From 86ccafcb75b8dc81a86b49b83cb8c70646f4b151 Mon Sep 17 00:00:00 2001
From: DLBPointon <damonlbp@hotmail.co.uk>
Date: Fri, 7 Feb 2025 14:29:31 +0000
Subject: [PATCH] Update

---
 assets/test-local.yaml | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)
 create mode 100755 assets/test-local.yaml

diff --git a/assets/test-local.yaml b/assets/test-local.yaml
new file mode 100755
index 0000000..c5e9ab5
--- /dev/null
+++ b/assets/test-local.yaml
@@ -0,0 +1,33 @@
+# 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