Mercurial > repos > galaxytrakr > hfp_centriflaken_awsbatch

comparison 0.4.2/workflows/spades_only.nf @ 0:082e0091e813 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload
author galaxytrakr
date Fri, 29 May 2026 13:27:47 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:082e0091e813
1 // Define any required imports for this specific workflow
2 import java.nio.file.Paths
3 import nextflow.file.FileHelper
4
5 // Include any necessary methods
6 include { \
7 summaryOfParams; stopNow; fastqEntryPointHelp; sendMail; \
8 addPadding; wrapUpHelp } from "${params.routines}"
9 include { spadesHelp } from "${params.toolshelp}${params.fs}spades"
10
11
12 // Exit if help requested before any subworkflows
13 if (params.help) {
14 log.info help()
15 exit 0
16 }
17
18 // Include any necessary modules and subworkflows
19 include { PROCESS_FASTQ } from "${params.subworkflows}${params.fs}process_fastq"
20 include { SPADES_ASSEMBLE } from "${params.modules}${params.fs}spades${params.fs}assemble${params.fs}main"
21 include { DUMP_SOFTWARE_VERSIONS } from "${params.modules}${params.fs}custom${params.fs}dump_software_versions${params.fs}main"
22
23
24
25 /*
26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
27 INPUTS AND ANY CHECKS FOR THE CENTRIFLAKEN-HY WORKFLOW
28 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
29 */
30
31 def spades_custom_hmm = (params.spades_hmm ? file ( "${params.spades_hmm}" ) : false)
32 def reads_platform = 0
33
34 reads_platform += (params.input ? 1 : 0)
35
36 if (spades_custom_hmm && !spades_custom_hmm.exists()) {
37 stopNow("Please check if the following SPAdes' custom HMM directory\n" +
38 "path is valid:\n${params.spades_hmm}\nCannot proceed further!")
39 }
40
41 if (reads_platform < 1 || reads_platform == 0) {
42 stopNow("Please mention at least one absolute path to input folder which contains\n" +
43 "FASTQ files sequenced using the --input option.\n" +
44 "Ex: --input (Illumina or Generic short reads in FASTQ format)")
45 }
46
47 /*
48 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
49 RUN THE CENTRIFLAKEN-HY WORKFLOW
50 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
51 */
52
53 workflow SPADES_ONLY {
54 main:
55 ch_dummy = Channel.fromPath("${params.dummyfile}")
56 ch_dummy2 = Channel.fromPath("${params.dummyfile2}")
57
58 log.info summaryOfParams()
59
60 PROCESS_FASTQ()
61 .processed_reads
62 .set { ch_processed_reads }
63
64 PROCESS_FASTQ
65 .out
66 .versions
67 .set { software_versions }
68
69 // As of 06/02/2022, with the upcoming newer versions of NextFlow, we will be able to do
70 // allowNull: true for both input and output, but until then, we have to use dummy files.
71 // and work arounds.
72 // https://github.com/nextflow-io/nextflow/pull/2893
73
74 SPADES_ASSEMBLE (
75 ch_processed_reads
76 .combine(ch_dummy)
77 .combine(ch_dummy2)
78 )
79
80 SPADES_ASSEMBLE
81 .out
82 .assembly
83 .set { ch_assembly }
84
85 software_versions
86 .mix ( SPADES_ASSEMBLE.out.versions.ifEmpty(null) )
87 .set { software_versions }
88
89
90 DUMP_SOFTWARE_VERSIONS (
91 software_versions
92 .unique()
93 .collectFile(name: 'collected_versions.yml')
94 )
95 }
96
97 /*
98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
99 ON COMPLETE, SHOW GORY DETAILS OF ALL PARAMS WHICH WILL BE HELPFUL TO DEBUG
100 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
101 */
102
103 workflow.onComplete {
104 if (workflow.success) {
105 sendMail()
106 }
107 }
108
109 workflow.onError {
110 sendMail()
111 }
112
113 /*
114 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
115 HELPER METHODS FOR CENTRIFLAKEN-HY WORKFLOW
116 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
117 */
118
119 def help() {
120
121 Map helptext = [:]
122
123 helptext.putAll (
124 fastqEntryPointHelp() +
125 spadesHelp(params).text +
126 wrapUpHelp()
127 )
128
129 return addPadding(helptext)
130 }