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