Mercurial > repos > fubar > egapx_runner

comparison nf/ui.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 // main nextflow script for EGAPx ui execution
3 // prepare data channels and call main subworkflow
4
5 nextflow.enable.dsl=2
6
7 include { egapx } from './subworkflows/ncbi/main'
8 include { only_gnomon } from './subworkflows/ncbi/only_gnomon'
9
10 params.verbose = false
11
12
13 process export {
14 publishDir "${params.output}", mode: 'copy', saveAs: { fn -> fn.substring(fn.lastIndexOf('/')+1) }
15 input:
16 path out_files
17 path annot_builder_output, stageAs: 'annot_builder_output/*'
18 // path locus
19 output:
20 path "*", includeInputs: true
21 script:
22 """
23 echo "export script"
24 """
25 stub:
26 """
27 echo "export stub"
28 """
29 }
30
31
32 workflow {
33 // Parse input parameters
34 def input_params = params.get('input', [:])
35 def genome = input_params.get('genome', [])
36 def proteins = input_params.get('proteins', [])
37 def reads_query = input_params.get('reads_query', [])
38 def reads_ids = input_params.get('reads_ids', [])
39 def reads = input_params.get('reads', [])
40 def reads_metadata = input_params.get('reads_metadata', [])
41 def organelles = input_params.get('organelles', []) ?: []
42 def tax_id = input_params.get('taxid', [])
43 def hmm_params = input_params.get('hmm', []) ?: []
44 def hmm_taxid = input_params.get('hmm_taxid', []) ?: []
45 def softmask = input_params.get('softmask', []) ?: []
46 def max_intron = input_params.get('max_intron', [])
47 def genome_size_threshold = input_params.get('genome_size_threshold', [])
48 def rnaseq_alignments = input_params.get('rnaseq_alignments', []) ?: []
49 def protein_alignments = input_params.get('protein_alignments', []) ?: []
50 def task_params = params.get('tasks', [:])
51 def func_name = params.get('func_name', '')
52 if (params.verbose) {
53 println("input params:\ngenome ${genome}")
54 println("proteins ${proteins}")
55 println("reads_query ${reads_query}")
56 println("reads_ids ${reads_ids}")
57 println("reads ${reads}")
58 println("reads_metadata ${reads_metadata}")
59 println("organelles ${organelles}")
60 println("tax_id ${tax_id}")
61 println("hmm_params ${hmm_params}")
62 println("hmm_taxid ${hmm_taxid}")
63 println("softmask ${softmask}")
64 println("max_intron ${max_intron}")
65 println("genome_size_threshold ${genome_size_threshold}")
66 println("rnaseq_alignments ${rnaseq_alignments}")
67 println("protein_alignments ${protein_alignments}")
68 println("func_name ${func_name}")
69 // Keep it last as it is large
70 println("task_params ${task_params}")
71 }
72
73 if(func_name == 'only_gnomon') {
74 if (params.verbose) {
75 print('in gnomon block')
76 }
77 only_gnomon(genome, proteins, rnaseq_alignments, protein_alignments, organelles, tax_id, hmm_params, hmm_taxid, softmask, task_params)
78 export(only_gnomon.out.out_files, only_gnomon.out.evidence)
79 }
80 else {
81 if (params.verbose) {
82 print('in egapx block')
83 }
84 egapx(genome, proteins, reads_query, reads_ids, reads, reads_metadata, organelles, tax_id, hmm_params, hmm_taxid, softmask, max_intron, genome_size_threshold, task_params)
85 // export(egapx.out.out_files, egapx.out.annot_builder_output, egapx.out.locus)
86 export(egapx.out.out_files, egapx.out.annot_builder_output)
87 }
88 }