Adjusted parameter name for rg.curation.polish #7 #8

draeger-lab · Nov 18, 2024 · 755be41 · 755be41
1 parent 50f0b72
commit 755be41
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Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/src/specimen/cmpb/workflow.py b/src/specimen/cmpb/workflow.py
@@ -167,7 +167,7 @@ def between_analysis(model: Model, cfg:dict, step:str):
         current_libmodel = polish(current_libmodel, 
                                   email = config['tech-resources']['email'],
                                   id_db = config['general']['namespace'],
-                                  refseq_gff = config['general']['refseq_gff'],
+                                  gff = config['general']['gff'],
                                   protein_fasta = config['general']['protein_fasta'],
                                   lab_strain = config['cm-polish']['is_lab_strain'],
                                   kegg_organism_id = config['general']['kegg_organism_id'],

diff --git a/src/specimen/data/config/cmpb_config.yaml b/src/specimen/data/config/cmpb_config.yaml
@@ -31,7 +31,7 @@ general:
   stats_always_on: False     # Calculate the model statistics after every step
 
   # Options used by multiple steps of the workflow
-  refseq_gff: USER           # Path to RefSeq GFF file: 
+  gff: USER                  # Path to RefSeq/Genbank GFF file:
                              # Can be optionally provided for cm-polish.
   kegg_organism_id: USER     # KEGG ID of the organism: Required for gap analysis with 'KEGG'.
                              # Can be optionally provided for cm-polish.

diff --git a/src/specimen/util/set_up.py b/src/specimen/util/set_up.py
@@ -35,7 +35,7 @@
                              'mnx_chem_prop', 'mnx_chem_xref','mnx_reac_prop','mnx_reac_xref',
                              'media_analysis'] #: :meta: 
 CMPB_CONFIG_PATHS_REQUIRED = ['mediapath'] #: :meta:
-CMPB_CONFIG_PATHS_OPTIONAL = ['modelpath','full_genome_sequence','refseq_gff', 'protein_fasta',
+CMPB_CONFIG_PATHS_OPTIONAL = ['modelpath','full_genome_sequence','gff', 'protein_fasta',
                               'gene-table','reacs-table','gff','swissprot-dmnd',
                               'swissprot-mapping'] # :meta:
 PIPELINE_PATHS_OPTIONAL = {'hqtb':HQTB_CONFIG_PATH_OPTIONAL,