diff nf/subworkflows/ncbi/gnomon/diamond/main.nf @ 0:d9c5c5b87fec draft

planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nf/subworkflows/ncbi/gnomon/diamond/main.nf	Sat Aug 03 11:16:53 2024 +0000
@@ -0,0 +1,24 @@
+#!/usr/bin/env nextflow
+nextflow.enable.dsl=2
+
+include { merge_params; to_map; shellSplit } from '../../utilities'
+include { run_diamond_egap;} from '../../shared/diamond/main'
+
+
+workflow diamond_worker {
+    take:
+        gnomon_prot_ids
+        swiss_prot_ids
+        gnomon_prot_asn
+        swiss_prot_asn
+        parameters  // Map : extra parameter and parameter update
+    main:
+        String diamond_blastp_params = merge_params('--sam-query-len --very-sensitive --unal 0 --comp-based-stats 0 --masking 0', parameters, 'diamond_blastp')
+        String diamond_regular_params = merge_params('-ofmt seq-align-set -query-fmt seq-ids -subject-fmt seq-ids -output-prefix hits', parameters, 'diamond')
+        String diamond_egap_params = '-blastp-args \''  + diamond_blastp_params + '\' '  + diamond_regular_params
+        
+        run_diamond_egap(gnomon_prot_ids, swiss_prot_ids, gnomon_prot_asn, swiss_prot_asn, diamond_egap_params)
+
+    emit:
+        alignments = run_diamond_egap.out
+}