Update

assets/test-local.yaml

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+# General Vales for all subpiplines and modules
+assembly_id: grTriPseu1
+reference_hap1: /nfs/treeoflife-01/teams/tola/users/dp24/ear/TreeValTinyData/assembly/draft/grTriPseu1.fa
+reference_hap2: /nfs/treeoflife-01/teams/tola/users/dp24/ear/TreeValTinyData/assembly/draft/grTriPseu1-hap.fa
+reference_haplotigs: /nfs/treeoflife-01/teams/tola/users/dp24/ear/TreeValTinyData/assembly/draft/grTriPseu1-all_hap.fa
+
+# If a mapped bam already exists use the below + --mapped TRUE on the nextflow command else ignore.
+mapped_bam: []
+
+merquryfk:
+  fastk_hist: "./EMPTY.hist"
+  fastk_ktab: "./EMPTY.ktab"
+
+# Used by both subpipelines
+longread:
+  type: hifi
+  dir: /nfs/treeoflife-01/teams/tola/users/dp24/ear/TreeValTinyData/genomic_data/pacbio/
+
+curationpretext:
+  aligner: minimap2
+  telomere_motif: TTAGGG
+  hic_dir: /home/runner/work/ear/ear/TreeValTinyData/genomic_data/hic-arima/
+btk:
+  taxid: 352914
+  gca_accession: GCA_0001
+  lineages: "fungi_odb10"
+  nt_database: /home/runner/work/ascc/ascc/NT_database/
+  nt_database_prefix: 18S_fungal_sequences
+  diamond_uniprot_database_path: /home/runner/work/ascc/ascc/diamond/UP000000212_1234679_tax.dmnd
+  diamond_nr_database_path: /home/runner/work/ascc/ascc/diamond/UP000000212_1234679_tax.dmnd
+  ncbi_taxonomy_path: /home/runner/work/ascc/ascc/ncbi_taxdump/
+  ncbi_rankedlineage_path: /home/runner/work/ascc/ascc/ncbi_taxdump/rankedlineage.dmp
+  config: /home/runner/work/ear/ear/conf/sanger-tol-btk.config