never trust the linter

usegalaxy-eu · May 13, 2024 · 3993b0d · 3993b0d
1 parent ad31ecd
commit 3993b0d
Showing 1 changed file with 20 additions and 20 deletions.
diff --git a/files/galaxy/tpv/tools.yml b/files/galaxy/tpv/tools.yml
@@ -22,17 +22,17 @@ tools:
       - id: no-pulsar
         if: user is not None
         execute: |
-            from tpv.core.entities import Tag, TagSetManager, TagType
+          from tpv.core.entities import Tag, TagSetManager, TagType
 
-            user_preferences = user.extra_preferences
-            pulsar_tag = user_preferences.get("distributed_compute|remote_resources", "None")
-            pulsar_tag = Tag("scheduling", pulsar_tag, TagType.REQUIRE) if pulsar_tag != "None" else None
+          user_preferences = user.extra_preferences
+          pulsar_tag = user_preferences.get("distributed_compute|remote_resources", "None")
+          pulsar_tag = Tag("scheduling", pulsar_tag, TagType.REQUIRE) if pulsar_tag != "None" else None
 
-            entity.tpv_tags.tags = [
-                tag
-                for tag in entity.tpv_tags.tags
-                if tag != pulsar_tag
-            ]
+          entity.tpv_tags.tags = [
+              tag
+              for tag in entity.tpv_tags.tags
+              if tag != pulsar_tag
+          ]
 
     env:
       TEMP: /data/1/galaxy_db/tmp
@@ -282,13 +282,13 @@ tools:
         params:
           singularity_run_extra_arguments: "--env ALPHAFOLD_DB=/data/db/databases/alphafold_databases/2.3/,ALPHAFOLD_USE_GPU=False"
       - if: helpers.tool_version_gte(tool, '2.3.1+galaxy2')
-        params:
-          singularity_run_extra_arguments: "--env ALPHAFOLD_DB=/data/db/databases/alphafold_databases,ALPHAFOLD_USE_GPU=False"
         execute: |
           from random import SystemRandom
           if SystemRandom().random() < 0.10:
-              entity.gpus = 1
-              entity.params['singularity_run_extra_arguments'] = '--env ALPHAFOLD_DB=/data/db/databases/alphafold_databases,ALPHAFOLD_USE_GPU=True'
+            entity.gpus = 1
+            entity.params['singularity_run_extra_arguments'] = '--env ALPHAFOLD_DB=/data/db/databases/alphafold_databases,ALPHAFOLD_USE_GPU=True'
+          else:
+            entity.params['singularity_run_extra_arguments'] = '--env ALPHAFOLD_DB=/data/db/databases/alphafold_databases,ALPHAFOLD_USE_GPU=False"
         # tweak amount of requested memory depending on the AlphaFold model to be run
       - id: model_preset_multimer
         if: job.get_param_values(app).get("model_preset") == "multimer"
@@ -341,7 +341,7 @@ tools:
     cores: 1
     mem: 30
     params:
-      docker_run_extra_arguments: ' --gpus all '
+      docker_run_extra_arguments: " --gpus all "
     env:
       GPU_AVAILABLE: 1
   toolshed.g2.bx.psu.edu/repos/bgruening/whisper/whisper/.*:
@@ -715,7 +715,7 @@ tools:
     mem: 30
     gpus: 1
     params:
-      singularity_run_extra_arguments: ' --nv '
+      singularity_run_extra_arguments: " --nv "
     scheduling:
       require:
         - singularity
@@ -852,7 +852,7 @@ tools:
           Too much data, we cannot support such large Trinity assemblies with our
           backend. Please use another server for your job.
 
-  '.*mothur_.*':
+  ".*mothur_.*":
     cores: 1
     mem: 90
     params:
@@ -865,7 +865,7 @@ tools:
         # see https://github.com/galaxyproject/galaxy/issues/16121#issuecomment-1555153421
         ##- embedded-pulsar
 
-  '.*mothur_classify_seqs.*':
+  ".*mothur_classify_seqs.*":
     cores: 2
     mem: 20
     params:
@@ -878,7 +878,7 @@ tools:
         # see https://github.com/galaxyproject/galaxy/issues/16121#issuecomment-1555153421
         ##- embedded-pulsar
 
-  '.*bioext_bam2msa.*':
+  ".*bioext_bam2msa.*":
     params:
       docker_run_extra_arguments: --pids-limit 10000 --ulimit fsize=1000000000 --env TERM=vt100
       docker_volumes: "$_CONDOR_SCRATCH_DIR:rw,$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/data/db/:ro,/data/dnb01/galaxy_db/:ro,/data/dnb02/galaxy_db/:ro,/data/dnb-ds03/galaxy_db/:ro,/data/dnb05/galaxy_db/:ro,/data/dnb06/galaxy_db/:rw,/data/dnb07/galaxy_db/:rw,,/data/dnb08/galaxy_db/:rw,/data/dnb-ds02/galaxy_db/:ro,/data/dp01/galaxy_db/:rw,/data/0/galaxy_db/:ro,/data/1/galaxy_db/:ro,/data/2/galaxy_db/:ro,/data/3/galaxy_db/:ro,/data/4/galaxy_db/:ro,/data/5/galaxy_import/galaxy_user_data/:ro,/data/6/galaxy_db/:ro,/data/7/galaxy_db/:ro,/usr/local/tools/:ro"
@@ -888,7 +888,7 @@ tools:
         - docker
         - embedded-pulsar
 
-  'last_*':
+  "last_*":
     params:
       docker_run_extra_arguments: --pids-limit 10000 --ulimit fsize=1000000000 --env TERM=vt100
       docker_volumes: "$_CONDOR_SCRATCH_DIR:rw,$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/data/db/:ro,/data/dnb01/galaxy_db/:ro,/data/dnb02/galaxy_db/:ro,/data/dnb-ds03/galaxy_db/:ro,/data/dnb05/galaxy_db/:ro,/data/dnb06/galaxy_db/:rw,/data/dnb07/galaxy_db/:rw,/data/dp01/galaxy_db/:rw,/data/0/galaxy_db/:ro,/data/1/galaxy_db/:ro,/data/2/galaxy_db/:ro,/data/3/galaxy_db/:ro,/data/4/galaxy_db/:ro,/data/5/galaxy_import/galaxy_user_data/:ro,/data/6/galaxy_db/:ro,/data/7/galaxy_db/:ro,/usr/local/tools/:ro"
@@ -964,7 +964,7 @@ tools:
       require:
         - singularity
         - conda
-# Not for Pulsar, or is the file copied?
+  # Not for Pulsar, or is the file copied?
   toolshed.g2.bx.psu.edu/repos/climate/cds_essential_variability/cds_essential_variability/.*:
     env:
       COPERNICUS_CDSAPIRC_KEY_FILE: /data/db/data_managers/COPERNICUS_CDSAPIRC_KEY_FILE