Mercurial > repos > kkonganti > cfsan_bettercallsal

comparison 0.7.0/lib/routines.nf @ 17:0e7a0053e4a6

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author kkonganti
date Mon, 15 Jul 2024 10:42:02 -0400
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16:b90e5a7a3d4f 17:0e7a0053e4a6
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 nextflow.config.ConfigParser
10 // import groovy.json.JsonOutput
11
12 // ASCII logo
13 def pipelineBanner() {
14
15 def padding = (params.pad) ?: 30
16 Map fgcolors = getANSIColors()
17
18 def banner = [
19 name: "${fgcolors.magenta}${workflow.manifest.name}${fgcolors.reset}",
20 author: "${fgcolors.cyan}${workflow.manifest.author}${fgcolors.reset}",
21 // workflow: "${fgcolors.magenta}${params.pipeline}${fgcolors.reset}",
22 version: "${fgcolors.green}${workflow.manifest.version}${fgcolors.reset}",
23 center: "${fgcolors.green}${params.center}${fgcolors.reset}",
24 pad: padding
25 ]
26
27 manifest = addPadding(banner)
28
29 return """${fgcolors.white}${dashedLine(type: '=')}${fgcolors.magenta}
30 (o)
31 ___ _ __ _ _ __ ___ ___
32 / __|| '_ \\ | || '_ \\ / _ \\/ __|
33 | (__ | |_) || || |_) || __/\\__ \\
34 \\___|| .__/ |_|| .__/ \\___||___/
35 | | | |
36 |_| |_|${fgcolors.reset}
37 ${dashedLine()}
38 ${fgcolors.blue}A collection of modular pipelines at CFSAN, FDA.${fgcolors.reset}
39 ${dashedLine()}
40 ${manifest}
41 ${dashedLine(type: '=')}
42 """.stripIndent()
43 }
44
45 // Add padding to keys so that
46 // they indent nicely on the
47 // terminal
48 def addPadding(values) {
49
50 def pad = (params.pad) ?: 30
51 values.pad = pad
52
53 def padding = values.pad.toInteger()
54 def nocapitalize = values.nocapitalize
55 def stopnow = values.stopNow
56 def help = values.help
57
58 values.removeAll {
59 k, v -> [
60 'nocapitalize',
61 'pad',
62 'stopNow',
63 'help'
64 ].contains(k)
65 }
66
67 values.keySet().each { k ->
68 v = values[k]
69 s = params.linewidth - (pad + 5)
70 if (v.toString().size() > s && !stopnow) {
71 def sen = ''
72 // v.toString().findAll(/.{1,${s}}\b(?:\W*|\s*)/).each {
73 // sen += ' '.multiply(padding + 2) + it + '\n'
74 // }
75 v.toString().eachMatch(/.{1,${s}}(?=.*)\b|\w+/) {
76 sen += ' '.multiply(padding + 2) + it.trim() + '\n'
77 }
78 values[k] = (
79 help ? sen.replaceAll(/^(\n|\s)*/, '') : sen.trim()
80 )
81 } else {
82 values[k] = (help ? v + "\n" : v)
83 }
84 k = k.replaceAll(/\./, '_')
85 }
86
87 return values.findResults {
88 k, v -> nocapitalize ?
89 k.padRight(padding) + ': ' + v :
90 k.capitalize().padRight(padding) + ': ' + v
91 }.join("\n")
92 }
93
94 // Method for error messages
95 def stopNow(msg) {
96
97 Map fgcolors = getANSIColors()
98 Map errors = [:]
99
100 if (msg == null) {
101 msg = "Unknown error"
102 }
103
104 errors['stopNow'] = true
105 errors["${params.cfsanpipename} - ${params.pipeline} - ERROR"] = """
106 ${fgcolors.reset}${dashedLine()}
107 ${fgcolors.red}${msg}${fgcolors.reset}
108 ${dashedLine()}
109 """.stripIndent()
110 // println dashedLine() // defaults to stdout
111 // log.info addPadding(errors) // prints to stdout
112 exit 1, "\n" + dashedLine() +
113 "${fgcolors.red}\n" + addPadding(errors)
114 }
115
116 // Method to validate 4 required parameters
117 // if input for entry point is FASTQ files
118 def validateParamsForFASTQ() {
119 switch (params) {
120 case { params.metadata == null && params.input == null }:
121 stopNow("Either metadata CSV file with 5 required columns\n" +
122 "in order: sample, fq1, fq2, strandedness, single_end or \n" +
123 "input directory of only FASTQ files (gzipped or unzipped) should be provided\n" +
124 "using --metadata or --input options.\n" +
125 "None of these two options were provided!")
126 break
127 case { params.metadata != null && params.input != null }:
128 stopNow("Either metadata or input directory of FASTQ files\n" +
129 "should be provided using --metadata or --input options.\n" +
130 "Using both these options is not allowed!")
131 break
132 case { params.output == null }:
133 stopNow("Please mention output directory to store all results " +
134 "using --output option!")
135 break
136 }
137 return 1
138 }
139
140 // Method to print summary of parameters
141 // before running
142 def summaryOfParams() {
143
144 def pipeline_specific_config = new ConfigParser().setIgnoreIncludes(true).parse(
145 file("${params.workflowsconf}${params.fs}${params.pipeline}.config").text
146 )
147 Map fgcolors = getANSIColors()
148 Map globalparams = [:]
149 Map localparams = params.subMap(
150 pipeline_specific_config.params.keySet().toList() + params.logtheseparams
151 )
152
153 if (localparams !instanceof Map) {
154 stopNow("Need a Map of paramters. We got: " + localparams.getClass())
155 }
156
157 if (localparams.size() != 0) {
158 localparams['nocapitalize'] = true
159 globalparams['nocapitalize'] = true
160 globalparams['nextflow_version'] = "${nextflow.version}"
161 globalparams['nextflow_build'] = "${nextflow.build}"
162 globalparams['nextflow_timestamp'] = "${nextflow.timestamp}"
163 globalparams['workflow_projectDir'] = "${workflow.projectDir}"
164 globalparams['workflow_launchDir'] = "${workflow.launchDir}"
165 globalparams['workflow_workDir'] = "${workflow.workDir}"
166 globalparams['workflow_container'] = "${workflow.container}"
167 globalparams['workflow_containerEngine'] = "${workflow.containerEngine}"
168 globalparams['workflow_runName'] = "${workflow.runName}"
169 globalparams['workflow_sessionId'] = "${workflow.sessionId}"
170 globalparams['workflow_profile'] = "${workflow.profile}"
171 globalparams['workflow_start'] = "${workflow.start}"
172 globalparams['workflow_commandLine'] = "${workflow.commandLine}"
173 return """${dashedLine()}
174 Summary of the current workflow (${fgcolors.magenta}${params.pipeline}${fgcolors.reset}) parameters
175 ${dashedLine()}
176 ${addPadding(localparams)}
177 ${dashedLine()}
178 ${fgcolors.cyan}N E X T F L O W${fgcolors.reset} - ${fgcolors.magenta}${params.cfsanpipename}${fgcolors.reset} - Runtime metadata
179 ${dashedLine()}
180 ${addPadding(globalparams)}
181 ${dashedLine()}""".stripIndent()
182 }
183 return 1
184 }
185
186 // Method to display
187 // Return dashed line either '-'
188 // type or '=' type
189 def dashedLine(Map defaults = [:]) {
190
191 Map fgcolors = getANSIColors()
192 def line = [color: 'white', type: '-']
193
194 if (!defaults.isEmpty()) {
195 line.putAll(defaults)
196 }
197
198 return fgcolors."${line.color}" +
199 "${line.type}".multiply(params.linewidth) +
200 fgcolors.reset
201 }
202
203 // Return slurped keys parsed from JSON
204 def slurpJson(file) {
205 def slurped = null
206 def jsonInst = new JsonSlurper()
207
208 try {
209 slurped = jsonInst.parse(new File ("${file}"))
210 }
211 catch (Exception e) {
212 log.error 'Please check your JSON schema. Invalid JSON file: ' + file
213 }
214
215 // Declare globals for the nanofactory
216 // workflow.
217 return [keys: slurped.keySet().toList(), cparams: slurped]
218 }
219
220 // Default help text in a map if the entry point
221 // to a pipeline is FASTQ files.
222 def fastqEntryPointHelp() {
223
224 Map helptext = [:]
225 Map fgcolors = getANSIColors()
226
227 helptext['Workflow'] = "${fgcolors.magenta}${params.pipeline}${fgcolors.reset}"
228 helptext['Author'] = "${fgcolors.cyan}${params.workflow_built_by}${fgcolors.reset}"
229 helptext['Version'] = "${fgcolors.green}${params.workflow_version}${fgcolors.reset}\n"
230 helptext['Usage'] = "cpipes --pipeline ${params.pipeline} [options]\n"
231 helptext['Required'] = ""
232 helptext['--input'] = "Absolute path to directory containing FASTQ files. " +
233 "The directory should contain only FASTQ files as all the " +
234 "files within the mentioned directory will be read. " +
235 "Ex: --input /path/to/fastq_pass"
236 helptext['--output'] = "Absolute path to directory where all the pipeline " +
237 "outputs should be stored. Ex: --output /path/to/output"
238 helptext['Other options'] = ""
239 helptext['--metadata'] = "Absolute path to metadata CSV file containing five " +
240 "mandatory columns: sample,fq1,fq2,strandedness,single_end. The fq1 and fq2 " +
241 "columns contain absolute paths to the FASTQ files. This option can be used in place " +
242 "of --input option. This is rare. Ex: --metadata samplesheet.csv"
243 helptext['--fq_suffix'] = "The suffix of FASTQ files (Unpaired reads or R1 reads or Long reads) if " +
244 "an input directory is mentioned via --input option. Default: ${params.fq_suffix}"
245 helptext['--fq2_suffix'] = "The suffix of FASTQ files (Paired-end reads or R2 reads) if an input directory is mentioned via " +
246 "--input option. Default: ${params.fq2_suffix}"
247 helptext['--fq_filter_by_len'] = "Remove FASTQ reads that are less than this many bases. " +
248 "Default: ${params.fq_filter_by_len}"
249 helptext['--fq_strandedness'] = "The strandedness of the sequencing run. This is mostly needed " +
250 "if your sequencing run is RNA-SEQ. For most of the other runs, it is probably safe to use " +
251 "unstranded for the option. Default: ${params.fq_strandedness}"
252 helptext['--fq_single_end'] = "SINGLE-END information will be auto-detected but this option forces " +
253 "PAIRED-END FASTQ files to be treated as SINGLE-END so only read 1 information is included in " +
254 "auto-generated samplesheet. Default: ${params.fq_single_end}"
255 helptext['--fq_filename_delim'] = "Delimiter by which the file name is split to obtain sample name. " +
256 "Default: ${params.fq_filename_delim}"
257 helptext['--fq_filename_delim_idx'] = "After splitting FASTQ file name by using the --fq_filename_delim option," +
258 " all elements before this index (1-based) will be joined to create final sample name." +
259 " Default: ${params.fq_filename_delim_idx}"
260
261 return helptext
262 }
263
264 // Show concise help text if configured within the main workflow.
265 def conciseHelp(def tool = null) {
266 Map fgcolors = getANSIColors()
267
268 tool ?= "fastp"
269 tools = tool?.tokenize(',')
270
271 return """
272 ${dashedLine()}
273 Show configurable CLI options for each tool within ${fgcolors.magenta}${params.pipeline}${fgcolors.reset}
274 ${dashedLine()}
275 Ex: cpipes --pipeline ${params.pipeline} --help
276 """ + (tools.size() > 1 ? "Ex: cpipes --pipeline ${params.pipeline} --help ${tools[0]}"
277 + """
278 Ex: cpipes --pipeline ${params.pipeline} --help ${tools[0]},${tools[1]}
279 ${dashedLine()}""".stripIndent() : """Ex: cpipes --pipeline ${params.pipeline} --help ${tool}
280 ${dashedLine()}""".stripIndent())
281
282 }
283
284 // Wrap help text with the following options
285 def wrapUpHelp() {
286
287 return [
288 'Help options' : "",
289 '--help': "Display this message.\n",
290 'help': true,
291 'nocapitalize': true
292 ]
293 }
294
295 // Method to send email on workflow complete.
296 def sendMail() {
297
298 if (params.user_email == null) {
299 return 1
300 }
301
302 def pad = (params.pad) ?: 30
303 def contact_emails = [
304 stakeholder: (params.workflow_blueprint_by ?: 'Not defined'),
305 author: (params.workflow_built_by ?: 'Not defined')
306 ]
307 def msg = """
308 ${pipelineBanner()}
309 ${summaryOfParams()}
310 ${params.cfsanpipename} - ${params.pipeline}
311 ${dashedLine()}
312 Please check the following directory for N E X T F L O W
313 reports. You can view the HTML files directly by double clicking
314 them on your workstation.
315 ${dashedLine()}
316 ${params.tracereportsdir}
317 ${dashedLine()}
318 Please send any bug reports to CFSAN Dev Team or the author or
319 the stakeholder of the current pipeline.
320 ${dashedLine()}
321 Error messages (if any)
322 ${dashedLine()}
323 ${workflow.errorMessage}
324 ${workflow.errorReport}
325 ${dashedLine()}
326 Contact emails
327 ${dashedLine()}
328 ${addPadding(contact_emails)}
329 ${dashedLine()}
330 Thank you for using ${params.cfsanpipename} - ${params.pipeline}!
331 ${dashedLine()}
332 """.stripIndent()
333
334 def mail_cmd = [
335 'sendmail',
336 '-f', 'noreply@gmail.com',
337 '-F', 'noreply',
338 '-t', "${params.user_email}"
339 ]
340
341 def email_subject = "${params.cfsanpipename} - ${params.pipeline}"
342 Map fgcolors = getANSIColors()
343
344 if (workflow.success) {
345 email_subject += ' completed successfully!'
346 }
347 else if (!workflow.success) {
348 email_subject += ' has failed!'
349 }
350
351 try {
352 ['env', 'bash'].execute() << """${mail_cmd.join(' ')}
353 Subject: ${email_subject}
354 Mime-Version: 1.0
355 Content-Type: text/html
356 <pre>
357 ${msg.replaceAll(/\x1b\[[0-9;]*m/, '')}
358 </pre>
359 """.stripIndent()
360 } catch (all) {
361 def warning_msg = "${fgcolors.yellow}${params.cfsanpipename} - ${params.pipeline} - WARNING"
362 .padRight(pad) + ':'
363 log.info """
364 ${dashedLine()}
365 ${warning_msg}
366 ${dashedLine()}
367 Could not send mail with the sendmail command!
368 ${dashedLine()}
369 """.stripIndent()
370 }
371 return 1
372 }
373
374 // Set ANSI colors for any and all
375 // STDOUT or STDERR
376 def getANSIColors() {
377
378 Map fgcolors = [:]
379
380 fgcolors['reset'] = "\033[0m"
381 fgcolors['black'] = "\033[0;30m"
382 fgcolors['red'] = "\033[0;31m"
383 fgcolors['green'] = "\033[0;32m"
384 fgcolors['yellow'] = "\033[0;33m"
385 fgcolors['blue'] = "\033[0;34m"
386 fgcolors['magenta'] = "\033[0;35m"
387 fgcolors['cyan'] = "\033[0;36m"
388 fgcolors['white'] = "\033[0;37m"
389
390 return fgcolors
391 }