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comparison nf/subworkflows/ncbi/gnomon-training-iteration/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 //nextflow.preview.recursion=true
4
5
6 include { gnomon_training_iteration; gnomon_training_iteration as gnomon_training_iteration2;
7 gnomon_training_iteration as gnomon_training_iteration3; gnomon_training_iteration as gnomon_training_iteration4 } from './utilities'
8
9
10 workflow gnomon_training_iterations {
11 take:
12 models_file
13 genome_asn
14 proteins_asn
15 chainer_alignments
16 chainer_evidence_denylist
17 chainer_gap_fill_allowlist
18 chainer_trusted_genes
19 chainer_scaffolds
20 gnomon_softmask_lds2
21 gnomon_softmask_lds2_source
22 gnomon_scaffolds
23 max_intron
24 parameters
25 main:
26 gnomon_training_iteration(models_file, genome_asn, proteins_asn ,chainer_alignments,chainer_evidence_denylist,chainer_gap_fill_allowlist,
27 chainer_trusted_genes, chainer_scaffolds, gnomon_softmask_lds2,
28 gnomon_softmask_lds2_source, gnomon_scaffolds, max_intron, parameters)
29 gnomon_training_iteration2(gnomon_training_iteration.out.hmm_params_file, genome_asn, proteins_asn ,chainer_alignments,
30 chainer_evidence_denylist,chainer_gap_fill_allowlist, chainer_trusted_genes, chainer_scaffolds, gnomon_softmask_lds2,
31 gnomon_softmask_lds2_source, gnomon_scaffolds, max_intron, parameters)
32 gnomon_training_iteration3(gnomon_training_iteration2.out.hmm_params_file, genome_asn, proteins_asn ,chainer_alignments,
33 chainer_evidence_denylist,chainer_gap_fill_allowlist, chainer_trusted_genes, chainer_scaffolds, gnomon_softmask_lds2,
34 gnomon_softmask_lds2_source, gnomon_scaffolds, max_intron, parameters)
35 gnomon_training_iteration4(gnomon_training_iteration3.out.hmm_params_file, genome_asn, proteins_asn ,chainer_alignments,
36 chainer_evidence_denylist,chainer_gap_fill_allowlist, chainer_trusted_genes, chainer_scaffolds, gnomon_softmask_lds2,
37 gnomon_softmask_lds2_source, gnomon_scaffolds, max_intron, parameters)
38
39 emit:
40 hmm_params_file = gnomon_training_iteration4.out.hmm_params_file
41 }
42
43 workflow gnomon_no_training {
44 take:
45 hmm
46 main:
47 process_no_training(hmm)
48 emit:
49 hmm_params_file = process_no_training.out.file
50 }
51
52 process process_no_training
53 {
54 input:
55 val hmm
56 output:
57 path "*.params" , emit: 'file'
58 script:
59 """
60 curl -O ${hmm}
61 """
62 stub:
63 """
64 touch hmm.params
65 """
66 }
67
68
69 /*
70
71 //experimental (preview.recursion)
72 // to be used in the future
73 workflow gnomon_training_iterations {
74 take:
75 models_file
76 genome_asn
77 proteins_asn
78 chainer_alignments
79 chainer_evidence_denylist
80 chainer_gap_fill_allowlist
81 chainer_trusted_genes
82 chainer_scaffolds
83 gnomon_softmask_lds2
84 gnomon_softmask_lds2_source
85 gnomon_scaffolds
86 max_intron
87 parameters
88 main:
89 gnomon_training_iteration
90 .recurse(models_file, genome_asn, proteins_asn ,chainer_alignments,chainer_evidence_denylist,chainer_gap_fill_allowlist,
91 chainer_trusted_genes, chainer_scaffolds, gnomon_softmask_lds2,
92 gnomon_softmask_lds2_source, gnomon_scaffolds, max_intron, parameters)
93 .times(4)
94 emit:
95 hmm_params_file = gnomon_training_iteration.out.hmm_params_file
96 }
97
98 */