Corrections to yaml file

sanger-tol · Nov 22, 2023 · dcf727e · dcf727e
1 parent f26b906
commit dcf727e
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Showing 3 changed files with 16 additions and 15 deletions.
diff --git a/assets/github_testing/TreeValTinyTest.yaml b/assets/github_testing/TreeValTinyTest.yaml
@@ -1,16 +1,16 @@
 assembly:
-  level: scaffold
+  assem_level: scaffold
   sample_id: grTriPseu1
   latin_name: to_provide_taxonomic_rank
-  classT: fungi
-  asmVersion: 1
-  dbVersion: "1"
-  gevalType: DTOL
+  defined_class: fungi
+  assem_version: 1
+  project_id: DTOL
 reference_file: /home/runner/work/treeval/treeval/TreeValTinyData/assembly/draft/grTriPseu1.fa
 assem_reads:
-  pacbio: /home/runner/work/treeval/treeval/TreeValTinyData/genomic_data/pacbio/
-  hic: /home/runner/work/treeval/treeval/TreeValTinyData/genomic_data/hic-arima/
-  supplementary: path
+  longread_type: hifi
+  longread_data: /home/runner/work/treeval/treeval/TreeValTinyData/genomic_data/pacbio/
+  hic_data: /home/runner/work/treeval/treeval/TreeValTinyData/genomic_data/hic-arima/
+  supplementary_data: path
 alignment:
   data_dir: /home/runner/work/treeval/treeval/TreeValTinyData/gene_alignment_data/
   common_name: "" # For future implementation (adding bee, wasp, ant etc)

diff --git a/assets/local_testing/nxOscDF5033-BGA.yaml b/assets/local_testing/nxOscDF5033-BGA.yaml
@@ -1,9 +1,10 @@
 assembly:
+  assem_level: scaffold
   sample_id: Oscheius_DF5033
   latin_name: to_provide_taxonomic_rank # Not currently in use
-  classT: nematode
-  asmVersion: 1
-  gevalType: DTOL
+  defined_class: nematode
+  assem_version: 1
+  project_id: DTOL
 reference_file: /workspace/treeval-curation/Oscheius_DF5033/genomic_data/Oscheius_DF5033.fa
 assem_reads:
   pacbio: /workspace/treeval-curation/Oscheius_DF5033/pacbio/

diff --git a/assets/local_testing/nxOscSUBSET.yaml b/assets/local_testing/nxOscSUBSET.yaml
@@ -1,10 +1,10 @@
 assembly:
-  level: scaffold
+  assem_level: scaffold
   sample_id: OscheiusSUBSET
   latin_name: to_provide_taxonomic_rank
-  classT: nematode
-  asmVersion: 1
-  gevalType: DTOL
+  defined_class: nematode
+  assem_version: 1
+  project_id: DTOL
 reference_file: /lustre/scratch123/tol/resources/treeval/treeval-testdata/TreeValSmallData/Oscheius_SUBSET/assembly/draft/SUBSET_genome/Oscheius_SUBSET.fasta
 #/lustre/scratch123/tol/resources/treeval/nextflow_test_data/Oscheius_DF5033/assembly/draft/DF5033.hifiasm.noTelos.20211120/DF5033.noTelos.hifiasm.purged.noCont.noMito.fasta
 assem_reads: