Integrated file workflow as alt to database

workflows/cath-shared-files.nf

@@ -26,7 +26,7 @@ process create_cath_dataset_from_files {
     grep -F -f uniprot_ids_csv all_af_uniprot_md5_csv > filtered_af_uniprot_md5_csv
     cath-af-cli create-cath-dataset-from-files \
         --src_af_uniprot_md5 filtered_crh_csv \
-        --src_crh filtered_af_crh \
+        --src_decorated_crh ${params.src_decorated_crh } \
         --csv_uniprot_ids uniprot_ids_csv \
         --csv_uniprot_md5 ${params.uniprot_md5_csv_fn} \
         --gene3d_crh_output ${params.gene3d_crh_output_fn} \

workflows/cath-wf-test-files.nf

@@ -0,0 +1,52 @@
+#!/usr/bin/env nextflow
+nextflow.enable.dsl=2
+
+// Params defined before include are also used in the processes
+params.dataset_name = 'dataset10'//'dataset200000'
+params.dataset_dir = "$workflow.launchDir/tests/fixtures/${params.dataset_name}/${params.dataset_name}"
+params.publish_dir = "$workflow.launchDir/results-${params.dataset_name}"
+
+
+params.uniprot_md5_csv_fn = "uniprot_md5.csv"
+params.uniprot_ids_csv_fn = "uniprot_ids.csv"
+params.gene3d_crh_output_fn = "gene3d_crh_output.csv"
+params.af_domainlist_ids_csv_fn = "af_domainlist_ids.csv"
+params.af_chainlist_ids_csv_fn = "af_chainlist_ids.csv"
+params.af_cath_orig_annotations_csv_fn = "af_cath_orig_annotations.csv"
+
+params.src_decorated_crh = "${params.dataset_dir}.decorated_crh.csv"
+params.src_af_uniprot_md5 = "${params.dataset_dir}.af_uniprot_md5.csv"
+params.csv_uniprot_md5 = "${params.dataset_dir}.uniprot_ids.csv"
+params.gene3d_crh_output = "${params.dataset_dir}.gene_3d_crh.csv"
+params.af_domainlist_ids = "${params.dataset_dir}.csv"
+params.af_chainlist_ids = "${params.dataset_dir}.csv"
+
+
+
+// Processes to include from the shared module
+include { create_cath_dataset_from_files } from './cath-shared-files'
+
+// Submodule workflows to include
+include { GATHER_CIF } from './cath-module-core'
+include { AF_ANNOTATE_DOMAINS_CIF } from './cath-module-kinfams'
+
+// Params defined after include are used locally
+params.uniprot_domain_ids_csv_fn = "uniprot_domain_ids.csv"
+params.all_crh_csv = "${params.dataset_dir}.af_uniprot_md5.csv"
+params.all_af_uniprot_md5 = "${params.dataset_dir}.uniprot_ids.csv"
+
+
+
+
+workflow {
+
+    //The first 2 are commented out due to missing domain file in dataset10 - dataset10.uniprot_domain_ids.csv 
+
+    def uniprot_domain_ids_path = "${params.dataset_dir}.${params.uniprot_domain_ids_csv_fn}"
+
+    GATHER_CIF(uniprot_domain_ids_path)
+
+    def uniprot_csv_ch = AF_ANNOTATE_DOMAINS_CIF()
+
+    def uniprot_dataset = create_cath_dataset_from_files(uniprot_csv_ch, params.all_crh_csv, params.all_af_uniprot_md5)            
+}

workflows/cath-wf-test.nf

@@ -0,0 +1,25 @@
+#!/usr/bin/env nextflow
+nextflow.enable.dsl=2
+
+// Params defined before include are also used in the processes
+params.dataset_name = 'dataset100'
+
+// Processes to include from the shared module
+include { create_cath_dataset_from_db } from './cath-shared-database'
+
+// Submodule workflows to include
+include { GATHER_CIF } from './cath-module-core'
+include { AF_ANNOTATE_DOMAINS_CIF } from './cath-module-kinfams'
+
+// Params defined after include are used locally
+params.dataset_dir = "$workflow.launchDir/tests/fixtures/${params.dataset_name}"
+params.uniprot_domain_ids_csv_fn = "${params.dataset_name}.uniprot_domain_ids.csv"
+
+workflow {
+
+    def uniprot_domain_ids_path = "${params.dataset_dir}/${params.uniprot_domain_ids_csv_fn}"
+
+    GATHER_CIF(uniprot_domain_ids_path)
+
+    def uniprot_csv_ch = AF_ANNOTATE_DOMAINS_CIF()            
+}