Mercurial > repos > galaxytrakr > hfp_bettercallsal_awsbatch

comparison 1.0.0/lib/routines.nf @ 0:801b85b03a17 draft default tip

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author galaxytrakr
date Thu, 28 May 2026 20:31:42 +0000
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-1:000000000000 0:801b85b03a17
1 // Hold methods to print:
2 // 1. Colored logo.
3 // 2. Summary of parameters.
4 // 3. Single dashed line.
5 // 4. Double dashed line.
6 //
7
8 import groovy.json.JsonSlurper
9 import groovy.util.ConfigSlurper
10 // import nextflow.config.ConfigParser
11 // import nextflow.config.ConfigBuilder
12 // import groovy.json.JsonOutput
13
14 // ASCII logo
15 def pipelineBanner() {
16
17 def padding = (params.pad) ?: 30
18 Map fgcolors = getANSIColors()
19
20 def banner = [
21 name: "${fgcolors.magenta}${workflow.manifest.name}${fgcolors.reset}",
22 author: "${fgcolors.cyan}${workflow.manifest.author}${fgcolors.reset}",
23 // workflow: "${fgcolors.magenta}${params.pipeline}${fgcolors.reset}",
24 version: "${fgcolors.green}${workflow.manifest.version}${fgcolors.reset}",
25 center: "${fgcolors.green}${params.center}${fgcolors.reset}",
26 pad: padding
27 ]
28
29 manifest = addPadding(banner)
30
31 return """${fgcolors.white}${dashedLine(type: '=')}${fgcolors.magenta}
32 (o)
33 ___ _ __ _ _ __ ___ ___
34 / __|| '_ \\ | || '_ \\ / _ \\/ __|
35 | (__ | |_) || || |_) || __/\\__ \\
36 \\___|| .__/ |_|| .__/ \\___||___/
37 | | | |
38 |_| |_|${fgcolors.reset}
39 ${dashedLine()}
40 ${fgcolors.blue}A collection of modular pipelines at CFSAN, FDA.${fgcolors.reset}
41 ${dashedLine()}
42 ${manifest}
43 ${dashedLine(type: '=')}
44 """.stripIndent()
45 }
46
47 // Add padding to keys so that
48 // they indent nicely on the
49 // terminal
50 def addPadding(values) {
51
52 def pad = (params.pad) ?: 30
53 values.pad = pad
54
55 def padding = values.pad.toInteger()
56 def nocapitalize = values.nocapitalize
57 def stopnow = values.stopNow
58 def help = values.help
59
60 values.removeAll {
61 k, v -> [
62 'nocapitalize',
63 'pad',
64 'stopNow',
65 'help'
66 ].contains(k)
67 }
68
69 values.keySet().each { k ->
70 v = values[k]
71 s = params.linewidth - (pad + 5)
72 if (v.toString().size() > s && !stopnow) {
73 def sen = ''
74 // v.toString().findAll(/.{1,${s}}\b(?:\W*|\s*)/).each {
75 // sen += ' '.multiply(padding + 2) + it + '\n'
76 // }
77 v.toString().eachMatch(/.{1,${s}}(?=.*)\b|\w+/) {
78 sen += ' '.multiply(padding + 2) + it.trim() + '\n'
79 }
80 values[k] = (
81 help ? sen.replaceAll(/^(\n|\s)*/, '') : sen.trim()
82 )
83 } else {
84 values[k] = (help ? v + "\n" : v)
85 }
86 k = k.replaceAll(/\./, '_')
87 }
88
89 return values.findResults {
90 k, v -> nocapitalize ?
91 k.padRight(padding) + ': ' + v :
92 k.capitalize().padRight(padding) + ': ' + v
93 }.join("\n")
94 }
95
96 // Method for error messages
97 def stopNow(msg) {
98
99 Map fgcolors = getANSIColors()
100 Map errors = [:]
101
102 if (msg == null) {
103 msg = "Unknown error"
104 }
105
106 errors['stopNow'] = true
107 errors["${params.cfsanpipename} - ${params.pipeline} - ERROR"] = """
108 ${fgcolors.reset}${dashedLine()}
109 ${fgcolors.red}${msg}${fgcolors.reset}
110 ${dashedLine()}
111 """.stripIndent()
112 // println dashedLine() // defaults to stdout
113 // log.info addPadding(errors) // prints to stdout
114 exit 1, "\n" + dashedLine() +
115 "${fgcolors.red}\n" + addPadding(errors)
116 }
117
118 // Method to validate 4 required parameters
119 // if input for entry point is FASTQ files
120 def validateParamsForFASTQ() {
121 switch (params) {
122 case { params.metadata == null && params.input == null }:
123 stopNow("Either metadata CSV file with 5 required columns\n" +
124 "in order: sample, fq1, fq2, strandedness, single_end or \n" +
125 "input directory of only FASTQ files (gzipped or unzipped) should be provided\n" +
126 "using --metadata or --input options.\n" +
127 "None of these two options were provided!")
128 break
129 case { params.metadata != null && params.input != null }:
130 stopNow("Either metadata or input directory of FASTQ files\n" +
131 "should be provided using --metadata or --input options.\n" +
132 "Using both these options is not allowed!")
133 break
134 case { params.output == null }:
135 stopNow("Please mention output directory to store all results " +
136 "using --output option!")
137 break
138 }
139 return 1
140 }
141
142 // Method to print summary of parameters
143 // before running
144 def summaryOfParams() {
145
146 // def pipeline_specific_config = pipeline_specific_config = new ConfigParser().setIgnoreIncludes(true).parse(
147 // file("${params.workflowsconf}${params.fs}${params.pipeline}.config").text
148 // )
149 def pipeline_specific_config = new ConfigSlurper().parse(
150 file("${params.workflowsconf}${params.fs}${params.pipeline}.config").text
151 )
152
153 Map fgcolors = getANSIColors()
154 Map globalparams = [:]
155 Map localparams = params.subMap(
156 pipeline_specific_config.params.keySet().toList() + params.logtheseparams
157 )
158
159 if (localparams !instanceof Map) {
160 stopNow("Need a Map of paramters. We got: " + localparams.getClass())
161 }
162
163 if (localparams.size() != 0) {
164 localparams['nocapitalize'] = true
165 globalparams['nocapitalize'] = true
166 globalparams['nextflow_version'] = "${nextflow.version}"
167 globalparams['nextflow_build'] = "${nextflow.build}"
168 globalparams['nextflow_timestamp'] = "${nextflow.timestamp}"
169 globalparams['workflow_projectDir'] = "${workflow.projectDir}"
170 globalparams['workflow_launchDir'] = "${workflow.launchDir}"
171 globalparams['workflow_workDir'] = "${workflow.workDir}"
172 globalparams['workflow_container'] = "${workflow.container}"
173 globalparams['workflow_containerEngine'] = "${workflow.containerEngine}"
174 globalparams['workflow_runName'] = "${workflow.runName}"
175 globalparams['workflow_sessionId'] = "${workflow.sessionId}"
176 globalparams['workflow_profile'] = "${workflow.profile}"
177 globalparams['workflow_start'] = "${workflow.start}"
178 globalparams['workflow_commandLine'] = "${workflow.commandLine}"
179 return """${dashedLine()}
180 Summary of the current workflow (${fgcolors.magenta}${params.pipeline}${fgcolors.reset}) parameters
181 ${dashedLine()}
182 ${addPadding(localparams)}
183 ${dashedLine()}
184 ${fgcolors.cyan}N E X T F L O W${fgcolors.reset} - ${fgcolors.magenta}${params.cfsanpipename}${fgcolors.reset} - Runtime metadata
185 ${dashedLine()}
186 ${addPadding(globalparams)}
187 ${dashedLine()}""".stripIndent()
188 }
189 return 1
190 }
191
192 // Method to display
193 // Return dashed line either '-'
194 // type or '=' type
195 def dashedLine(Map defaults = [:]) {
196
197 Map fgcolors = getANSIColors()
198 def line = [color: 'white', type: '-']
199
200 if (!defaults.isEmpty()) {
201 line.putAll(defaults)
202 }
203
204 return fgcolors."${line.color}" +
205 "${line.type}".multiply(params.linewidth) +
206 fgcolors.reset
207 }
208
209 // Return slurped keys parsed from JSON
210 def slurpJson(file) {
211 def slurped = null
212 def jsonInst = new JsonSlurper()
213
214 try {
215 slurped = jsonInst.parse(new File ("${file}"))
216 }
217 catch (Exception e) {
218 log.error 'Please check your JSON schema. Invalid JSON file: ' + file
219 }
220
221 // Declare globals for the nanofactory
222 // workflow.
223 return [keys: slurped.keySet().toList(), cparams: slurped]
224 }
225
226 // Default help text in a map if the entry point
227 // to a pipeline is FASTQ files.
228 def fastqEntryPointHelp() {
229
230 Map helptext = [:]
231 Map fgcolors = getANSIColors()
232
233 helptext['Workflow'] = "${fgcolors.magenta}${params.pipeline}${fgcolors.reset}"
234 helptext['Author'] = "${fgcolors.cyan}${params.workflow_built_by}${fgcolors.reset}"
235 helptext['Version'] = "${fgcolors.green}${params.workflow_version}${fgcolors.reset}\n"
236 helptext['Usage'] = "cpipes --pipeline ${params.pipeline} [options]\n"
237 helptext['Required'] = ""
238 helptext['--input'] = "Absolute path to directory containing FASTQ files. " +
239 "The directory should contain only FASTQ files as all the " +
240 "files within the mentioned directory will be read. " +
241 "Ex: --input /path/to/fastq_pass"
242 helptext['--output'] = "Absolute path to directory where all the pipeline " +
243 "outputs should be stored. Ex: --output /path/to/output"
244 helptext['Other options'] = ""
245 helptext['--metadata'] = "Absolute path to metadata CSV file containing five " +
246 "mandatory columns: sample,fq1,fq2,strandedness,single_end. The fq1 and fq2 " +
247 "columns contain absolute paths to the FASTQ files. This option can be used in place " +
248 "of --input option. This is rare. Ex: --metadata samplesheet.csv"
249 helptext['--fq_suffix'] = "The suffix of FASTQ files (Unpaired reads or R1 reads or Long reads) if " +
250 "an input directory is mentioned via --input option. Default: ${params.fq_suffix}"
251 helptext['--fq2_suffix'] = "The suffix of FASTQ files (Paired-end reads or R2 reads) if an input directory is mentioned via " +
252 "--input option. Default: ${params.fq2_suffix}"
253 helptext['--fq_filter_by_len'] = "Remove FASTQ reads that are less than this many bases. " +
254 "Default: ${params.fq_filter_by_len}"
255 helptext['--fq_strandedness'] = "The strandedness of the sequencing run. This is mostly needed " +
256 "if your sequencing run is RNA-SEQ. For most of the other runs, it is probably safe to use " +
257 "unstranded for the option. Default: ${params.fq_strandedness}"
258 helptext['--fq_single_end'] = "SINGLE-END information will be auto-detected but this option forces " +
259 "PAIRED-END FASTQ files to be treated as SINGLE-END so only read 1 information is included in " +
260 "auto-generated samplesheet. Default: ${params.fq_single_end}"
261 helptext['--fq_filename_delim'] = "Delimiter by which the file name is split to obtain sample name. " +
262 "Default: ${params.fq_filename_delim}"
263 helptext['--fq_filename_delim_idx'] = "After splitting FASTQ file name by using the --fq_filename_delim option," +
264 " all elements before this index (1-based) will be joined to create final sample name." +
265 " Default: ${params.fq_filename_delim_idx}"
266
267 return helptext
268 }
269
270 // Show concise help text if configured within the main workflow.
271 def conciseHelp(def tool = null) {
272 Map fgcolors = getANSIColors()
273
274 tool ?= "fastp"
275 tools = tool?.tokenize(',')
276
277 return """
278 ${dashedLine()}
279 Show configurable CLI options for each tool within ${fgcolors.magenta}${params.pipeline}${fgcolors.reset}
280 ${dashedLine()}
281 Ex: cpipes --pipeline ${params.pipeline} --help
282 """ + (tools.size() > 1 ? "Ex: cpipes --pipeline ${params.pipeline} --help ${tools[0]}"
283 + """
284 Ex: cpipes --pipeline ${params.pipeline} --help ${tools[0]},${tools[1]}
285 ${dashedLine()}""".stripIndent() : """Ex: cpipes --pipeline ${params.pipeline} --help ${tool}
286 ${dashedLine()}""".stripIndent())
287
288 }
289
290 // Wrap help text with the following options
291 def wrapUpHelp() {
292
293 return [
294 'Help options' : "",
295 '--help': "Display this message.\n",
296 'help': true,
297 'nocapitalize': true
298 ]
299 }
300
301 // Method to send email on workflow complete.
302 def sendMail() {
303
304 if (params.user_email == null) {
305 return 1
306 }
307
308 def pad = (params.pad) ?: 30
309 def contact_emails = [
310 stakeholder: (params.workflow_blueprint_by ?: 'Not defined'),
311 author: (params.workflow_built_by ?: 'Not defined')
312 ]
313 def msg = """
314 ${pipelineBanner()}
315 ${summaryOfParams()}
316 ${params.cfsanpipename} - ${params.pipeline}
317 ${dashedLine()}
318 Please check the following directory for N E X T F L O W
319 reports. You can view the HTML files directly by double clicking
320 them on your workstation.
321 ${dashedLine()}
322 ${params.tracereportsdir}
323 ${dashedLine()}
324 Please send any bug reports to CFSAN Dev Team or the author or
325 the stakeholder of the current pipeline.
326 ${dashedLine()}
327 Error messages (if any)
328 ${dashedLine()}
329 ${workflow.errorMessage}
330 ${workflow.errorReport}
331 ${dashedLine()}
332 Contact emails
333 ${dashedLine()}
334 ${addPadding(contact_emails)}
335 ${dashedLine()}
336 Thank you for using ${params.cfsanpipename} - ${params.pipeline}!
337 ${dashedLine()}
338 """.stripIndent()
339
340 def mail_cmd = [
341 'sendmail',
342 '-f', 'noreply@gmail.com',
343 '-F', 'noreply',
344 '-t', "${params.user_email}"
345 ]
346
347 def email_subject = "${params.cfsanpipename} - ${params.pipeline}"
348 Map fgcolors = getANSIColors()
349
350 if (workflow.success) {
351 email_subject += ' completed successfully!'
352 }
353 else if (!workflow.success) {
354 email_subject += ' has failed!'
355 }
356
357 try {
358 ['env', 'bash'].execute() << """${mail_cmd.join(' ')}
359 Subject: ${email_subject}
360 Mime-Version: 1.0
361 Content-Type: text/html
362 <pre>
363 ${msg.replaceAll(/\x1b\[[0-9;]*m/, '')}
364 </pre>
365 """.stripIndent()
366 } catch (all) {
367 def warning_msg = "${fgcolors.yellow}${params.cfsanpipename} - ${params.pipeline} - WARNING"
368 .padRight(pad) + ':'
369 log.info """
370 ${dashedLine()}
371 ${warning_msg}
372 ${dashedLine()}
373 Could not send mail with the sendmail command!
374 ${dashedLine()}
375 """.stripIndent()
376 }
377 return 1
378 }
379
380 // Set ANSI colors for any and all
381 // STDOUT or STDERR
382 def getANSIColors() {
383
384 Map fgcolors = [:]
385
386 fgcolors['reset'] = "\033[0m"
387 fgcolors['black'] = "\033[0;30m"
388 fgcolors['red'] = "\033[0;31m"
389 fgcolors['green'] = "\033[0;32m"
390 fgcolors['yellow'] = "\033[0;33m"
391 fgcolors['blue'] = "\033[0;34m"
392 fgcolors['magenta'] = "\033[0;35m"
393 fgcolors['cyan'] = "\033[0;36m"
394 fgcolors['white'] = "\033[0;37m"
395
396 return fgcolors
397 }