#332 file name changes in var file

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