Mercurial > repos > kkonganti > hfp_nowayout

comparison 0.5.0/workflows/nowayout.nf @ 0:97cd2f532efe

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planemo upload
author kkonganti
date Mon, 31 Mar 2025 14:50:40 -0400
parents
children 3539fbeb4230
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-1:000000000000 0:97cd2f532efe
1 // Define any required imports for this specific workflow
2 import java.nio.file.Paths
3 import java.util.zip.GZIPInputStream
4 import java.io.FileInputStream
5 import nextflow.file.FileHelper
6
7
8 // Include any necessary methods
9 include { \
10 summaryOfParams; stopNow; fastqEntryPointHelp; sendMail; \
11 addPadding; wrapUpHelp } from "${params.routines}"
12 include { fastpHelp } from "${params.toolshelp}${params.fs}fastp"
13 include { kmaalignHelp } from "${params.toolshelp}${params.fs}kmaalign"
14 include { seqkitgrepHelp } from "${params.toolshelp}${params.fs}seqkitgrep"
15 include { salmonidxHelp } from "${params.toolshelp}${params.fs}salmonidx"
16 include { sourmashsketchHelp } from "${params.toolshelp}${params.fs}sourmashsketch"
17 include { sourmashgatherHelp } from "${params.toolshelp}${params.fs}sourmashgather"
18 include { sfhpyHelp } from "${params.toolshelp}${params.fs}sfhpy"
19 include { gsalkronapyHelp } from "${params.toolshelp}${params.fs}gsalkronapy"
20 include { kronaktimporttextHelp } from "${params.toolshelp}${params.fs}kronaktimporttext"
21
22 // Exit if help requested before any subworkflows
23 if (params.help) {
24 log.info help()
25 exit 0
26 }
27
28
29 // Include any necessary modules and subworkflows
30 include { PROCESS_FASTQ } from "${params.subworkflows}${params.fs}process_fastq"
31 include { FASTP } from "${params.modules}${params.fs}fastp${params.fs}main"
32 include { KMA_ALIGN } from "${params.modules}${params.fs}kma${params.fs}align${params.fs}main"
33 include { OTF_GENOME } from "${params.modules}${params.fs}otf_genome${params.fs}main"
34 include { SEQKIT_GREP } from "${params.modules}${params.fs}seqkit${params.fs}grep${params.fs}main"
35 include { SALMON_INDEX } from "${params.modules}${params.fs}salmon${params.fs}index${params.fs}main"
36 include { SALMON_QUANT } from "${params.modules}${params.fs}salmon${params.fs}quant${params.fs}main"
37 include { SOURMASH_SKETCH } from "${params.modules}${params.fs}sourmash${params.fs}sketch${params.fs}main"
38 include { SOURMASH_SKETCH \
39 as REDUCE_DB_IDX } from "${params.modules}${params.fs}sourmash${params.fs}sketch${params.fs}main"
40 include { SOURMASH_GATHER } from "${params.modules}${params.fs}sourmash${params.fs}gather${params.fs}main"
41 include { NOWAYOUT_RESULTS } from "${params.modules}${params.fs}nowayout_results${params.fs}main"
42 include { KRONA_KTIMPORTTEXT } from "${params.modules}${params.fs}krona${params.fs}ktimporttext${params.fs}main"
43 include { DUMP_SOFTWARE_VERSIONS } from "${params.modules}${params.fs}custom${params.fs}dump_software_versions${params.fs}main"
44 include { MULTIQC } from "${params.modules}${params.fs}multiqc${params.fs}main"
45
46 /*
47 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
48 INPUTS AND ANY CHECKS FOR THE BETTERCALLSAL WORKFLOW
49 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
50 */
51
52 def reads_platform = 0
53 reads_platform += (params.input ? 1 : 0)
54
55 if (reads_platform < 1 || reads_platform == 0) {
56 stopNow("Please mention at least one absolute path to input folder which contains\n" +
57 "FASTQ files sequenced using the --input option.\n" +
58 "Ex: --input (Illumina or Generic short reads in FASTQ format)")
59 }
60
61 params.fastp_adapter_fasta ? checkMetadataExists(params.fastp_adapter_fasta, 'Adapter sequences FASTA') : null
62 checkMetadataExists(params.lineages_csv, 'Lineages CSV')
63 checkMetadataExists(params.kmaalign_idx, 'KMA Indices')
64 checkMetadataExists(params.ref_fna, 'FASTA reference')
65
66 ch_sourmash_lin = file( params.lineages_csv )
67
68
69 /*
70 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 RUN THE BETTERCALLSAL WORKFLOW
72 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
73 */
74
75 workflow NOWAYOUT {
76 main:
77 log.info summaryOfParams()
78
79 PROCESS_FASTQ()
80
81 PROCESS_FASTQ.out.versions
82 .set { software_versions }
83
84 PROCESS_FASTQ.out.processed_reads
85 .set { ch_processed_reads }
86
87 ch_processed_reads
88 .map { meta, fastq ->
89 meta.get_kma_hit_accs = true
90 meta.salmon_decoys = params.dummyfile
91 meta.salmon_lib_type = (params.salmonalign_libtype ?: false)
92 meta.kma_t_db = params.kmaalign_idx
93 [ meta, fastq ]
94 }
95 .filter { meta, fastq ->
96 fq_file = ( fastq.getClass().toString() =~ /ArrayList/ ? fastq : [ fastq ] )
97 fq_gzip = new GZIPInputStream( new FileInputStream( fq_file[0].toAbsolutePath().toString() ) )
98 fq_gzip.read() != -1
99 }
100 .set { ch_processed_reads }
101
102 FASTP( ch_processed_reads )
103
104 FASTP.out.json
105 .map { meta, json ->
106 json
107 }
108 .collect()
109 .set { ch_multiqc }
110
111 KMA_ALIGN(
112 FASTP.out.passed_reads
113 .map { meta, fastq ->
114 [meta, fastq, []]
115 }
116 )
117
118 OTF_GENOME(
119 KMA_ALIGN.out.hits
120 .join(KMA_ALIGN.out.frags)
121 )
122
123 OTF_GENOME.out.reads_extracted
124 .filter { meta, fasta ->
125 fa_file = ( fasta.getClass().toString() =~ /ArrayList/ ? fasta : [ fasta ] )
126 fa_gzip = new GZIPInputStream( new FileInputStream( fa_file[0].toAbsolutePath().toString() ) )
127 fa_gzip.read() != -1
128 }
129 .set { ch_mito_aln_reads }
130
131 SEQKIT_GREP(
132 KMA_ALIGN.out.hits
133 .filter { meta, mapped_refs ->
134 patterns = file( mapped_refs )
135 patterns.size() > 0
136 }
137 .map { meta, mapped_refs ->
138 [meta, params.ref_fna, mapped_refs]
139 }
140 )
141
142 SALMON_INDEX( SEQKIT_GREP.out.fastx )
143
144 SALMON_QUANT(
145 ch_mito_aln_reads
146 .join( SALMON_INDEX.out.idx )
147 )
148
149 REDUCE_DB_IDX(
150 SEQKIT_GREP.out.fastx,
151 true,
152 false,
153 'db'
154 )
155
156 SOURMASH_SKETCH(
157 ch_mito_aln_reads,
158 false,
159 false,
160 'query'
161 )
162
163 SOURMASH_GATHER(
164 SOURMASH_SKETCH.out.signatures
165 .join( REDUCE_DB_IDX.out.signatures ),
166 [], [], [], []
167 )
168
169 // SOURMASH_TAX_METAGENOME(
170 // SOURMASH_GATHER.out.result
171 // .groupTuple(by: [0])
172 // .map { meta, csv ->
173 // [ meta, csv, ch_sourmash_lin ]
174 // }
175 // )
176
177 // SOURMASH_TAX_METAGENOME.out.csv
178 // .map { meta, csv ->
179 // csv
180 // }
181 // .set { ch_lin_csv }
182
183 // SOURMASH_TAX_METAGENOME.out.tsv
184 // .tap { ch_lin_krona }
185 // .map { meta, tsv ->
186 // tsv
187 // }
188 // .tap { ch_lin_tsv }
189
190 SOURMASH_GATHER.out.result
191 .groupTuple(by: [0])
192 .map { meta, csv ->
193 [ csv ]
194 }
195 .concat(
196 SALMON_QUANT.out.results
197 .map { meta, salmon_res ->
198 [ salmon_res ]
199 }
200 )
201 .concat(
202 SOURMASH_GATHER.out.failed
203 .map { meta, failed ->
204 [ failed ]
205 }
206 )
207 .concat( OTF_GENOME.out.failed )
208 .collect()
209 .flatten()
210 .collect()
211 .set { ch_gene_abn }
212
213 NOWAYOUT_RESULTS( ch_gene_abn, ch_sourmash_lin )
214
215 NOWAYOUT_RESULTS.out.tsv
216 .flatten()
217 .filter { tsv -> tsv.toString() =~ /.*${params.krona_res_suffix}$/ }
218 .map { tsv ->
219 meta = [:]
220 meta.id = "${params.cfsanpipename}_${params.pipeline}_krona"
221 [ meta, tsv ]
222 }
223 .groupTuple(by: [0])
224 .set { ch_lin_krona }
225
226 // ch_lin_tsv
227 // .mix( ch_lin_csv )
228 // .collect()
229 // .set { ch_lin_summary }
230
231 // SOURMASH_TAX_METAGENOME.out.txt
232 // .map { meta, txt ->
233 // txt
234 // }
235 // .collect()
236 // .set { ch_lin_kreport }
237
238 // NOWAYOUT_RESULTS(
239 // ch_lin_summary
240 // .concat( SOURMASH_GATHER.out.failed )
241 // .concat( OTF_GENOME.out.failed )
242 // .collect()
243 // )
244
245 KRONA_KTIMPORTTEXT( ch_lin_krona )
246
247 DUMP_SOFTWARE_VERSIONS(
248 software_versions
249 .mix (
250 FASTP.out.versions,
251 KMA_ALIGN.out.versions,
252 SEQKIT_GREP.out.versions,
253 REDUCE_DB_IDX.out.versions,
254 SOURMASH_SKETCH.out.versions,
255 SOURMASH_GATHER.out.versions,
256 SALMON_INDEX.out.versions,
257 SALMON_QUANT.out.versions,
258 NOWAYOUT_RESULTS.out.versions,
259 KRONA_KTIMPORTTEXT.out.versions
260 )
261 .unique()
262 .collectFile(name: 'collected_versions.yml')
263 )
264
265 DUMP_SOFTWARE_VERSIONS.out.mqc_yml
266 .concat(
267 ch_multiqc,
268 NOWAYOUT_RESULTS.out.mqc_yml
269 )
270 .collect()
271 .flatten()
272 .collect()
273 .set { ch_multiqc }
274
275 MULTIQC( ch_multiqc )
276 }
277
278 /*
279 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
280 ON COMPLETE, SHOW GORY DETAILS OF ALL PARAMS WHICH WILL BE HELPFUL TO DEBUG
281 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
282 */
283
284 workflow.onComplete {
285 if (workflow.success) {
286 sendMail()
287 }
288 }
289
290 workflow.onError {
291 sendMail()
292 }
293
294 /*
295 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
296 METHOD TO CHECK METADATA EXISTENCE
297 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
298 */
299
300 def checkMetadataExists(file_path, msg) {
301 file_path_obj = file( file_path )
302
303 if (msg.toString().find(/(?i)KMA/)) {
304 if (!file_path_obj.parent.exists() || file_path_obj.parent.size() == 0) {
305 stopNow("Please check if your ${msg}\n" +
306 "[ ${file_path} ]\nexists and that the files are not of size 0.")
307 }
308 }
309 else if (!file_path_obj.exists() || file_path_obj.size() == 0) {
310 stopNow("Please check if your ${msg} file\n" +
311 "[ ${file_path} ]\nexists and is not of size 0.")
312 }
313 }
314
315 /*
316 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
317 HELP TEXT METHODS FOR BETTERCALLSAL WORKFLOW
318 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
319 */
320
321 def help() {
322
323 Map helptext = [:]
324
325 helptext.putAll (
326 fastqEntryPointHelp() +
327 fastpHelp(params).text +
328 kmaalignHelp(params).text +
329 seqkitgrepHelp(params).text +
330 salmonidxHelp(params).text +
331 sourmashsketchHelp(params).text +
332 sourmashgatherHelp(params).text +
333 sfhpyHelp(params).text +
334 gsalkronapyHelp(params).text +
335 kronaktimporttextHelp(params).text +
336 wrapUpHelp()
337 )
338
339 return addPadding(helptext)
340 }