From 7f1ccb0a32d748bed899a6768d58ec17077d2cc4 Mon Sep 17 00:00:00 2001 From: ecwood Date: Wed, 26 Jul 2023 14:14:07 -0700 Subject: [PATCH] #332 file name changes in var file --- snakemake-config-var.yaml | 32 ++++++++++++++++---------------- 1 file changed, 16 insertions(+), 16 deletions(-) diff --git a/snakemake-config-var.yaml b/snakemake-config-var.yaml index 1747d067..faca9512 100644 --- a/snakemake-config-var.yaml +++ b/snakemake-config-var.yaml @@ -15,7 +15,7 @@ ont_output_nodes_file: ${BUILD_DIR}/${ont_output_base}${nodes_suffix}${test_suff ont_output_edges_file: ${BUILD_DIR}/${ont_output_base}${edges_suffix}${test_suffix}.jsonl semmeddb_extraction_base: extract-semmeddb -semmeddb_conversion_base: semmeddb_tuple_list_json_to_kg_json +semmeddb_conversion_base: semmeddb_tuplelist_json_to_kg_jsonl semmeddb_output_base: kg2-semmeddb semmeddb_extraction_script: ${CODE_DIR}/${semmeddb_extraction_base}.sh semmeddb_extraction_log: ${BUILD_DIR}/${semmeddb_extraction_base}${test_suffix}.log @@ -27,7 +27,7 @@ semmeddb_output_nodes_file: ${BUILD_DIR}/${semmeddb_output_base}${nodes_suffix}$ semmeddb_output_edges_file: ${BUILD_DIR}/${semmeddb_output_base}${edges_suffix}${test_suffix}.jsonl uniprotkb_extraction_base: extract-uniprotkb -uniprotkb_conversion_base: uniprotkb_dat_to_json +uniprotkb_conversion_base: uniprotkb_dat_to_kg_jsonl uniprotkb_output_base: kg2-uniprotkb uniprotkb_extraction_script: ${CODE_DIR}/${uniprotkb_extraction_base}.sh uniprotkb_extraction_log: ${BUILD_DIR}/${uniprotkb_extraction_base}${test_suffix}.log @@ -38,7 +38,7 @@ uniprotkb_output_nodes_file: ${BUILD_DIR}/${uniprotkb_output_base}${nodes_suffix uniprotkb_output_edges_file: ${BUILD_DIR}/${uniprotkb_output_base}${edges_suffix}${test_suffix}.jsonl ensembl_extraction_base: extract-ensembl -ensembl_conversion_base: ensembl_json_to_kg_json +ensembl_conversion_base: ensembl_json_to_kg_jsonl ensembl_output_base: kg2-ensembl ensembl_extraction_script: ${CODE_DIR}/${ensembl_extraction_base}.sh ensembl_extraction_log: ${BUILD_DIR}/${ensembl_extraction_base}${test_suffix}.log @@ -71,7 +71,7 @@ chembl_output_nodes_file: ${BUILD_DIR}/${chembl_output_base}${nodes_suffix}${tes chembl_output_edges_file: ${BUILD_DIR}/${chembl_output_base}${edges_suffix}${test_suffix}.jsonl ncbigene_extraction_base: extract-ncbigene -ncbigene_conversion_base: ncbigene_tsv_to_kg_json +ncbigene_conversion_base: ncbigene_tsv_to_kg_jsonl ncbigene_output_base: kg2-ncbigene ncbigene_extraction_script: ${CODE_DIR}/${ncbigene_extraction_base}.sh ncbigene_extraction_log: ${BUILD_DIR}/${ncbigene_extraction_base}${test_suffix}.log @@ -93,7 +93,7 @@ dgidb_output_nodes_file: ${BUILD_DIR}/${dgidb_output_base}${nodes_suffix}${test_ dgidb_output_edges_file: ${BUILD_DIR}/${dgidb_output_base}${edges_suffix}${test_suffix}.jsonl repodb_extraction_base: extract-repodb -repodb_conversion_base: repodb_csv_to_kg_json +repodb_conversion_base: repodb_csv_to_kg_jsonl repodb_output_base: kg2-repodb repodb_extraction_script: ${CODE_DIR}/${repodb_extraction_base}.sh repodb_extraction_log: ${BUILD_DIR}/${repodb_extraction_base}${test_suffix}.log @@ -105,7 +105,7 @@ repodb_output_nodes_file: ${BUILD_DIR}/${repodb_output_base}${nodes_suffix}${tes repodb_output_edges_file: ${BUILD_DIR}/${repodb_output_base}${edges_suffix}${test_suffix}.jsonl drugbank_extraction_base: extract-drugbank -drugbank_conversion_base: drugbank_xml_to_kg_json +drugbank_conversion_base: drugbank_xml_to_kg_jsonl drugbank_output_base: kg2-drugbank drugbank_extraction_script: ${CODE_DIR}/${drugbank_extraction_base}.sh drugbank_extraction_log: ${BUILD_DIR}/${drugbank_extraction_base}${test_suffix}.log @@ -116,7 +116,7 @@ drugbank_output_nodes_file: ${BUILD_DIR}/${drugbank_output_base}${nodes_suffix}$ drugbank_output_edges_file: ${BUILD_DIR}/${drugbank_output_base}${edges_suffix}${test_suffix}.jsonl smpdb_extraction_base: extract-smpdb -smpdb_conversion_base: smpdb_csv_to_kg_json +smpdb_conversion_base: smpdb_csv_to_kg_jsonl smpdb_output_base: kg2-smpdb smpdb_extraction_script: ${CODE_DIR}/${smpdb_extraction_base}.sh smpdb_extraction_log: ${BUILD_DIR}/${smpdb_extraction_base}${test_suffix}.log @@ -128,7 +128,7 @@ smpdb_output_nodes_file: ${BUILD_DIR}/${smpdb_output_base}${nodes_suffix}${test_ smpdb_output_edges_file: ${BUILD_DIR}/${smpdb_output_base}${edges_suffix}${test_suffix}.jsonl hmdb_extraction_base: extract-hmdb -hmdb_conversion_base: hmdb_xml_to_kg_json +hmdb_conversion_base: hmdb_xml_to_kg_jsonl hmdb_output_base: kg2-hmdb hmdb_extraction_script: ${CODE_DIR}/${hmdb_extraction_base}.sh hmdb_extraction_log: ${BUILD_DIR}/${hmdb_extraction_base}${test_suffix}.log @@ -139,7 +139,7 @@ hmdb_output_nodes_file: ${BUILD_DIR}/${hmdb_output_base}${nodes_suffix}${test_su hmdb_output_edges_file: ${BUILD_DIR}/${hmdb_output_base}${edges_suffix}${test_suffix}.jsonl go_annotations_extraction_base: extract-go-annotations -go_annotations_conversion_base: go_gpa_to_kg_json +go_annotations_conversion_base: go_gpa_to_kg_jsonl go_annotations_output_base: kg2-go-annotations go_annotations_extraction_script: ${CODE_DIR}/${go_annotations_extraction_base}.sh go_annotations_extraction_log: ${BUILD_DIR}/${go_annotations_extraction_base}${test_suffix}.log @@ -150,7 +150,7 @@ go_annotations_output_nodes_file: ${BUILD_DIR}/${go_annotations_output_base}${no go_annotations_output_edges_file: ${BUILD_DIR}/${go_annotations_output_base}${edges_suffix}${test_suffix}.jsonl reactome_extraction_base: extract-reactome -reactome_conversion_base: reactome_mysql_to_kg_json +reactome_conversion_base: reactome_mysql_to_kg_jsonl reactome_output_base: kg2-reactome reactome_extraction_script: ${CODE_DIR}/${reactome_extraction_base}.sh reactome_extraction_log: ${BUILD_DIR}/${reactome_extraction_base}${test_suffix}.log @@ -161,7 +161,7 @@ reactome_output_nodes_file: ${BUILD_DIR}/${reactome_output_base}${nodes_suffix}$ reactome_output_edges_file: ${BUILD_DIR}/${reactome_output_base}${edges_suffix}${test_suffix}.jsonl mirbase_extraction_base: extract-mirbase -mirbase_conversion_base: mirbase_dat_to_kg_json +mirbase_conversion_base: mirbase_dat_to_kg_jsonl mirbase_output_base: kg2-mirbase mirbase_extraction_script: ${CODE_DIR}/${mirbase_extraction_base}.sh mirbase_extraction_log: ${BUILD_DIR}/${mirbase_extraction_base}${test_suffix}.log @@ -172,7 +172,7 @@ mirbase_output_nodes_file: ${BUILD_DIR}/${mirbase_output_base}${nodes_suffix}${t mirbase_output_edges_file: ${BUILD_DIR}/${mirbase_output_base}${edges_suffix}${test_suffix}.jsonl jensenlab_extraction_base: extract-jensenlab -jensenlab_conversion_base: jensenlab_tsv_to_kg_json +jensenlab_conversion_base: jensenlab_tsv_to_kg_jsonl jensenlab_output_base: kg2-jensenlab jensenlab_extraction_script: ${CODE_DIR}/${jensenlab_extraction_base}.sh jensenlab_extraction_log: ${BUILD_DIR}/${jensenlab_extraction_base}${test_suffix}.log @@ -183,7 +183,7 @@ jensenlab_output_nodes_file: ${BUILD_DIR}/${jensenlab_output_base}${nodes_suffix jensenlab_output_edges_file: ${BUILD_DIR}/${jensenlab_output_base}${edges_suffix}${test_suffix}.jsonl drugcentral_extraction_base: extract-drugcentral -drugcentral_conversion_base: drugcentral_json_to_kg_json +drugcentral_conversion_base: drugcentral_json_to_kg_jsonl drugcentral_output_base: kg2-drugcentral drugcentral_extraction_script: ${CODE_DIR}/${drugcentral_extraction_base}.sh drugcentral_extraction_log: ${BUILD_DIR}/${drugcentral_extraction_base}${test_suffix}.log @@ -195,7 +195,7 @@ drugcentral_output_nodes_file: ${BUILD_DIR}/${drugcentral_output_base}${nodes_su drugcentral_output_edges_file: ${BUILD_DIR}/${drugcentral_output_base}${edges_suffix}${test_suffix}.jsonl intact_extraction_base: extract-intact -intact_conversion_base: intact_tsv_to_kg_json +intact_conversion_base: intact_tsv_to_kg_jsonl intact_output_base: kg2-intact intact_extraction_script: ${CODE_DIR}/${intact_extraction_base}.sh intact_extraction_log: ${BUILD_DIR}/${intact_extraction_base}${test_suffix}.log @@ -206,7 +206,7 @@ intact_output_nodes_file: ${BUILD_DIR}/${intact_output_base}${nodes_suffix}${tes intact_output_edges_file: ${BUILD_DIR}/${intact_output_base}${edges_suffix}${test_suffix}.jsonl disgenet_extraction_base: extract-disgenet -disgenet_conversion_base: disgenet_tsv_to_kg_json +disgenet_conversion_base: disgenet_tsv_to_kg_jsonl disgenet_output_base: kg2-disgenet disgenet_extraction_script: ${CODE_DIR}/${disgenet_extraction_base}.sh disgenet_extraction_log: ${BUILD_DIR}/${disgenet_extraction_base}${test_suffix}.log @@ -217,7 +217,7 @@ disgenet_output_nodes_file: ${BUILD_DIR}/${disgenet_output_base}${nodes_suffix}$ disgenet_output_edges_file: ${BUILD_DIR}/${disgenet_output_base}${edges_suffix}${test_suffix}.jsonl kegg_extraction_base: extract-kegg -kegg_conversion_base: kegg_json_to_kg_json +kegg_conversion_base: kegg_json_to_kg_jsonl kegg_output_base: kg2-kegg kegg_extraction_script: ${CODE_DIR}/${kegg_extraction_base}.sh kegg_extraction_log: ${BUILD_DIR}/${kegg_extraction_base}${test_suffix}.log