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comparison 1.0.0/subworkflows/process_fastq.nf @ 0:0a8dda29956e draft default tip

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planemo upload
author galaxytrakr
date Thu, 28 May 2026 20:41:10 +0000
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-1:000000000000 0:0a8dda29956e
1 // Include any necessary methods and modules
2 include { stopNow; validateParamsForFASTQ } from "${params.routines}"
3 include { GEN_SAMPLESHEET } from "${params.modules}${params.fs}gen_samplesheet${params.fs}main"
4 include { SAMPLESHEET_CHECK } from "${params.modules}${params.fs}samplesheet_check${params.fs}main"
5 include { CAT_FASTQ } from "${params.modules}${params.fs}cat${params.fs}fastq${params.fs}main"
6 include { SEQKIT_SEQ } from "${params.modules}${params.fs}seqkit${params.fs}seq${params.fs}main"
7
8 // Validate 4 required workflow parameters if
9 // FASTQ files are the input for the
10 // entry point.
11 validateParamsForFASTQ()
12
13 // Start the subworkflow
14 workflow PROCESS_FASTQ {
15 main:
16 versions = Channel.empty()
17 input_ch = Channel.empty()
18 reads = Channel.empty()
19
20 def input = file( (params.input ?: params.metadata) )
21
22 if (params.input) {
23 def fastq_files = []
24
25 if (params.fq_suffix == null) {
26 stopNow("We need to know what suffix the FASTQ files ends with inside the\n" +
27 "directory. Please use the --fq_suffix option to indicate the file\n" +
28 "suffix by which the files are to be collected to run the pipeline on.")
29 }
30
31 if (params.fq_strandedness == null) {
32 stopNow("We need to know if the FASTQ files inside the directory\n" +
33 "are sequenced using stranded or non-stranded sequencing. This is generally\n" +
34 "required if the sequencing experiment is RNA-SEQ. For almost all of the other\n" +
35 "cases, you can probably use the --fq_strandedness unstranded option to indicate\n" +
36 "that the reads are unstranded.")
37 }
38
39 if (params.fq_filename_delim == null || params.fq_filename_delim_idx == null) {
40 stopNow("We need to know the delimiter of the filename of the FASTQ files.\n" +
41 "By default the filename delimiter is _ (underscore). This delimiter character\n" +
42 "is used to split and assign a group name. The group name can be controlled by\n" +
43 "using the --fq_filename_delim_idx option (1-based). For example, if the FASTQ\n" +
44 "filename is WT_REP1_001.fastq, then to create a group WT, use the following\n" +
45 "options: --fq_filename_delim _ --fq_filename_delim_idx 1")
46 }
47
48 if (!input.exists()) {
49 stopNow("The input directory,\n${params.input}\ndoes not exist!")
50 }
51
52 input.eachFileRecurse {
53 it.name.endsWith("${params.fq_suffix}") ? fastq_files << it : fastq_files << null
54 }
55
56 if (fastq_files.findAll{ it != null }.size() == 0) {
57 stopNow("The input directory,\n${params.input}\nis empty! or does not " +
58 "have FASTQ files ending with the suffix: ${params.fq_suffix}")
59 }
60
61 GEN_SAMPLESHEET( Channel.fromPath(params.input, type: 'dir') )
62 GEN_SAMPLESHEET.out.csv.set{ input_ch }
63 versions.mix( GEN_SAMPLESHEET.out.versions )
64 .set { versions }
65 } else if (params.metadata) {
66 if (!input.exists()) {
67 stopNow("The metadata CSV file,\n${params.metadata}\ndoes not exist!")
68 }
69
70 if (input.size() <= 0) {
71 stopNow("The metadata CSV file,\n${params.metadata}\nis empty!")
72 }
73
74 Channel.fromPath(params.metadata, type: 'file')
75 .set { input_ch }
76 }
77
78 SAMPLESHEET_CHECK( input_ch )
79 .csv
80 .splitCsv( header: true, sep: ',')
81 .map { create_fastq_channel(it) }
82 .groupTuple(by: [0])
83 .branch {
84 meta, fastq ->
85 single : fastq.size() == 1
86 return [ meta, fastq.flatten() ]
87 multiple : fastq.size() > 1
88 return [ meta, fastq.flatten() ]
89 }
90 .set { reads }
91
92 CAT_FASTQ( reads.multiple )
93 .catted_reads
94 .mix( reads.single )
95 .set { processed_reads }
96
97 if (params.fq_filter_by_len.toInteger() > 0) {
98 SEQKIT_SEQ( processed_reads )
99 .fastx
100 .set { processed_reads }
101
102 versions.mix( SEQKIT_SEQ.out.versions.first().ifEmpty(null) )
103 .set { versions }
104 }
105
106 versions.mix(
107 SAMPLESHEET_CHECK.out.versions,
108 CAT_FASTQ.out.versions.first().ifEmpty(null)
109 )
110 .set { versions }
111
112 emit:
113 processed_reads
114 versions
115 }
116
117 // Function to get list of [ meta, [ fq1, fq2 ] ]
118 def create_fastq_channel(LinkedHashMap row) {
119
120 def meta = [:]
121 meta.id = row.sample
122 meta.single_end = row.single_end.toBoolean()
123 meta.strandedness = row.strandedness
124 meta.id = meta.id.split(params.fq_filename_delim)[0..params.fq_filename_delim_idx.toInteger() - 1]
125 .join(params.fq_filename_delim)
126 meta.id = (meta.id =~ /\./ ? meta.id.take(meta.id.indexOf('.')) : meta.id)
127
128 def array = []
129
130 if (!file(row.fq1).exists()) {
131 stopNow("Please check input metadata CSV. The following Read 1 FASTQ file does not exist!" +
132 "\n${row.fq1}")
133 }
134 if (meta.single_end) {
135 array = [ meta, [ file(row.fq1) ] ]
136 } else {
137 if (!file(row.fq2).exists()) {
138 stopNow("Please check input metadata CSV. The following Read 2 FASTQ file does not exist!" +
139 "\n${row.fq2}")
140 }
141 array = [ meta, [ file(row.fq1), file(row.fq2) ] ]
142 }
143 return array
144 }