forked from genomicsITER/NanoCLUST
-
Notifications
You must be signed in to change notification settings - Fork 0
/
main.nf
692 lines (570 loc) · 25.5 KB
/
main.nf
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
#!/usr/bin/env nextflow
/*
========================================================================================
nf-core/nanoclust
========================================================================================
nf-core/nanoclust Analysis Pipeline.
#### Homepage / Documentation
https://github.com/nf-core/nanoclust
----------------------------------------------------------------------------------------
*/
log.info nfcoreHeader()
def helpMessage() {
log.info"""
Usage:
The typical command for running the pipeline is as follows:
nextflow run nf-core/nanoclust --reads 'reads.fastq' --db "path/to/db" --tax "path/to/taxdb" -profile conda
Mandatory arguments:
--reads Path to input data (must be surrounded with quotes)
-profile Configuration profile to use. Can use multiple (comma separated)
Available: conda, docker, singularity, awsbatch, test and more.
UMAP and HDBSCAN clustering parameters:
--umap_set_size Number of reads used to perform the UMAP+HDBSCAN clustering (100000)
--cluster_sel_epsilon Minimun distance to separate clusters. (0.5)
--min_cluster_size Minimum number of reads to call a independent cluster (100)
--min_read_length Minimum number of base pair in sequence reads (1400)
--max_read_length Maximum number of base pair in sequence reads (1700)
--avg_amplicon_size Average size for the sequenced amplicon (ie: 1.5k for 16S/1.8k for 18S)
Other options:
--demultiplex Set this parameter if you file is a pooled sample
--demultiplex_porechop Same as --demultiplex but uses Porechop for the task
--kit (Only with --demultiplex) Barcoding kit (RAB204) {Auto,PBC096,RBK004,NBD104/NBD114,PBK004/LWB001,RBK001,RAB204,VMK001,PBC001,NBD114,NBD103/NBD104,DUAL,RPB004/RLB001}
--umap_set_size Number of reads used to perform the UMAP+HDBSCAN clustering (100000)
--cluster_sel_epsilon Minimun distance to separate clusters. (0.5)
--min_cluster_size Minimum number of reads to call a independent cluster (100)
--polishing_reads Number of reads used for polishing (100)
--db Path to local BLAST database. If not specified, search will be done againts NCBI 16S Microbial
--tax Path to taxdb database which contains the names for the --db entries
--outdir The output directory where the results will be saved
--email Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits
--email_on_fail Same as --email, except only send mail if the workflow is not successful
--maxMultiqcEmailFileSize Theshold size for MultiQC report to be attached in notification email. If file generated by pipeline exceeds the threshold, it will not be attached (Default: 25MB)
-name Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic.
""".stripIndent()
}
// Show help message
if (params.help) {
helpMessage()
exit 0
}
/*
* SET UP CONFIGURATION VARIABLES
*/
def racon_warnings = []
if(params.demultiplex) {
Channel.fromPath(params.reads).set { multiplexed_reads }
}
else if(params.demultiplex_porechop){
Channel.fromPath(params.reads).set { multiplexed_reads_porechop }
}
else{
Channel.fromPath(params.reads).set { reads }
}
// Has the run name been specified by the user?
// this has the bonus effect of catching both -name and --name
custom_runName = params.name
if (!(workflow.runName ==~ /[a-z]+_[a-z]+/)) {
custom_runName = workflow.runName
}
// Stage config files
ch_multiqc_config = file(params.multiqc_config, checkIfExists: true)
ch_output_docs = file("$baseDir/docs/3pipeline_output.md", checkIfExists: true)
// Header log info
//log.info nfcoreHeader()
def summary = [:]
if (workflow.revision) summary['Pipeline Release'] = workflow.revision
summary['Run Name'] = custom_runName ?: workflow.runName
// TODO nf-core: Report custom parameters here
summary['Reads'] = params.reads
summary['Max Resources'] = "$params.max_memory memory, $params.max_cpus cpus, $params.max_time time per job"
if (workflow.containerEngine) summary['Container'] = "$workflow.containerEngine - $workflow.container"
summary['Output dir'] = params.outdir
summary['Launch dir'] = workflow.launchDir
summary['Working dir'] = workflow.workDir
summary['Script dir'] = workflow.projectDir
summary['User'] = workflow.userName
summary['Config Profile'] = workflow.profile
if (params.config_profile_description) summary['Config Description'] = params.config_profile_description
if (params.config_profile_contact) summary['Config Contact'] = params.config_profile_contact
if (params.config_profile_url) summary['Config URL'] = params.config_profile_url
if (params.email || params.email_on_fail) {
summary['E-mail Address'] = params.email
summary['E-mail on failure'] = params.email_on_fail
summary['MultiQC maxsize'] = params.maxMultiqcEmailFileSize
}
log.info summary.collect { k,v -> "${k.padRight(18)}: $v" }.join("\n")
log.info "-\033[2m--------------------------------------------------\033[0m-"
// Check the hostnames against configured profiles
checkHostname()
def create_workflow_summary(summary) {
def yaml_file = workDir.resolve('workflow_summary_mqc.yaml')
yaml_file.text = """
id: 'nf-core-nanoclust-summary'
description: " - this information is collected when the pipeline is started."
section_name: 'nf-core/nanoclust Workflow Summary'
section_href: 'https://github.com/nf-core/nanoclust'
plot_type: 'html'
data: |
<dl class=\"dl-horizontal\">
${summary.collect { k,v -> " <dt>$k</dt><dd><samp>${v ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>" }.join("\n")}
</dl>
""".stripIndent()
return yaml_file
}
/*
* Parse software version numbers
*/
/*
process get_software_versions {
publishDir "${params.outdir}/pipeline_info", mode: 'copy',
saveAs: { filename ->
if (filename.indexOf(".csv") > 0) filename
else null
}
output:
file 'software_versions_mqc.yaml' into software_versions_yaml
file "software_versions.csv"
script:
// TODO nf-core: Get all tools to print their version number here
"""
echo $workflow.manifest.version > v_pipeline.txt
echo $workflow.nextflow.version > v_nextflow.txt
"""
} */
/*
* STEP 1 - Quality control
*/
good_reads = 0
cluster_count = []
if(params.demultiplex) {
process demultiplex {
publishDir "${params.outdir}/demultiplexed_samples", mode: 'copy'
input:
file(reads) from multiplexed_reads
output:
file("barcode*.fastq") into reads mode flatten
script:
kit = params.kit
"""
qcat -f $reads -k $kit --trim -t ${task.cpus} -b .
"""
}
}
if(params.demultiplex_porechop){
process demultiplex_porechop {
input:
file(reads) from multiplexed_reads_porechop
output:
file("BC*.fastq") into reads mode flatten
script:
"""
porechop -i "${reads}" -t 4 -b .
"""
}
}
process QC {
input:
file(reads) from reads
output:
tuple env(barcode), file("*qced_reads_set.fastq") into reads_fastqc, qc_results
script:
"""
barcode=${reads.baseName}
fastp -i $reads -q 8 -l ${params.min_read_length} --length_limit ${params.max_read_length} -o \$barcode\\_qced_reads.fastq
#perl prinseq-lite.pl -fastq $reads -out_good qced_reads -min_len 1400 -max_len 1700 -log qc_log -min_qual_mean 8
head -n\$(( ${params.umap_set_size}*4 )) \$barcode\\_qced_reads.fastq > \$barcode\\_qced_reads_set.fastq
"""
}
process fastqc {
publishDir "${params.outdir}/fastqc_rawdata", mode: 'copy',
saveAs: {filename -> filename.indexOf(".zip") > 0 ? "zips/$filename" : "$filename"}
input:
set val(name), file(reads) from reads_fastqc
output:
file "*_fastqc.{zip,html}" into fastqc_results
script:
"""
fastqc -q $reads
"""
}
if(params.multiqc){
process multiqc {
publishDir "${params.outdir}/MultiQC", mode: 'copy'
input:
file ('fastqc/*') from fastqc_results.collect().ifEmpty([])
output:
file "*multiqc_report.html"
file "*_data"
script:
"""
multiqc .
"""
}
}
process kmer_freqs {
memory { 7.GB * task.attempt }
time { 1.hour * task.attempt }
errorStrategy { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
maxRetries 3
input:
tuple val(barcode), file(qced_reads) from qc_results
output:
file "freqs.txt" into freqs
tuple val(barcode), file(qced_reads) into freqs_qc_results
script:
"""
kmer_freq.py -r $qced_reads > freqs.txt
"""
}
process read_clustering {
time { 1.hour * task.attempt }
errorStrategy { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
maxRetries 3
publishDir "${params.outdir}/${barcode}/", mode: 'copy', pattern: 'hdbscan.output.*'
input:
file(kmer_freqs) from freqs
tuple val(barcode), file(qced_reads) from freqs_qc_results
output:
tuple val(barcode), file('hdbscan.output.tsv'), file(qced_reads) into clustering_out
file('*.png')
script:
template "umap_hdbscan.py"
}
process split_by_cluster {
input:
tuple val(barcode), file(clusters), file(qced_reads) from clustering_out
output:
tuple val(barcode), file('*[0-9]*.log'), file('*[0-9]*.fastq') into cluster_reads mode flatten
script:
"""
sed 's/\\srunid.*//g' $qced_reads > only_id_header_readfile.fastq
CLUSTERS_CNT=\$(awk '(\$5 ~ /[0-9]/) {print \$5}' $clusters | sort -nr | uniq | head -n1)
for ((i = 0 ; i <= \$CLUSTERS_CNT ; i++));
do
cluster_id=\$i
awk -v cluster="\$cluster_id" '(\$5 == cluster) {print \$1}' $clusters > \$cluster_id\\_ids.txt
seqtk subseq only_id_header_readfile.fastq \$cluster_id\\_ids.txt > \$cluster_id.fastq
READ_COUNT=\$(( \$(awk '{print \$1/4}' <(wc -l \$cluster_id.fastq)) ))
echo -n "\$cluster_id;\$READ_COUNT" > \$cluster_id.log
done
"""
}
process read_correction {
memory { 7.GB * task.attempt }
time { 1.hour * task.attempt }
errorStrategy { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
maxRetries 3
input:
tuple val(barcode), file(cluster_log), file(reads) from cluster_reads
output:
tuple val(barcode), val(cluster_id), file('*_racon_.log'), file('corrected_reads.correctedReads.fasta') into corrected_reads
script:
count=params.polishing_reads
cluster_id=cluster_log.baseName
"""
head -n\$(( $count*4 )) $reads > subset.fastq
canu -correct -p corrected_reads -nanopore-raw subset.fastq genomeSize=${params.avg_amplicon_size} stopOnLowCoverage=1 minInputCoverage=2 minReadLength=500 minOverlapLength=200
gunzip corrected_reads.correctedReads.fasta.gz
READ_COUNT=\$(( \$(awk '{print \$1/2}' <(wc -l corrected_reads.correctedReads.fasta)) ))
cat $cluster_log > ${cluster_id}_racon.log
echo -n ";$count;\$READ_COUNT;" >> ${cluster_id}_racon.log && cp ${cluster_id}_racon.log ${cluster_id}_racon_.log
"""
}
process draft_selection {
publishDir "${params.outdir}/${barcode}/cluster${cluster_id}", mode: 'copy', pattern: 'draft_read.fasta'
errorStrategy 'retry'
input:
tuple val(barcode), val(cluster_id), file(cluster_log), file(reads) from corrected_reads
output:
tuple val(barcode), val(cluster_id), file('*_draft.log'), file('draft_read.fasta'), file(reads) into draft
script:
"""
split -l 2 $reads split_reads
find split_reads* > read_list.txt
fastANI --ql read_list.txt --rl read_list.txt -o fastani_output.ani -t 48 -k 16 --fragLen 160
DRAFT=\$(awk 'NR>1{name[\$1] = \$1; arr[\$1] += \$3; count[\$1] += 1} END{for (a in arr) {print arr[a] / count[a], name[a] }}' fastani_output.ani | sort -rg | cut -d " " -f2 | head -n1)
cat \$DRAFT > draft_read.fasta
ID=\$(head -n1 draft_read.fasta | sed 's/>//g')
cat $cluster_log > ${cluster_id}_draft.log
echo -n \$ID >> ${cluster_id}_draft.log
"""
}
process racon_pass {
memory { 7.GB * task.attempt }
time { 1.hour * task.attempt }
errorStrategy { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
maxRetries 3
input:
tuple val(barcode), val(cluster_id), file(cluster_log), file(draft_read), file(corrected_reads) from draft
output:
tuple val(barcode), val(cluster_id), file(cluster_log), file('racon_consensus.fasta'), file(corrected_reads), env(success) into racon_output
script:
"""
success=1
minimap2 -ax map-ont --no-long-join -r100 -a $draft_read $corrected_reads -o aligned.sam
if racon --quality-threshold=9 -w 250 $corrected_reads aligned.sam $draft_read > racon_consensus.fasta ; then
success=1
else
success=0
cat $draft_read > racon_consensus.fasta
fi
"""
}
process medaka_pass {
memory { 7.GB * task.attempt }
time { 1.hour * task.attempt }
errorStrategy { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
maxRetries 3
publishDir "${params.outdir}/${barcode}/cluster${cluster_id}", mode: 'copy', pattern: 'consensus_medaka.fasta/consensus.fasta'
input:
tuple val(barcode), val(cluster_id), file(cluster_log), file(draft), file(corrected_reads), val(success) from racon_output
output:
tuple val(barcode), val(cluster_id), file(cluster_log), file('consensus_medaka.fasta/consensus.fasta') into final_consensus
script:
if(success == "0"){
log.warn """Sample $barcode : Racon correction for cluster $cluster_id failed due to not enough overlaps. Taking draft read as consensus"""
racon_warnings.add("""Sample $barcode : Racon correction for cluster $cluster_id failed due to not enough overlaps. Taking draft read as consensus""")
}
"""
if medaka_consensus -i $corrected_reads -d $draft -o consensus_medaka.fasta -t 4 -m r941_min_high_g303 ; then
echo "Command succeeded"
else
cat $draft > consensus_medaka.fasta
fi
"""
}
def resolve_blast_db_path (path) {
if(path ==~ /^\/.*/)
path
else if(path ==~ /^\.\/.*/)
"$projectDir/" + path
else if(workflow.profile == 'conda' || workflow.profile == 'test,conda')
"$baseDir/" + path
else
"/tmp/" + path
}
process consensus_classification {
publishDir "${params.outdir}/${barcode}/cluster${cluster_id}", mode: 'copy', pattern: 'consensus_classification.csv'
time '3m'
errorStrategy { sleep(1000); return 'retry' }
maxRetries 5
input:
tuple val(barcode), val(cluster_id), file(cluster_log), file(consensus) from final_consensus
output:
file('consensus_classification.csv')
tuple val(barcode), file('*_blast.log') into classifications_ch
script:
db = resolve_blast_db_path(params.db)
taxdb = resolve_blast_db_path(params.tax)
if(!params.db)
"""
blastn -query $consensus -db nr -remote -entrez_query "Bacteria [Organism]" -task blastn -dust no -outfmt "10 staxids sscinames evalue length score pident" -evalue 11 -max_hsps 50 -max_target_seqs 5 > consensus_classification.csv
cat $cluster_log > ${cluster_id}_blast.log
echo -n ";" >> ${cluster_id}_blast.log
BLAST_OUT=\$(cut -d";" -f1,2,4,5 consensus_classification.csv | head -n1)
echo \$BLAST_OUT >> ${cluster_id}_blast.log
"""
else
"""
export BLASTDB=
export BLASTDB=\$BLASTDB:$taxdb
blastn -query $consensus -db $db -task blastn -dust no -outfmt "10 sscinames staxids evalue length pident" -evalue 11 -max_hsps 50 -max_target_seqs 5 | sed 's/,/;/g' > consensus_classification.csv
#DECIDE FINAL CLASSIFFICATION
cat $cluster_log > ${cluster_id}_blast.log
echo -n ";" >> ${cluster_id}_blast.log
BLAST_OUT=\$(cut -d";" -f1,2,4,5 consensus_classification.csv | head -n1)
echo \$BLAST_OUT >> ${cluster_id}_blast.log
"""
}
process join_results {
publishDir "${params.outdir}/${barcode}", mode: 'copy'
input:
tuple val(barcode), file(logs) from classifications_ch.groupTuple()
output:
tuple val(barcode), file('*.nanoclust_out.txt') into output_table_ch
script:
"""
echo "id;reads_in_cluster;used_for_consensus;reads_after_corr;draft_id;sciname;taxid;length;per_ident" > ${barcode}.nanoclust_out.txt
for i in $logs; do
cat \$i >> ${barcode}.nanoclust_out.txt
done
"""
}
process get_abundances {
publishDir "${params.outdir}/${barcode}", mode: 'copy'
input:
tuple val(barcode), file(table) from output_table_ch
output:
tuple val(barcode), file('*.csv') into abundance_table_ch mode flatten
script:
template "get_abundance.py"
}
process plot_abundances {
publishDir "${params.outdir}/${barcode}", mode: 'copy'
input:
tuple val(barcode), file(table) from abundance_table_ch
output:
file("*.png")
script:
template "plot_abundances_pool.py"
}
process output_documentation {
publishDir "${params.outdir}/pipeline_info", mode: 'copy'
input:
file output_docs from ch_output_docs
output:
file "results_description.html"
script:
"""
markdown_to_html.py $output_docs -o results_description.html
"""
}
/*
* Completion e-mail notification
*/
workflow.onComplete {
// Set up the e-mail variables
def subject = "[nf-core/nanoclust] Successful: $workflow.runName"
if (!workflow.success) {
subject = "[nf-core/nanoclust] FAILED: $workflow.runName"
}
def email_fields = [:]
email_fields['version'] = workflow.manifest.version
email_fields['runName'] = custom_runName ?: workflow.runName
email_fields['success'] = workflow.success
email_fields['dateComplete'] = workflow.complete
email_fields['duration'] = workflow.duration
email_fields['exitStatus'] = workflow.exitStatus
email_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
email_fields['errorReport'] = (workflow.errorReport ?: 'None')
email_fields['commandLine'] = workflow.commandLine
email_fields['projectDir'] = workflow.projectDir
email_fields['summary'] = summary
email_fields['summary']['Date Started'] = workflow.start
email_fields['summary']['Date Completed'] = workflow.complete
email_fields['summary']['Pipeline script file path'] = workflow.scriptFile
email_fields['summary']['Pipeline script hash ID'] = workflow.scriptId
if (workflow.repository) email_fields['summary']['Pipeline repository Git URL'] = workflow.repository
if (workflow.commitId) email_fields['summary']['Pipeline repository Git Commit'] = workflow.commitId
if (workflow.revision) email_fields['summary']['Pipeline Git branch/tag'] = workflow.revision
if (workflow.container) email_fields['summary']['Docker image'] = workflow.container
email_fields['summary']['Nextflow Version'] = workflow.nextflow.version
email_fields['summary']['Nextflow Build'] = workflow.nextflow.build
email_fields['summary']['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
// TODO nf-core: If not using MultiQC, strip out this code (including params.maxMultiqcEmailFileSize)
// On success try attach the multiqc report
def mqc_report = null
try {
if (workflow.success) {
mqc_report = multiqc_report.getVal()
if (mqc_report.getClass() == ArrayList) {
log.warn "[nf-core/nanoclust] Found multiple reports from process 'multiqc', will use only one"
mqc_report = mqc_report[0]
}
}
} catch (all) {
log.warn "[nf-core/nanoclust] Could not attach MultiQC report to summary email"
}
// Check if we are only sending emails on failure
email_address = params.email
if (!params.email && params.email_on_fail && !workflow.success) {
email_address = params.email_on_fail
}
// Render the TXT template
def engine = new groovy.text.GStringTemplateEngine()
def tf = new File("$baseDir/assets/email_template.txt")
def txt_template = engine.createTemplate(tf).make(email_fields)
def email_txt = txt_template.toString()
// Render the HTML template
def hf = new File("$baseDir/assets/email_template.html")
def html_template = engine.createTemplate(hf).make(email_fields)
def email_html = html_template.toString()
// Render the sendmail template
def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, baseDir: "$baseDir", mqcFile: mqc_report, mqcMaxSize: params.maxMultiqcEmailFileSize.toBytes() ]
def sf = new File("$baseDir/assets/sendmail_template.txt")
def sendmail_template = engine.createTemplate(sf).make(smail_fields)
def sendmail_html = sendmail_template.toString()
// Send the HTML e-mail
if (email_address) {
try {
if ( params.plaintext_email ){ throw GroovyException('Send plaintext e-mail, not HTML') }
// Try to send HTML e-mail using sendmail
[ 'sendmail', '-t' ].execute() << sendmail_html
log.info "[nf-core/nanoclust] Sent summary e-mail to $email_address (sendmail)"
} catch (all) {
// Catch failures and try with plaintext
[ 'mail', '-s', subject, email_address ].execute() << email_txt
log.info "[nf-core/nanoclust] Sent summary e-mail to $email_address (mail)"
}
}
// Write summary e-mail HTML to a file
def output_d = new File( "${params.outdir}/pipeline_info/" )
if (!output_d.exists()) {
output_d.mkdirs()
}
def output_hf = new File( output_d, "pipeline_report.html" )
output_hf.withWriter { w -> w << email_html }
def output_tf = new File( output_d, "pipeline_report.txt" )
output_tf.withWriter { w -> w << email_txt }
c_reset = params.monochrome_logs ? '' : "\033[0m";
c_purple = params.monochrome_logs ? '' : "\033[0;35m";
c_green = params.monochrome_logs ? '' : "\033[0;32m";
c_red = params.monochrome_logs ? '' : "\033[0;31m";
if (workflow.stats.ignoredCount > 0 && workflow.success) {
log.info "${c_purple}Warning, pipeline completed, but with errored process(es) ${c_reset}"
log.info "${c_red}Number of ignored errored process(es) : ${workflow.stats.ignoredCount} ${c_reset}"
log.info "${c_green}Number of successfully ran process(es) : ${workflow.stats.succeedCount} ${c_reset}"
}
if (workflow.success) {
log.info "${c_purple}[nf-core/nanoclust]${c_green} Pipeline completed successfully${c_reset}"
if(!racon_warnings.isEmpty()){
racon_warnings.each{log.warn "$it"}
}
} else {
checkHostname()
log.info "${c_purple}[nf-core/nanoclust]${c_red} Pipeline completed with errors${c_reset}"
}
}
def nfcoreHeader(){
// Log colors ANSI codes
c_reset = params.monochrome_logs ? '' : "\033[0m";
c_dim = params.monochrome_logs ? '' : "\033[2m";
c_black = params.monochrome_logs ? '' : "\033[0;30m";
c_green = params.monochrome_logs ? '' : "\033[0;32m";
c_yellow = params.monochrome_logs ? '' : "\033[0;33m";
c_blue = params.monochrome_logs ? '' : "\033[0;34m";
c_purple = params.monochrome_logs ? '' : "\033[0;35m";
c_cyan = params.monochrome_logs ? '' : "\033[0;36m";
c_white = params.monochrome_logs ? '' : "\033[0;37m";
c_red = params.monochrome_logs ? '' : "\033[0;31m";
return """
-${c_dim}--------------------------------------------------${c_reset}-
${c_green} _ __ ${c_red} ________ __ _____________${c_reset}
${c_green} / | / /___ _____ ____ ${c_red} / ____/ / / / / / ___/_ __/${c_reset}
${c_green} / |/ / __ `/ __ \\/ __ \\ ${c_red} / / / / / / / /\\__ \\ / / ${c_reset}
${c_green} / /| / /_/ / / / / /_/ / ${c_red} / /___/ /___/ /_/ /___/ // / ${c_reset}
${c_green} /_/ |_/\\__,_/_/ /_/\\____/ ${c_red} \\____/_____/\\____//____//_/ ${c_reset}
${c_purple} NanoCLUST v${workflow.manifest.version}${c_reset}
-${c_dim}--------------------------------------------------${c_reset}-
""".stripIndent()
}
def checkHostname(){
def c_reset = params.monochrome_logs ? '' : "\033[0m"
def c_white = params.monochrome_logs ? '' : "\033[0;37m"
def c_red = params.monochrome_logs ? '' : "\033[1;91m"
def c_yellow_bold = params.monochrome_logs ? '' : "\033[1;93m"
if (params.hostnames) {
def hostname = "hostname".execute().text.trim()
params.hostnames.each { prof, hnames ->
hnames.each { hname ->
if (hostname.contains(hname) && !workflow.profile.contains(prof)) {
log.error "====================================================\n" +
" ${c_red}WARNING!${c_reset} You are running with `-profile $workflow.profile`\n" +
" but your machine hostname is ${c_white}'$hostname'${c_reset}\n" +
" ${c_yellow_bold}It's highly recommended that you use `-profile $prof${c_reset}`\n" +
"============================================================"
}
}
}
}
}