
     mem: 40
     rules:
-    - id: interproscan_metagenome_input_rule
+    - id: tpvdb_interproscan_metagenome_input_rule
       if: input_size > 0.9
       cores: 10
       mem: 80
@@ -322,7 +322,7 @@ tools:
     mem: 8
   toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/.*:
     rules:
-    - id: tp_sort_header_tool_large_input_rule
+    - id: tpvdb_tp_sort_header_tool_large_input_rule
       if: input_size > 0.8
       mem: 10
   toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/.*:
@@ -444,7 +444,7 @@ tools:
     mem: 20
   toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS.*:
     rules:
-    - id: EMBOSS_large_input_rule
+    - id: tpvdb_EMBOSS_large_input_rule
       if: input_size > 0.6
       mem: 10
   'toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: fuzztran39/.*':
@@ -488,7 +488,7 @@ tools:
     cores: 8
     mem: 40
     rules:
-    - id: pulsar_rule
+    - id: tpvdb_ncbi_blastp_wrapper_pulsar_rule
       if: |
         helpers.job_args_match(job, app, {'db_opts': {'db_opts_selector': 'db'}})
       scheduling:
@@ -561,7 +561,7 @@ tools:
     env:
       TERM: vt100
     rules:
-    - id: lotus2_small_input_rule
+    - id: tpvdb_lotus2_small_input_rule
       if: input_size < 0.1
       mem: 8
   toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/t_coffee/.*:
@@ -1275,7 +1275,7 @@ tools:
   toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/.*:
     mem: 30
     rules:
-    - id: fasttree_small_input_rule
+    - id: tpvdb_fasttree_small_input_rule
       if: input_size < 0.005
       mem: 8
   toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/.*:
@@ -1289,7 +1289,7 @@ tools:
     cores: 8
     mem: 40
     rules:
-    - id: funannotate_annotate_large_input
+    - id: tpvdb_funannotate_annotate_large_input_rule
       if: input_size > 3.2
       mem: 62
   toolshed.g2.bx.psu.edu/repos/iuc/funannotate_clean/funannotate_clean/.*:
@@ -2210,7 +2210,7 @@ tools:
   toolshed.g2.bx.psu.edu/repos/iuc/novoplasty/novoplasty/.*:
     mem: 40
     rules:
-    - id: novoplasty_small_input_rule
+    - id: tpvdb_novoplasty_small_input_rule
       if: input_size < 0.2
       mem: 8
   toolshed.g2.bx.psu.edu/repos/iuc/ont_fast5_api_compress_fast5/ont_fast5_api_compress_fast5/.*:

From 57811be8feb3b7838f406a228ae6b1ba576da611 Mon Sep 17 00:00:00 2001
From: cat-bro <cathjb@gmail.com>
Date: Fri, 23 May 2025 14:22:31 +1000
Subject: [PATCH 2/2] fix existing format errors

---
 tools.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tools.yml b/tools.yml
index f0da3fd..916dd3c 100644
--- a/tools.yml
+++ b/tools.yml
@@ -2581,12 +2581,12 @@ tools:
     mem: 32
   toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_fillpeaks/abims_xcms_fillPeaks/.*:
     mem: 32
-  toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_retcor/abims_xcms_retcor/.*:
-    mem: 32
   toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_group/.*:
     mem: 32
   toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_merge/abims_xcms_merge/.*:
     mem: 32
+  toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_retcor/abims_xcms_retcor/.*:
+    mem: 32
   toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/.*:
     cores: 8
     mem: 28
@@ -2678,8 +2678,8 @@ tools:
     cores: 4
     mem: 32
   toolshed.g2.bx.psu.edu/repos/recetox/recetox_aplcms_align_features/recetox_aplcms_align_features/.*:
-    mem: 64
     cores: 4
+    mem: 64
   toolshed.g2.bx.psu.edu/repos/recetox/recetox_aplcms_compute_clusters/recetox_aplcms_compute_clusters/.*:
     mem: 16