-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathmain.nf
1371 lines (1085 loc) · 50.3 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
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
#!/usr/bin/env nextflow
/*
========================================================================================
nf-core/umisrnaseqv
========================================================================================
nf-core/umisrnaseqv Analysis Pipeline.
#### Homepage / Documentation
https://github.com/nf-core/umisrnaseqv
----------------------------------------------------------------------------------------
*/
def helpMessage() {
// TODO nf-core: Add to this help message with new command line parameters
log.info nfcoreHeader()
log.info"""
Usage:
The typical command for running the pipeline is as follows:
nextflow run nf-core/umisrnaseqv --input '*_R{1,2}.fastq.gz' -profile docker
nextflow run umisrnaseqv -profile conda --input 'samplesheet.csv' (../Proyectos/ctDNA/muestras_ctDNA_test/muestras_ctDNA_test_filt/samplesheet.csv)
nextflow run umisrnaseqv -profile conda --input ../Proyectos/ctDNA/muestras_ctDNA_test/muestras_ctDNA_test_filt/samplesheet.csv
Mandatory arguments:
--input [file] Path to input data (must be surrounded with quotes)
-profile [str] Configuration profile to use. Can use multiple (comma separated)
Available: conda, docker, singularity, test, awsbatch, <institute> and more
Options:
--genome [str] Name of iGenomes reference
--single_end [bool] Specifies that the input is single-end reads
References If not specified in the configuration file or you wish to overwrite any of the references
--fasta [file] Path to fasta reference
Other options:
--outdir [file] The output directory where the results will be saved
--publish_dir_mode [str] Mode for publishing results in the output directory. Available: symlink, rellink, link, copy, copyNoFollow, move (Default: copy)
--email [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 [email] Same as --email, except only send mail if the workflow is not successful
--max_multiqc_email_size [str] Threshold 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 [str] Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic
AWSBatch options:
--awsqueue [str] The AWSBatch JobQueue that needs to be set when running on AWSBatch
--awsregion [str] The AWS Region for your AWS Batch job to run on
--awscli [str] Path to the AWS CLI tool
""".stripIndent()
}
// Show help message
if (params.help) {
helpMessage()
exit 0
}
/*
* VALIDATE INPUTS
*/
if (params.input) { ch_input = file(params.input, checkIfExists: true) } else { exit 1, "Cannot carry out the analysis, input samplesheet file not specified!" }
if (params.fasta) { ch_fasta = file(params.fasta, checkIfExists: true) } else { exit 1, "Cannot carry out the analysis, reference genome file not specified!"}
if (params.bwa_index) { ch_bwa_index = Channel.fromPath( params.bwa_index, type: 'dir', checkIfExists: true ) } else {
if (params.skip_get_bwa_index) {
exit 1, "Cannot carry out the analysis! BWA index not specified! Please, provide a valid path to BWA index or don't skip BWA index obtention (skip_get_bwa_index = false)!"
}
}
if (params.picard_merge_dict) { ch_dict = Channel.fromPath( params.picard_merge_dict, type: 'dir', checkIfExists: true ) } else {
if (params.skip_get_picard_merge_dict) {
exit 1, "Cannot carry out the analysis! Reference dictionary for Picard BAM merge not specified! Please, provide a valid path to reference dictionary or don't skip Reference dictionary obtention (skip_get_picard_merge_dict = false)!"
}
}
if (params.index_mutect2) {ch_index_mutect2 = file(params.index_mutect2, checkIfExists: true) }
if (params.bed) { ch_bed = file(params.bed, checkIfExists: true) } else { exit 1, "Cannot carry out the analysis, bed file for variants detection not specified!"}
if (params.germline) { ch_germline = file(params.germline, checkIfExists: true) } else { exit 1, "Cannot carry out the analysis, germline vcf file for variants detection by Mutect2 not specified!"}
if (params.normal) { ch_normal = file(params.normal, checkIfExists: true) } else { exit 1, "Cannot carry out the analysis, normal vcf file for variants detection by Mutect2 not specified!"}
if (params.annovar_database) { ch_annovar_database = Channel.fromPath( params.annovar_database, type: 'dir', checkIfExists: true ) } else { exit 1, "Cannot carry out the analysis, annovar database not specified!"}
// Check if reference genome exists in the config file
if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
exit 1, "The provided genome '${params.genome}' is not available in the Genome file. Currently the available genomes are ${params.genomes.keySet().join(", ")}"
}
params.fasta = params.genome ? params.genomes[ params.genome ].fasta ?: false : false
params.gff = params.genome ? params.genomes[ params.genome ].gff ?: false : false
//vr?
/*
if (params.fasta) {
file(params.fasta, checkIfExists: true)
lastPath = params.fasta.lastIndexOf(File.separator)
lastExt = params.fasta.lastIndexOf(".")
fasta_base = params.fasta.substring(lastPath+1)
index_base = params.fasta.substring(lastPath+1,lastExt)
if (params.fasta.endsWith('.gz')) {
fasta_base = params.fasta.substring(lastPath+1,lastExt)
index_base = fasta_base.substring(0,fasta_base.lastIndexOf("."))
}
} else {
exit 1, "Reference genome fasta file not specified!"
}
*/
//params.fasta = params.genome ? params.genomes[ params.genome ].fasta ?: false : false
//if (params.fasta) { ch_fasta = file(params.fasta, checkIfExists: true) }
// Has the run name been specified by the user?
// this has the bonus effect of catching both -name and --name
custom_runName = params.name
if (!(workflow.runName ==~ /[a-z]+_[a-z]+/)) {
custom_runName = workflow.runName
}
// Stage config files
ch_multiqc_config = file("$projectDir/assets/multiqc_config.yaml", checkIfExists: true)
ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty()
ch_output_docs = file("$projectDir/docs/output.md", checkIfExists: true)
ch_output_docs_images = file("$projectDir/docs/images/", checkIfExists: true)
// Check AWS batch settings
if (workflow.profile.contains('awsbatch')) {
// AWSBatch sanity checking
if (!params.awsqueue || !params.awsregion) exit 1, "Specify correct --awsqueue and --awsregion parameters on AWSBatch!"
// Check outdir paths to be S3 buckets if running on AWSBatch
// related: https://github.com/nextflow-io/nextflow/issues/813
if (!params.outdir.startsWith('s3:')) exit 1, "Outdir not on S3 - specify S3 Bucket to run on AWSBatch!"
// Prevent trace files to be stored on S3 since S3 does not support rolling files.
if (params.tracedir.startsWith('s3:')) exit 1, "Specify a local tracedir or run without trace! S3 cannot be used for tracefiles."
}
// 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['Input'] = params.input
summary['Fasta Ref'] = params.fasta
summary['Data Type'] = params.single_end ? 'Single-End' : 'Paired-End'
summary['Max Resources'] = "$params.max_memory memory, $params.max_cpus cpus, $params.max_time time per job"
if (workflow.containerEngine) summary['Container'] = "$workflow.containerEngine - $workflow.container"
summary['Output dir'] = params.outdir
summary['Launch dir'] = workflow.launchDir
summary['Working dir'] = workflow.workDir
summary['Script dir'] = workflow.projectDir
summary['User'] = workflow.userName
if (workflow.profile.contains('awsbatch')) {
summary['AWS Region'] = params.awsregion
summary['AWS Queue'] = params.awsqueue
summary['AWS CLI'] = params.awscli
}
summary['Config Profile'] = workflow.profile
if (params.config_profile_description) summary['Config Profile Description'] = params.config_profile_description
if (params.config_profile_contact) summary['Config Profile Contact'] = params.config_profile_contact
if (params.config_profile_url) summary['Config Profile URL'] = params.config_profile_url
summary['Config Files'] = workflow.configFiles.join(', ')
if (params.email || params.email_on_fail) {
summary['E-mail Address'] = params.email
summary['E-mail on failure'] = params.email_on_fail
summary['MultiQC maxsize'] = params.max_multiqc_email_size
}
log.info summary.collect { k,v -> "${k.padRight(18)}: $v" }.join("\n")
log.info "-\033[2m--------------------------------------------------\033[0m-"
// Check the hostnames against configured profiles
checkHostname()
///////////////////////////////////////////////////////////////////
/* */
/* UNZIP/UNTAR REFERENCE FILES */
/* */
///////////////////////////////////////////////////////////////////
/*
* PREPROCESSING: Uncompress genome fasta file
*/
/*
if (params.fasta) {
file(params.fasta, checkIfExists: true)
if (params.fasta.endsWith('.gz')) {
process GUNZIP_FASTA {
label 'error_retry'
if (params.save_reference) {
publishDir "${params.outdir}/genome", mode: params.publish_dir_mode
}
input:
path fasta from params.fasta
output:
path "$unzip" into ch_fasta
script:
unzip = fasta.toString() - '.gz'
"""
pigz -f -d -p $task.cpus $fasta
"""
}
} else {
ch_fasta = file(params.fasta)
}
}
*/
/*
* PREPROCESSING 1: Reformat samplesheet and check validity
*/
process CHECK_SAMPLESHEET {
conda '/mnt/home/users/b02_cimes_uma/elpz/.conda/envs/env_umis_picasso'
tag "$samplesheet"
input:
path samplesheet from ch_input
output:
path samplesheet into ch_reformat_input
script:
"""
check_samplesheet.py $samplesheet
"""
}
// Function to get list of [ sample_id, [ fastq_1, fastq_2 ], fastq_3 ]
def validate_input(LinkedHashMap sample) {
def sample_id = sample.sample_id
def fastq_1 = sample.fastq_1
def fastq_2 = sample.fastq_2
def umis = sample.umis
def array = []
array = [ sample_id, [ fastq_1, fastq_2 ], umis ]
return array
}
/*
* Create channels for input fastq files
*/
ch_reformat_input
.splitCsv(header:true, sep:',')
.map { validate_input(it) }
.into { ch_fastqc
ch_trimgalore }
/*
* PREPROCESSING 2: Duplicate reference genome
*/
process DUPLICATE_REF_GENOME {
conda '/mnt/home/users/b02_cimes_uma/elpz/.conda/envs/env_umis_picasso'
tag "$fasta"
input:
path fasta from ch_fasta
output:
path fasta into ch_fasta_bwamap,
ch_fasta_bwaindex,
ch_fasta_picarddict,
ch_fasta_bwamapcons,
ch_fasta_filtercons,
ch_fasta_clipbam,
ch_fasta_index_mutect2,
ch_fasta_mutect2,
ch_fasta_vardict
script:
"""
echo $fasta
"""
}
/*
* PREPROCESSING 3: Get adn Duplicate BWA index
*/
if (!params.bwa_index) {
process BWAINDEX {
conda '/mnt/home/users/b02_cimes_uma/elpz/.conda/envs/env_umis_picasso'
tag "$sample"
label 'process_high'
//label 'process_low'
publishDir "${params.outdir}/bwamap/bwaindex", mode: params.publish_dir_mode
input:
path fasta from ch_fasta_bwaindex
output:
path "index" into ch_bwa_index
script:
"""
mkdir index
mv $fasta ./index/reference_genome.fna
bwa index ./index/reference_genome.fna
"""
}
}
process DUPLICATE_BWAINDEX {
conda '/mnt/home/users/b02_cimes_uma/elpz/.conda/envs/env_umis_picasso'
tag "$index"
input:
path index from ch_bwa_index
output: //
path index into ch_bwa_index_nocons,
ch_bwa_index_cons
script:
"""
echo $index
"""
}
/*
* PREPROCESSING 4: Get and Duplicate Picard dictionary
*/
if (!params.picard_merge_dict) {
process DICT {
conda '/mnt/home/users/b02_cimes_uma/elpz/.conda/envs/env_umis_picasso'
tag "$dict"
label 'process_medium'
publishDir "${params.outdir}/dict", mode: params.publish_dir_mode
input:
path fasta from ch_fasta_picarddict
output:
path "*dict" into ch_dict
script:
"""
picard CreateSequenceDictionary $fasta
"""
}
}
process DUPLICATE_DICT {
conda '/mnt/home/users/b02_cimes_uma/elpz/.conda/envs/env_umis_picasso'
tag "$dict"
input:
path dict from ch_dict
output:
path dict into ch_picard_merge_dict_nocons,
ch_picard_merge_dict_cons,
ch_mutect2_dict
script:
"""
echo $dict
"""
}
/*
* PREPROCESSING 5: Duplicate bed file for Vardict and Mutect2 variants calling
*/
if (params.bed) {
process DUPLICATE_VARIANTS_BED {
conda '/mnt/home/users/b02_cimes_uma/elpz/.conda/envs/env_umis_picasso'
tag "$bed"
input:
path bed from ch_bed
output:
path bed into ch_mutect2_bed,
ch_vardict_bed
script:
"""
echo $bed
"""
}
}
/*
* PREPROCESSING 6: Duplicate variants panels for Mutect2 variants calling
*/
process DUPLICATE_PANEL_NORMAL_MUTECT2 {
conda '/mnt/home/users/b02_cimes_uma/elpz/.conda/envs/env_umis_picasso'
tag "$vcf_normal"
input:
path vcf_normal from ch_normal
output:
path vcf_normal into ch_normal_index,
ch_normal_vcalling
script:
"""
echo $vcf_normal
"""
}
process DUPLICATE_PANEL_GERMLINE_MUTECT2 {
conda '/mnt/home/users/b02_cimes_uma/elpz/.conda/envs/env_umis_picasso'
tag "$vcf_germline"
input:
path vcf_germline from ch_germline
output:
path vcf_germline into ch_germline_index,
ch_germline_vcalling
script:
"""
echo $vcf_germline
"""
}
/*
* PREPROCESSING 7: Duplicate Annovar database
*/
if (params.annovar_database) {
process DUPLICATE_ANNOVAR_DATABASE {
conda '/mnt/home/users/b02_cimes_uma/elpz/.conda/envs/env_umis_picasso'
tag "$database"
input:
path database from ch_annovar_database
output:
path database into ch_annovar_mutect2_database,
ch_annovar_vardict_database
script:
"""
echo $database
"""
}
}
/*
* STEP 1: FastQC on input reads after merging libraries from the same sample
*/
process FASTQC {
conda '/mnt/home/users/b02_cimes_uma/elpz/.conda/envs/env_umis_picasso'
tag "$sample"
//label 'process_low'
label 'process_medium'
publishDir "${params.outdir}/1_fastqc/$sample", mode: params.publish_dir_mode,
saveAs: { filename ->
filename.endsWith(".zip") ? "zips/$filename" : filename
}
when:
!params.skip_fastqc
input:
tuple val(sample), path(reads), path(umis) from ch_fastqc
output:
path "*.{zip,html}" into ch_fastqc_raw_reports_mqc
script:
"""
fastqc --quiet --threads $task.cpus $reads
"""
}
/*
* STEP 2 - Trimgalore adapter trimming and quality filtering
*/
if (!params.skip_trimgalore_trimming) {
process TRIMGALORE {
conda '/mnt/home/users/b02_cimes_uma/elpz/.conda/envs/env_umis_picasso'
tag "$sample"
label 'process_medium'
//label 'process_low'
publishDir "${params.outdir}/2_trimgalore/$sample", mode: params.publish_dir_mode
input:
tuple val(sample), path(reads), path(umis) from ch_trimgalore
output:
tuple val(sample), path("*val_{1,2}.fq.gz"), path(umis) into ch_umisfiltering
script:
"""
trim_galore --fastqc --paired --cores 4 --gzip --output_dir ./ ${reads[0]} ${reads[1]}
"""
}
} else {
ch_trimgalore
.into { ch_umisfiltering }
}
/*
* STEP 3 - UMIs filtering after reads adapter trimming and quality filtering
*/
if (!params.skip_umis_filtering) {
process UMIS_FILTERING {
conda '/mnt/home/users/b02_cimes_uma/elpz/.conda/envs/env_umis_picasso'
tag "$sample"
label 'process_medium'
//label 'process_low'
publishDir "${params.outdir}/3_umis_filtering/$sample", mode: params.publish_dir_mode,
saveAs: { filename ->
if (filename.endsWith(".trimmed.UMIs.fastq.gz")) filename
}
input:
tuple val(sample), path(reads), path(umis) from ch_umisfiltering
output:
tuple val(sample), path(reads), path("*.trimmed.UMIs.fastq.gz") into ch_fastqtobam
script:
"""
keep_surviving_trimIds.Alfon.pl ${reads[1]} $umis | gzip > ${sample}.trimmed.UMIs.fastq.gz
"""
}
} else {
ch_umisfiltering
.into { ch_fastqtobam }
}
/*
if (!params.skip_umis_filtering) {
process UMIS_FILTERING {
conda '/mnt/home/users/b02_cimes_uma/elpz/.conda/envs/env_umis_picasso'
tag "$sample"
label 'process_medium'
//label 'process_low'
publishDir "${params.outdir}/3_umis_filtering/$sample", mode: params.publish_dir_mode,
saveAs: { filename ->
if (filename.endsWith(".trimmed.UMIs.fastq.gz")) filename
}
input:
tuple val(sample), path(reads), path(umis) from ch_umisfiltering
output:
tuple val(sample), path(reads), path("*.trimmed.UMIs.fastq.gz") into ch_fastqtobam
script:
"""
reads_1_nc=\$(echo "${reads[1]}" | rev | cut -c4- | rev)
umis_nc=\$(echo "$umis" | rev | cut -c4- | rev)
gzip -d --force ${reads[1]}
gzip -d --force $umis
keep_surviving_trimids_v2.py \$reads_1_nc \$umis_nc ${sample}.trimmed.UMIs.fastq
gzip ${sample}.trimmed.UMIs.fastq
gzip --force \$reads_1_nc
"""
}
} else {
ch_umisfiltering
.into { ch_fastqtobam }
}
*/
/*
* STEP 4 - Fastq to Bam conversion for sorting reads
*/
process SORTFASTQTOBAM {
conda '/mnt/home/users/b02_cimes_uma/elpz/.conda/envs/env_umis_picasso'
tag "$sample"
label 'process_medium'
//label 'process_low'
publishDir "${params.outdir}/4_sortfastqtobam/$sample", mode: params.publish_dir_mode
input:
tuple val(sample), path(reads), path(umis) from ch_fastqtobam
output:
tuple val(sample), path("*.unmapWUMI.srt.bam") into ch_bwamap
script:
"""
fgbio FastqToBam -i ${reads[0]} ${reads[1]} $umis -o ./${sample}.unmapWUMI.bam --read-structures +T +T 10M --sample=$sample --library=$sample
picard SortSam INPUT=./${sample}.unmapWUMI.bam OUTPUT=${sample}.unmapWUMI.srt.bam SORT_ORDER=queryname
"""
}
/*
* STEP 5 - Reads mapping and UMIs merge
*/
/*
if ( !params.skip_get_bwa_index && !params.bwa_index) {
process BWAINDEX {
conda '/mnt/home/users/b02_cimes_uma/elpz/.conda/envs/env_umis_picasso'
tag "$sample"
//label 'process_high'
label 'process_low'
publishDir "${params.outdir}/bwaindex", mode: params.publish_dir_mode
input:
path fasta from ch_fasta_bwaindex
output:
path "./" into ch_bwa_index
script:
"""
bwa index $fasta
"""
}
}
*/
/*
if ( !params.bwa_index) {
process BWAINDEX {
conda '/mnt/home/users/b02_cimes_uma/elpz/.conda/envs/env_umis_picasso'
tag "$sample"
//label 'process_high'
label 'process_low'
publishDir "${params.outdir}/bwaindex", mode: params.publish_dir_mode
input:
path fasta from ch_fasta_bwaindex
output:
path "index" into ch_bwa_index
script:
"""
mkdir index
mv $fasta ./index/${fasta}
cd index
bwa index $fasta
"""
}
}
*/
/*
if (!params.bwa_index) {
process BWAINDEX {
conda '/mnt/home/users/b02_cimes_uma/elpz/.conda/envs/env_umis_picasso'
tag "$sample"
//label 'process_high'
label 'process_low'
publishDir "${params.outdir}/bwamap/bwaindex", mode: params.publish_dir_mode
input:
path fasta from ch_fasta_bwaindex
output:
path "index" into ch_bwa_index
script:
"""
mkdir index
mv $fasta ./index/reference_genome.fna
bwa index ./index/reference_genome.fna
"""
}
}
*/
process BWAMAP {
conda '/mnt/home/users/b02_cimes_uma/elpz/.conda/envs/env_umis_picasso'
tag "$sample"
label 'process_high'
//label 'process_low'
publishDir "${params.outdir}/5_bwamap/$sample", mode: params.publish_dir_mode
input:
tuple val(sample), path(bam), path(path_index), path(fasta), path(dict) from ch_bwamap.combine(ch_bwa_index_nocons).combine(ch_fasta_bwamap).combine(ch_picard_merge_dict_nocons)
output:
tuple val(sample), path("*.mappedWUMI.bam") into ch_group_reads_by_umi
script:
"""
picard SamToFastq I=$bam F=${sample}.unmapWUMI.srt.fq INTERLEAVE=true
bwa mem -p -t 8 ${path_index}/*.fasta ${sample}.unmapWUMI.srt.fq > ${sample}.mapWUMI.sam
picard SortSam INPUT=${sample}.mapWUMI.sam OUTPUT=${sample}.mapWUMI.srt.sam SORT_ORDER=queryname
samtools view -Sb ${sample}.mapWUMI.srt.sam > ${sample}.mapWUMI.srt.bam
picard MergeBamAlignment UNMAPPED_BAM=$bam ALIGNED_BAM=${sample}.mapWUMI.srt.bam O=${sample}.mappedWUMI.bam R=$fasta SO=coordinate ALIGNER_PROPER_PAIR_FLAGS=true MAX_GAPS=-1 ORIENTATIONS=FR VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true
"""
}
/*
* STEP 6 - Reads grouping by UMI
*/
process GROUPREADSBYUMI {
conda '/mnt/home/users/b02_cimes_uma/elpz/.conda/envs/env_umis_picasso'
tag "$sample"
label 'process_medium'
publishDir "${params.outdir}/6_groupreadsbyumi/$sample", mode: params.publish_dir_mode
input:
tuple val(sample), path(bam) from ch_group_reads_by_umi
output:
tuple val(sample), path("*.mapWUMI.gbu.bam") into ch_call_molecular_consensus
script:
"""
mkdir logs
fgbio GroupReadsByUmi -s Adjacency -i $bam -o ${sample}.mapWUMI.gbu.bam -f ${sample}.mappedWUMI.gbu.hist.txt > logs/${sample}.GroupReadsByUmi.out 2>logs/${sample}.GroupReadsByUmi.err
"""
}
/*
* STEP 7 - Get Molecular Consensus for every read set grouped by UMIs
*/
process CALLMOLECULARCONSENSUS {
conda '/mnt/home/users/b02_cimes_uma/elpz/.conda/envs/env_umis_picasso'
tag "$sample"
label 'process_medium'
publishDir "${params.outdir}/7_callmolecularconsensus/$sample", mode: params.publish_dir_mode
input:
tuple val(sample), path(bam) from ch_call_molecular_consensus
output:
tuple val(sample), path("*.mappedWUMI.gbu.cons_unmap.bam") into ch_bwamap_cons
script:
"""
mkdir logs
fgbio CallMolecularConsensusReads --input $bam --output ${sample}.mappedWUMI.gbu.cons_unmap.bam --min-reads=1 --reject ${sample}.mappedWUMI.gbu.cons_rej.bam > logs/${sample}_CallMolecularConsensusReads.out 2>logs/${sample}_CallMolecularConsensusReads.error
"""
}
/*
* STEP 8 - Consensus reads mapping and UMIs merge
*/
process BWAMAPCONS {
conda '/mnt/home/users/b02_cimes_uma/elpz/.conda/envs/env_umis_picasso'
tag "$sample"
label 'process_high'
publishDir "${params.outdir}/8_bwamapcons/$sample", mode: params.publish_dir_mode
input:
tuple val(sample), path(bam), path(path_index), path(fasta), path(dict) from ch_bwamap_cons.combine(ch_bwa_index_cons).combine(ch_fasta_bwamapcons).combine(ch_picard_merge_dict_cons)
output:
tuple val(sample), path("*.mappedWUMI.gbu.bam") into ch_filtercons
script:
"""
picard SamToFastq RGT=A I=$bam F=${sample}.mapWUMI.gbu.fq INTERLEAVE=true
bwa mem -p -t 8 ${path_index}/*.fasta ${sample}.mapWUMI.gbu.fq > ${sample}.mapWUMI.gbu.sam
picard SortSam INPUT=${sample}.mapWUMI.gbu.sam OUTPUT=${sample}.mapWUMI.gbu.srt.sam SORT_ORDER=queryname
samtools view -Sb ${sample}.mapWUMI.gbu.srt.sam > ${sample}.mapWUMI.gbu.srt.bam
picard MergeBamAlignment UNMAPPED_BAM=$bam ALIGNED_BAM=${sample}.mapWUMI.gbu.srt.bam O=${sample}.mappedWUMI.gbu.bam R=$fasta SO=coordinate ALIGNER_PROPER_PAIR_FLAGS=true MAX_GAPS=-1 ORIENTATIONS=FR VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true
"""
}
/*
* STEP 9 - Consensus reads filtering
*/
process FILTERCONS {
conda '/mnt/home/users/b02_cimes_uma/elpz/.conda/envs/env_umis_picasso'
tag "$sample"
label 'process_medium'
publishDir "${params.outdir}/9_filtercons/$sample", mode: params.publish_dir_mode
input:
tuple val(sample), path(bam), path(fasta) from ch_filtercons.combine(ch_fasta_filtercons)
output:
tuple val(sample), path("*.mappedWUMI.FCons.min2.bam") into ch_clipbam
script:
"""
mkdir logs
fgbio FilterConsensusReads -M 2 -N 30 -i $bam -o ${sample}.mappedWUMI.FCons.min2.bam -r $fasta > logs/${sample}.FilterConsensusReads.min2.out 2> logs/${sample}.FilterConsensusReads.min2.err
"""
}
/*
* STEP 10 - Overlapping reads filtering
*/
process CLIPBAM {
conda '/mnt/home/users/b02_cimes_uma/elpz/.conda/envs/env_umis_picasso'
tag "$sample"
label 'process_medium'
publishDir "${params.outdir}/10_clipbam/$sample", mode: params.publish_dir_mode
input:
tuple val(sample), path(bam), path(fasta) from ch_clipbam.combine(ch_fasta_clipbam)
output:
tuple val(sample), path("*.mappedWUMI.FCons.min2.clip.bam") into ch_mutect2,
ch_vardict
script:
"""
mkdir logs
fgbio ClipBam -Xmx32000M --clip-overlapping-reads -i $bam -o ${sample}.mappedWUMI.FCons.min2.clip.bam -m ${sample}.mappedWUMI.FCons.min2.clip.metrics.txt -r $fasta > logs/${sample}.ClipBam.out 2> logs/${sample}.ClipBam.err
"""
}
/*
* STEP 11 - Mutect2 Variants Calling
*/
if (!params.index_mutect2) {
process INDEX_MUTECT2 {
conda '/mnt/home/users/b02_cimes_uma/elpz/.conda/envs/env_umis_picasso'
tag "$sample"
label 'process_medium'
publishDir "${params.outdir}/11_mutect2/index_mutect2", mode: params.publish_dir_mode
input:
path fasta from ch_fasta_index_mutect2
output:
tuple val(sample), path("*fai") into ch_index_mutect2
script:
"""
ref=\$(echo "$fasta" | rev | cut -c4- | rev)
gzip -d $fasta
samtools faidx \$ref
"""
}
}
process PANEL_NORMAL_INDEX_MUTECT2 {
conda '/mnt/home/users/b02_cimes_uma/elpz/.conda/envs/env_umis_picasso'
tag "$sample"
label 'process_medium'
publishDir "${params.outdir}/11_mutect2/index_mutect2", mode: params.publish_dir_mode
input:
path vcf_normal from ch_normal_index
output:
path "*.tbi" into ch_normal_index_vcalling
script:
"""
gatk IndexFeatureFile -I $vcf_normal
"""
}
process PANEL_GERMLINE_INDEX_MUTECT2 {
conda '/mnt/home/users/b02_cimes_uma/elpz/.conda/envs/env_umis_picasso'
tag "$sample"
label 'process_medium'
publishDir "${params.outdir}/11_mutect2/index_mutect2", mode: params.publish_dir_mode
input:
path vcf_germline from ch_germline_index
output:
path "*.tbi" into ch_germline_index_vcalling
script:
"""
gatk IndexFeatureFile -I $vcf_germline
"""
}
process MUTECT2 {
conda '/mnt/home/users/b02_cimes_uma/elpz/.conda/envs/env_umis_picasso'
tag "$sample"
label 'process_high'
publishDir "${params.outdir}/11_mutect2/$sample", mode: params.publish_dir_mode
input:
tuple val(sample), path(bam), path(fasta), path(bed), path(vcf_germline), path(vcf_normal), path(vcf_germline_index), path(vcf_normal_index), path(dict) from ch_mutect2.combine(ch_fasta_mutect2).combine(ch_mutect2_bed).combine(ch_germline_vcalling).combine(ch_normal_vcalling).combine(ch_germline_index_vcalling).combine(ch_normal_index_vcalling).combine(ch_mutect2_dict)
//path fasta from ch_fasta_mutect2
path index from ch_index_mutect2
//path bed from ch_mutect2_bed
//path vcf_germline from ch_germline_vcalling
//path vcf_normal from ch_normal_vcalling
//path vcf_germline_index from ch_germline_index_vcalling
//path vcf_normal_index from ch_normal_index_vcalling
//path dict from ch_mutect2_dict
output:
tuple val(sample), path("*.min2.clip.vcf.gz") into ch_mutect2_annovar
script:
"""
mkdir logs
gatk Mutect2 -R $fasta -I $bam -L $bed --germline-resource $vcf_germline --panel-of-normals $vcf_normal -O ${sample}.min2.clip.vcf.gz > logs/${sample}.mutect.min2.clip.out 2> logs/${sample}.mutect.min2.clip.err
"""
}
/*
* STEP 12 - Vardict Variants Calling
*/
/*
process VARDICT {
conda '/mnt/home/users/b02_cimes_uma/elpz/.conda/envs/env_umis_picasso'
tag "$sample"
label 'process_high'
publishDir "${params.outdir}/12_vardict/$sample", mode: params.publish_dir_mode
input:
tuple val(sample), path(bam), path(fasta), path(bed) from ch_vardict.combine(ch_fasta_vardict).combine(ch_vardict_bed)
output:
tuple val(sample), path("*.min2.clip.vcf.gz") into ch_vardict_annovar
script:
"""
vardict -G $fasta -f $params.af_thr -N $sample -b $bam -c 1 -S 2 -E 3 -g 5 $bed | teststrandbias.R | var2vcf_valid.pl -N $sample -E -f $params.af_thr
"""
}
*/
/*
* STEP 13 - Variants Annotations
*/
// ANOTACIÓN DE VARIANTES DETECTADAS CON MUTECT2 UTILIZANDO ANNOVAR //
process ANNOVAR_MUTECT2 {
conda '/mnt/home/users/b02_cimes_uma/elpz/.conda/envs/env_umis_picasso'
tag "$sample"
label 'process_high'
publishDir "${params.outdir}/13_annovar/$sample/annot_mutect2", mode: params.publish_dir_mode
input:
tuple val(sample), path(variants), path(database) from ch_mutect2_annovar.combine(ch_annovar_mutect2_database)
output:
tuple val(sample), path("*.txt") into ch_mutect2_annotations
script:
"""
table_annovar.pl $variants $database -buildver hg38 -out ${sample}.mutect2-anno-cos95.ensGene -remove -nastring . -protocol ensGene,cosmic95,tcgaBRCA,tcgaALL -operation g,f,f,f -vcfinput
"""
}