Merge pull request #421 from sanger-tol/schema_update

changed assem_id type

Author: weaglesBio

assets/local_testing/nxOscSUBSET.yaml

@@ -19,7 +19,7 @@ hic_data:
 kmer_profile:
   # kmer_length will act as input for kmer_read_cov fastk and as the name of folder in profile_dir
   kmer_length: 31
-  dir: /lustre/scratch123/tol/resources/treeval/treeval-testdata/TreeValSmallData/genomic_data/nxOscSpes1/pacbio/
+  profile: /lustre/scratch123/tol/resources/treeval/treeval-testdata/TreeValSmallData/genomic_data/nxOscSpes1/pacbio/
 alignment:
   genesets:
     - /lustre/scratch123/tol/resources/treeval/treeval-testdata/TreeValSmallData/gene_set/nematode/csv_data/CaenorhabditisElegans.WBcel235-data.csv

assets/schema_input.json

@@ -13,7 +13,7 @@
                     "errorMessage": "Assembly level must be provided"
                 },
                 "assem_version": {
-                    "type": "integer",
+                    "anyOf": [{ "type": "string" }, { "type": "integer" }],
                     "errorMessage": "Assembly version must be provided"
                 },
                 "sample_id": {

subworkflows/local/yaml_input/main.nf

@@ -55,7 +55,7 @@ workflow YAML_INPUT {
                 data.assem_reads.supplementary_data,
             )
             genesets: (id == "FULL" || id == "JBROWSE" ? data.alignment.genesets.collect { geneset_path -> file(geneset_path, checkIfExists: true) } : [])
-            synteny: (data.synteny ? data.synteny.collect { fasta -> file(fasta, checkIfExists: true) } : [])
+            synteny: (id == "FULL" || id == "JBROWSE" ? (data.synteny ? data.synteny.collect { fasta -> file(fasta, checkIfExists: true) } : []) : [])
             intron_size: (id == "FULL" ? data.intron.size : "")
             teloseq: data.telomere.teloseq
             busco_lineage: data.busco.lineage