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

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planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4
author fubar
date Sat, 03 Aug 2024 11:16:53 +0000
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-1:000000000000 0:d9c5c5b87fec
1 #!/usr/bin/env nextflow
2 nextflow.enable.dsl=2
3
4 include { merge_params; to_map; shellSplit } from '../../utilities'
5 include { run_diamond_egap;} from '../../shared/diamond/main'
6
7
8 workflow diamond_worker {
9 take:
10 gnomon_prot_ids
11 swiss_prot_ids
12 gnomon_prot_asn
13 swiss_prot_asn
14 parameters // Map : extra parameter and parameter update
15 main:
16 String diamond_blastp_params = merge_params('--sam-query-len --very-sensitive --unal 0 --comp-based-stats 0 --masking 0', parameters, 'diamond_blastp')
17 String diamond_regular_params = merge_params('-ofmt seq-align-set -query-fmt seq-ids -subject-fmt seq-ids -output-prefix hits', parameters, 'diamond')
18 String diamond_egap_params = '-blastp-args \'' + diamond_blastp_params + '\' ' + diamond_regular_params
19
20 run_diamond_egap(gnomon_prot_ids, swiss_prot_ids, gnomon_prot_asn, swiss_prot_asn, diamond_egap_params)
21
22 emit:
23 alignments = run_diamond_egap.out
24 }