-
Notifications
You must be signed in to change notification settings - Fork 45
/
.gitlab-ci.yml
441 lines (397 loc) · 46.7 KB
/
.gitlab-ci.yml
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
# Include shared CI
include:
- project: "epi2melabs/ci-templates"
file: "wf-containers.yaml"
# conda, mac, simg
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-variation/snp_demo.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "modules/local/wf-human-snp.nf modules/local/wf-human-sv.nf"
NF_IGNORE_PROCESSES: "hap,lookup_clair3_model,phase_contig_haplotag,cat_haplotagged_contigs,makeAlignmentReport.\
get_genome,aggregate_all_variants,aggregate_full_align_variants,aggregate_pileup_variants,create_candidates,\
evaluate_candidates,get_qual_filter,makeReport,make_chunks,merge_pileup_and_full_vars,output_snp,phase_contig,\
pileup_variants,post_clair_phase_contig,select_het_snps,vcfStats,phase_gvcf"
NF_WORKFLOW_OPTS: "--snp --sv --bam ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bam --bed ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bed --ref ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.fasta --clair3_model_path ${CI_PROJECT_NAME}/data/snp_demo/ont_r104_e81_sup_g5015 --phased --annotation_threads 4 --override_basecaller_cfg dna_r10.4.1_e8.2_400bps_hac_prom"
CI_FLAVOUR: "new"
PYTEST_CONTAINER_CONFIG_KEY: "e2l_base_tag"
check-models:
extends: .preflight
script:
- !reference [.install, nextflow] # requires nextflow to read config
- bash util/update_models_schema.sh . docker
- >
if ! diff nextflow_schema.json nextflow_schema.json.new; then
echo "Model schema requires updating."
exit 1
fi
docker-run:
artifacts:
when: always
paths:
- ${CI_PROJECT_NAME}
- .nextflow.log
exclude:
- ${CI_PROJECT_NAME}/**/*.bam
- ${CI_PROJECT_NAME}/**/*.cram
- ${CI_PROJECT_NAME}/**/*.fa
- ${CI_PROJECT_NAME}/**/*.fna
- ${CI_PROJECT_NAME}/**/*.fasta
- ${CI_PROJECT_NAME}/**/ref_cache/**
- ${CI_PROJECT_NAME}/data/**/*
# Define a 1D job matrix to inject a variable named MATRIX_NAME into
# the CI environment, we can use the value of MATRIX_NAME to determine
# which options to apply as part of the rules block below
# NOTE There is a slightly cleaner way to define this matrix to include
# the variables, but it is broken when using long strings! See CW-756
parallel:
matrix:
- MATRIX_NAME: [
"str-usersex",
"str-infersex",
"missing-ref",
"two-models",
"all_phased",
"all_phased_igv",
"all_unphased",
"snp_sv_mod_unphased",
"multibam",
"haplocheck_contaminated",
"multimods",
"multimods_realign",
"multimods_phase",
"haplocheck_mt",
"haplocheck_nomt",
"haplocheck_custommt_missing",
"run_all_no_report",
"gzref-bam-mod",
"gzref-bam-mod-hap",
"wf-human-snp_modelint",
"wf-human-snp_modelint_unphase",
"wf-human-snp_modelext",
"wf-human-snp_covblock",
"wf-human-snp_svrefine",
"wf-human-sv",
"wf-human-sv-phase",
"wf-human-cnv-spectre",
"wf-human-phase_all",
"wf-human-phase_all_lp",
"downsample",
"wf-human-snp_GVCF_unphased",
"wf-human-snp_GVCF_phased",
"wf-human-snp-gene-summary",
]
rules:
# NOTE As we're overriding the rules block for the included docker-run
# we must redefine this CI_COMMIT_BRANCH rule to prevent docker-run
# being incorrectly scheduled for "detached merge request pipelines" etc.
- if: ($CI_COMMIT_BRANCH == null || $CI_COMMIT_BRANCH == "dev-template")
when: never
# This test tries to run with a missing ref, and fails with an expected error.
- if: $MATRIX_NAME == "missing-ref"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-somatic-variation/wf-somatic-variation-demo.tar.gz && \
tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/ && \
wget -q -O ${CI_PROJECT_NAME}/data/wf-somatic-variation-demo/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/ref/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz; echo 'process { withName:minimap2_alignment { memory = '24.GB' } }' > ${CI_PROJECT_NAME}/data/mm2.config"
NF_PROCESS_FILES: "workflows/methyl.nf"
NF_IGNORE_PROCESSES: "modkit_phase,minimap2_ubam,index_ref_gzi,get_coverage,getVersions,getParams,failedQCReport,makeAlignmentReport,annotate_vcf,eval_downsampling,downsampling,modkit"
NF_WORKFLOW_OPTS: "--snp true --sv true --mod --cnv false --str false \
--bed ${CI_PROJECT_NAME}/data/wf-somatic-variation-demo/demo.bed \
--bam ${CI_PROJECT_NAME}/data/wf-somatic-variation-demo/20240213_0951_0-AN-DN__abcde123/bam_pass/normal/ \
--ref ${CI_PROJECT_NAME}/data/wf-somatic-variation-demo/GCA_000001405.15_GRCh38_no_alt_analysis_set_chr20.fasta \
--sample_name HOOT --ubam_map_threads 2 --ubam_sort_threads 1 --ubam_bam2fq_threads 1 --bam_min_coverage 0 \
--annotation false --modkit_threads 4 \
--override_basecaller_cfg [email protected] \
-c ${CI_PROJECT_NAME}/data/mm2.config"
ASSERT_NEXTFLOW_FAILURE: "yes"
ASSERT_NEXTFLOW_FAILURE_REXP : "GCA_000001405.15_GRCh38_no_alt_analysis_set_chr20.fasta not found"
# This test takes multiple input BAM files, concatenates them and process them.
- if: $MATRIX_NAME == "multibam"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-somatic-variation/wf-somatic-variation-demo.tar.gz && \
tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/ && \
wget -q -O ${CI_PROJECT_NAME}/data/wf-somatic-variation-demo/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/ref/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz; echo 'process { withName:minimap2_alignment { memory = '24.GB' } }' > ${CI_PROJECT_NAME}/data/mm2.config"
NF_PROCESS_FILES: "workflows/methyl.nf"
NF_IGNORE_PROCESSES: "modkit_phase,minimap2_ubam,index_ref_gzi,get_coverage,getVersions,getParams,failedQCReport,makeAlignmentReport,annotate_vcf,eval_downsampling,downsampling,modkit"
NF_WORKFLOW_OPTS: "--snp true --sv true --mod --cnv false --str false \
--bed ${CI_PROJECT_NAME}/data/wf-somatic-variation-demo/demo.bed \
--bam ${CI_PROJECT_NAME}/data/wf-somatic-variation-demo/20240213_0951_0-AN-DN__abcde123/bam_pass/normal/ \
--ref ${CI_PROJECT_NAME}/data/wf-somatic-variation-demo/GCA_000001405.15_GRCh38_no_alt_analysis_set_chr20.fna \
--sample_name HOOT --ubam_map_threads 2 --ubam_sort_threads 1 --ubam_bam2fq_threads 1 --bam_min_coverage 0 \
--annotation false --modkit_threads 4 \
--override_basecaller_cfg [email protected] \
-c ${CI_PROJECT_NAME}/data/mm2.config"
# This uses BAM with reads on chr6, chr20 and chrM. The chrM reads come from both HG001 and HG002, and should
# result contaminated at the haplocheck stage.
- if: $MATRIX_NAME == "haplocheck_contaminated"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-snp/wf-human-snp-v2.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "workflows/methyl.nf"
NF_IGNORE_PROCESSES: "modkit_phase,getVersions,getParams,failedQCReport,makeAlignmentReport"
NF_WORKFLOW_OPTS: "--snp false --sv false --mod true --cnv false --str false --bam ${CI_PROJECT_NAME}/data/wf-human-snp-v2/demo_chr6_chr20_chrM_unmap.bam --ref ${CI_PROJECT_NAME}/data/wf-human-snp-v2/chr6_chr20_chrM.fasta --bed ${CI_PROJECT_NAME}/data/wf-human-snp-v2/chr6_chr20_chrM.bed --bam_min_coverage 0 --override_basecaller_cfg [email protected] --haplocheck --annotation false"
# This process tests all subworkflows, and also requests phasing.
- if: $MATRIX_NAME == "all_phased"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-snp/wf-human-snp-v2.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "workflows/methyl.nf"
NF_IGNORE_PROCESSES: "merge_tsv,make_report,modkit,post_clair_contig_haplotag,post_clair_phase_contig,phase_gvcf,hap,phase_contig_haplotag,cat_haplotagged_contigs,phase_contig,getGenome,get_coverage,getVersions,getParams,failedQCReport,refine_with_sv,makeAlignmentReport"
NF_WORKFLOW_OPTS: "--snp true --sv true --mod true --cnv true --str true --bam ${CI_PROJECT_NAME}/data/wf-human-snp-v2/multimods_10k_hg38.bam --ref ${CI_PROJECT_NAME}/data/wf-human-snp-v2/chr6_chr20_chrM.fasta --bam_min_coverage 0 --annotation false --phased"
# This process tests all subworkflows, and also requests phasing.
- if: $MATRIX_NAME == "all_phased_igv"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-snp/wf-human-snp-v2.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "workflows/methyl.nf"
NF_IGNORE_PROCESSES: "merge_tsv,make_report,modkit,post_clair_contig_haplotag,post_clair_phase_contig,phase_gvcf,hap,phase_contig_haplotag,cat_haplotagged_contigs,phase_contig,getGenome,get_coverage,getVersions,getParams,failedQCReport,refine_with_sv,makeAlignmentReport"
NF_WORKFLOW_OPTS: "--igv --snp true --sv true --mod true --cnv true --str true --bam ${CI_PROJECT_NAME}/data/wf-human-snp-v2/multimods_10k_hg38.bam --ref ${CI_PROJECT_NAME}/data/wf-human-snp-v2/chr6_chr20_chrM.fasta --bam_min_coverage 0 --annotation false --phased"
# This process tests all subworkflows, but without phasing.
- if: $MATRIX_NAME == "all_unphased"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-snp/wf-human-snp-v2.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "workflows/methyl.nf"
NF_IGNORE_PROCESSES: "merge_tsv,make_report,modkit_phase,post_clair_contig_haplotag,post_clair_phase_contig,phase_gvcf,hap,phase_contig_haplotag,cat_haplotagged_contigs,phase_contig,getGenome,get_coverage,getVersions,getParams,failedQCReport,refine_with_sv,makeAlignmentReport"
NF_WORKFLOW_OPTS: "--snp true --sv true --mod true --cnv true --str true --bam ${CI_PROJECT_NAME}/data/wf-human-snp-v2/multimods_10k_hg38.bam --ref ${CI_PROJECT_NAME}/data/wf-human-snp-v2/chr6_chr20_chrM.fasta --bam_min_coverage 0 --annotation false"
# This process tests SNP, SV and MOD subworkflows, that shouldn't required to pass the phased channel around.
- if: $MATRIX_NAME == "snp_sv_mod_unphased"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-snp/wf-human-snp-v2.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "workflows/methyl.nf"
NF_IGNORE_PROCESSES: "merge_tsv,make_report,modkit_phase,post_clair_contig_haplotag,post_clair_phase_contig,phase_gvcf,hap,phase_contig_haplotag,cat_haplotagged_contigs,phase_contig,getGenome,get_coverage,getVersions,getParams,failedQCReport,refine_with_sv,makeAlignmentReport"
NF_WORKFLOW_OPTS: "--snp true --sv true --mod true --cnv false --str false --bam ${CI_PROJECT_NAME}/data/wf-human-snp-v2/multimods_10k_hg38.bam --ref ${CI_PROJECT_NAME}/data/wf-human-snp-v2/chr6_chr20_chrM.fasta --bam_min_coverage 0 --annotation false"
# This process checks the use with multiple modified bases concurrently.
- if: $MATRIX_NAME == "two-models"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-snp/wf-human-snp-v2.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/; echo 'process { withName:minimap2_alignment { memory = '24.GB' } }' > ${CI_PROJECT_NAME}/data/mm2.config"
NF_IGNORE_PROCESSES: "modkit_phase,post_clair_contig_haplotag,post_clair_phase_contig,phase_gvcf,hap,phase_contig_haplotag,cat_haplotagged_contigs,phase_contig,getGenome,get_coverage,getVersions,getParams,failedQCReport,refine_with_sv,makeAlignmentReport"
NF_WORKFLOW_OPTS: "--snp true --sv false --mod false --cnv false --str false --bam ${CI_PROJECT_NAME}/data/wf-human-snp-v2/multimodel.bam --ref ${CI_PROJECT_NAME}/data/wf-human-snp-v2/chr6_chr20_chrM.fasta --bam_min_coverage 0 --annotation false --ubam_map_threads 2 --ubam_sort_threads 1 --ubam_bam2fq_threads 1 -c ${CI_PROJECT_NAME}/data/mm2.config"
ASSERT_NEXTFLOW_FAILURE: "yes"
ASSERT_NEXTFLOW_FAILURE_REXP : "# INPUT DATA PROBLEM"
# This process checks the use with multiple modified bases concurrently.
- if: $MATRIX_NAME == "multimods"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-snp/wf-human-snp-v2.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "workflows/methyl.nf"
NF_IGNORE_PROCESSES: "modkit_phase,post_clair_contig_haplotag,post_clair_phase_contig,phase_gvcf,hap,phase_contig_haplotag,cat_haplotagged_contigs,phase_contig,getGenome,get_coverage,getVersions,getParams,failedQCReport,refine_with_sv,makeAlignmentReport"
NF_WORKFLOW_OPTS: "--snp false --sv false --mod true --cnv false --str false --bam ${CI_PROJECT_NAME}/data/wf-human-snp-v2/multimods_10k_hg38.bam --ref ${CI_PROJECT_NAME}/data/wf-human-snp-v2/chr6_chr20_chrM.fasta --bam_min_coverage 0 --override_basecaller_cfg [email protected] --annotation false"
# Realign an aligned BAM [CW-4104]
- if: $MATRIX_NAME == "multimods_realign"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-snp/wf-human-snp-v2.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/; wget -q -O ${CI_PROJECT_NAME}/data/human_g1k_v37.6_20_MT.fasta https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/ref/human_g1k_v37.6_20_MT.fasta; echo 'process { withName:minimap2_alignment { memory = '24.GB' } }' > ${CI_PROJECT_NAME}/data/mm2.config"
NF_PROCESS_FILES: "workflows/methyl.nf"
NF_IGNORE_PROCESSES: "modkit_phase,post_clair_contig_haplotag,post_clair_phase_contig,phase_gvcf,hap,phase_contig_haplotag,cat_haplotagged_contigs,phase_contig,getGenome,get_coverage,getVersions,getParams,failedQCReport,refine_with_sv,makeAlignmentReport"
NF_WORKFLOW_OPTS: "--snp false --sv false --mod true --cnv false --str false --bam ${CI_PROJECT_NAME}/data/wf-human-snp-v2/multimods_10k_hg38.bam --ref ${CI_PROJECT_NAME}/data/human_g1k_v37.6_20_MT.fasta --bam_min_coverage 0 --override_basecaller_cfg [email protected] --annotation false --ubam_map_threads 2 --ubam_sort_threads 1 --ubam_bam2fq_threads 1 -c ${CI_PROJECT_NAME}/data/mm2.config"
# This process checks the use with multiple modified bases concurrently, and using phase information.
- if: $MATRIX_NAME == "multimods_phase"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-snp/wf-human-snp-v2.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "workflows/methyl.nf"
NF_IGNORE_PROCESSES: "modkit,post_clair_contig_haplotag,post_clair_phase_contig,phase_gvcf,hap,phase_contig_haplotag,cat_haplotagged_contigs,phase_contig,getGenome,get_coverage,getVersions,getParams,failedQCReport,refine_with_sv,makeAlignmentReport"
NF_WORKFLOW_OPTS: "--snp false --sv false --mod true --cnv false --str false --phased --bam ${CI_PROJECT_NAME}/data/wf-human-snp-v2/multimods_10k_hg38.bam --ref ${CI_PROJECT_NAME}/data/wf-human-snp-v2/chr6_chr20_chrM.fasta --bam_min_coverage 0 --override_basecaller_cfg [email protected] --annotation false"
# This uses the Spectre dataset, that contains the mt genome, and should therefore run
# haplocheck.
- if: $MATRIX_NAME == "haplocheck_mt"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-spectre/spectre_demo.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "modules/local/wf-human-snp.nf"
NF_IGNORE_PROCESSES: "post_clair_contig_haplotag,post_clair_phase_contig,phase_gvcf,hap,phase_contig_haplotag,cat_haplotagged_contigs,phase_contig,getGenome,get_coverage,getVersions,getParams,failedQCReport,refine_with_sv,makeAlignmentReport"
NF_WORKFLOW_OPTS: "--snp true --sv false --mod false --cnv false --str false --bam ${CI_PROJECT_NAME}/data/spectre_demo/demo.bam --ref ${CI_PROJECT_NAME}/data/spectre_demo/GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta --bam_min_coverage 0 --haplocheck --annotation false --override_basecaller_cfg [email protected]"
# The SNP demo doesn't have the MT genome in the reference, and should fail with an expected error.
- if: $MATRIX_NAME == "haplocheck_nomt"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-variation/snp_demo.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "modules/local/wf-human-snp.nf"
NF_IGNORE_PROCESSES: "phase_gvcf,hap,phase_contig_haplotag,cat_haplotagged_contigs,phase_contig,getGenome,get_coverage,getVersions,getParams,failedQCReport,refine_with_sv,makeAlignmentReport"
NF_WORKFLOW_OPTS: "--snp --sv false --mod false --cnv false --str false --bam ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bam --bed ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bed --ref ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.fasta --override_basecaller_cfg dna_r10.4.1_e8.2_400bps_hac_prom --haplocheck --bam_min_coverage 0 --annotation false"
ASSERT_NEXTFLOW_FAILURE: "yes"
ASSERT_NEXTFLOW_FAILURE_REXP : "Unexpected number of mitochondrial chromosome found:"
# The SNP demo doesn't have the MT genome in the reference, and should fail with an expected error.
- if: $MATRIX_NAME == "haplocheck_custommt_missing"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-spectre/spectre_demo.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "modules/local/wf-human-snp.nf"
NF_IGNORE_PROCESSES: "post_clair_contig_haplotag,post_clair_phase_contig,phase_gvcf,hap,phase_contig_haplotag,cat_haplotagged_contigs,phase_contig,getGenome,get_coverage,getVersions,getParams,failedQCReport,refine_with_sv,makeAlignmentReport"
NF_WORKFLOW_OPTS: "--snp true --sv false --mod false --cnv false --str false --bam ${CI_PROJECT_NAME}/data/spectre_demo/demo.bam --ref ${CI_PROJECT_NAME}/data/spectre_demo/GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta --bam_min_coverage 0 --haplocheck --mitogenome myVerySpecialMt --annotation false --override_basecaller_cfg [email protected]"
ASSERT_NEXTFLOW_FAILURE: "yes"
ASSERT_NEXTFLOW_FAILURE_REXP : "Mitochondrial genome myVerySpecialMt not present in the reference"
- if: $MATRIX_NAME == "wf-human-snp_modelint"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-variation/snp_demo.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "modules/local/wf-human-snp.nf"
NF_IGNORE_PROCESSES: "phase_gvcf,hap,phase_contig_haplotag,cat_haplotagged_contigs,phase_contig,getGenome,get_coverage,getVersions,getParams,failedQCReport,refine_with_sv,makeAlignmentReport"
NF_WORKFLOW_OPTS: "--snp --sv false --mod false --cnv false --str false --bam ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bam --bed ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bed --ref ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.fasta --override_basecaller_cfg dna_r10.4.1_e8.2_400bps_hac_prom --phased --bam_min_coverage 0.00001 --annotation_threads 4"
- if: $MATRIX_NAME == "wf-human-snp_modelint_unphase"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-variation/snp_demo.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "modules/local/wf-human-snp.nf"
NF_IGNORE_PROCESSES: "hap,phase_contig_haplotag,post_clair_phase_contig,cat_haplotagged_contigs,phase_contig,getGenome,get_coverage,
getVersions,getParams,failedQCReport,refine_with_sv,makeAlignmentReport,post_clair_contig_haplotag,phase_gvcf"
NF_WORKFLOW_OPTS: "--snp --sv false --mod false --cnv false --str false --bam ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bam --bed ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bed --ref ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.fasta --override_basecaller_cfg dna_r10.4.1_e8.2_400bps_hac_prom --bam_min_coverage 0.00001 --annotation_threads 4"
- if: $MATRIX_NAME == "wf-human-snp_modelext"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-variation/snp_demo.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "modules/local/wf-human-snp.nf"
NF_IGNORE_PROCESSES: "phase_gvcf,hap,lookup_clair3_model,phase_contig,phase_contig_haplotag,cat_haplotagged_contigs,getGenome,get_coverage,getVersions,getParams,failedQCReport,refine_with_sv,makeAlignmentReport"
NF_WORKFLOW_OPTS: "--snp --sv false --mod false --cnv false --str false --bam ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bam --bed ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bed --ref ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.fasta --clair3_model_path ${CI_PROJECT_NAME}/data/snp_demo/ont_r104_e81_sup_g5015 --phased --bam_min_coverage 0.00001 --annotation_threads 4"
- if: $MATRIX_NAME == "wf-human-snp_covblock"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-variation/snp_demo.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "modules/local/wf-human-snp.nf"
NF_IGNORE_PROCESSES: "hap,lookup_clair3_model,phase_contig_haplotag,cat_haplotagged_contigs,post_clair_contig_haplotag,\
getGenome,aggregate_all_variants,aggregate_full_align_variants,aggregate_pileup_variants,create_candidates,\
evaluate_candidates,get_qual_filter,makeReport,make_chunks,merge_pileup_and_full_vars,output_snp,phase_contig,\
pileup_variants,post_clair_phase_contig,select_het_snps,vcfStats,refine_with_sv,annotate_vcf,bed_filter,phase_gvcf"
NF_WORKFLOW_OPTS: "--snp --sv false --mod false --cnv false --str false --bam ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bam --bed ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bed --ref ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.fasta --clair3_model_path ${CI_PROJECT_NAME}/data/snp_demo/ont_r104_e81_sup_g5015 --phased --bam_min_coverage 100 --override_basecaller_cfg dna_r10.4.1_e8.2_400bps_hac_prom"
- if: $MATRIX_NAME == "wf-human-snp_svrefine"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-variation/snp_demo.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "modules/local/wf-human-snp.nf"
NF_IGNORE_PROCESSES: "hap,lookup_clair3_model,phase_contig_haplotag,cat_haplotagged_contigs,makeAlignmentReport.\
get_genome,aggregate_all_variants,aggregate_full_align_variants,aggregate_pileup_variants,create_candidates,\
evaluate_candidates,get_qual_filter,makeReport,make_chunks,merge_pileup_and_full_vars,output_snp,phase_contig,\
pileup_variants,post_clair_phase_contig,select_het_snps,vcfStats,phase_gvcf"
NF_WORKFLOW_OPTS: "--snp --sv --mod false --cnv false --str false --bam ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bam --bed ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bed --ref ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.fasta --clair3_model_path ${CI_PROJECT_NAME}/data/snp_demo/ont_r104_e81_sup_g5015 --phased --annotation_threads 4 --override_basecaller_cfg dna_r10.4.1_e8.2_400bps_hac_prom"
- if: $MATRIX_NAME == "wf-human-sv"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-sv/demo_data.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "modules/local/wf-human-sv.nf"
NF_IGNORE_PROCESSES: "getAllChromosomesBed,minimap2_alignment,get_coverage,getVersions,getParams,failedQCReport,makeAlignmentReport,annotate_vcf"
NF_WORKFLOW_OPTS: "--snp false --sv --mod false --cnv false --str false --bam ${CI_PROJECT_NAME}/data/demo_data/test.bam --ref ${CI_PROJECT_NAME}/data/demo_data/chr20_human_g1k_v37_part.fasta.gz --bed ${CI_PROJECT_NAME}/data/demo_data/target.bed --tr_bed ${CI_PROJECT_NAME}/data/demo_data/human_hs37d5.trf.bed --bam_min_coverage 0.00001 --annotation_threads 4"
- if: $MATRIX_NAME == "wf-human-sv-phase"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-variation/snp_demo.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "modules/local/wf-human-sv.nf"
NF_IGNORE_PROCESSES: "getAllChromosomesBed,minimap2_alignment,get_coverage,getVersions,getParams,failedQCReport,makeAlignmentReport,annotate_vcf"
NF_WORKFLOW_OPTS: "--mod false --cnv false --str false --sv true --snp true --bam ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bam --bed ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bed --ref ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.fasta --clair3_model_path ${CI_PROJECT_NAME}/data/snp_demo/ont_r104_e81_sup_g5015 --annotation_threads 4 --phased"
- if: $MATRIX_NAME == "wf-human-cnv-spectre"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-spectre/spectre_demo.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "modules/local/wf-human-cnv.nf"
NF_IGNORE_PROCESSES: "get_coverage,getVersions,getParams,failedQCReport,makeAlignmentReport,phase_gvcf"
NF_WORKFLOW_OPTS: "--snp false --sv false --mod false --cnv --str false --bam ${CI_PROJECT_NAME}/data/spectre_demo/demo.bam --ref ${CI_PROJECT_NAME}/data/spectre_demo/GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta --bam_min_coverage 0.00001 --override_basecaller_cfg [email protected]"
- if: $MATRIX_NAME == "gzref-bam-mod-hap"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-somatic-variation/wf-somatic-variation-demo.tar.gz && \
tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/ && \
wget -q -O ${CI_PROJECT_NAME}/data/wf-somatic-variation-demo/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/ref/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz"
NF_PROCESS_FILES: "workflows/methyl.nf"
NF_IGNORE_PROCESSES: "minimap2_ubam,index_ref_gzi,get_coverage,getVersions,getParams,failedQCReport,makeAlignmentReport,annotate_vcf,eval_downsampling,downsampling,modkit"
NF_WORKFLOW_OPTS: "--snp false --sv false --mod --cnv false --str false --bed ${CI_PROJECT_NAME}/data/wf-somatic-variation-demo/demo.bed --bam ${CI_PROJECT_NAME}/data/wf-somatic-variation-demo/demo_normal.bam --ref ${CI_PROJECT_NAME}/data/wf-somatic-variation-demo/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa.gz --sample_name HOOT --ubam_map_threads 2 --ubam_sort_threads 1 --ubam_bam2fq_threads 1 --bam_min_coverage 0.00001 --phased --annotation false --modkit_threads 4 --override_basecaller_cfg [email protected]"
- if: $MATRIX_NAME == "gzref-bam-mod"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-somatic-variation/wf-somatic-variation-demo.tar.gz && \
tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/ && \
wget -q -O ${CI_PROJECT_NAME}/data/wf-somatic-variation-demo/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/ref/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz"
NF_PROCESS_FILES: "workflows/methyl.nf"
NF_IGNORE_PROCESSES: "minimap2_ubam,index_ref_gzi,get_coverage,getVersions,getParams,failedQCReport,makeAlignmentReport,annotate_vcf,eval_downsampling,downsampling,modkit_phase"
NF_WORKFLOW_OPTS: "--snp false --sv false --mod --cnv false --str false --bed ${CI_PROJECT_NAME}/data/wf-somatic-variation-demo/demo.bed --bam ${CI_PROJECT_NAME}/data/wf-somatic-variation-demo/demo_normal.bam --ref ${CI_PROJECT_NAME}/data/wf-somatic-variation-demo/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa.gz --sample_name HOOT --ubam_map_threads 2 --ubam_sort_threads 1 --ubam_bam2fq_threads 1 --bam_min_coverage 0.00001 --annotation false --modkit_threads 4 --override_basecaller_cfg [email protected]"
- if: $MATRIX_NAME == "downsample"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -qO ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-str/demo_data.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "workflows/methyl.nf"
NF_IGNORE_PROCESSES: "minimap2_ubam,index_ref_gzi,getGenome,get_coverage,getVersions,getParams,failedQCReport,makeAlignmentReport,eval_downsampling,downsampling,compress_bed,modkit_phase,annotate_vcf"
NF_WORKFLOW_OPTS: "--snp false --sv false --mod --annotation false --bam ${CI_PROJECT_NAME}/data/demo_data/demo.bam --ref ${CI_PROJECT_NAME}/data/demo_data/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa.gz \
--sample_name HOOT --ubam_map_threads 2 --ubam_sort_threads 1 \
--ubam_bam2fq_threads 1 --bam_min_coverage 0 --skip_annotation \
--downsample_coverage --downsample_coverage_target 10 --modkit_threads 4"
- if: $MATRIX_NAME == "str-usersex"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -qO ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-str/demo_data.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/ && wget -qO ${CI_PROJECT_NAME}/data/r1041_e82_400bps_sup_g615.tar.gz https://cdn.oxfordnanoportal.com/software/analysis/models/clair3/r1041_e82_400bps_sup_g615.tar.gz && tar -xvf ${CI_PROJECT_NAME}/data/r1041_e82_400bps_sup_g615.tar.gz -C ${CI_PROJECT_NAME}/data"
NF_PROCESS_FILES: "modules/local/wf-human-str.nf"
NF_IGNORE_PROCESSES: "get_coverage,getVersions,getParams,failedQCReport,makeAlignmentReport"
NF_WORKFLOW_OPTS: "--snp false --sv false --mod false --cnv false --str --bam ${CI_PROJECT_NAME}/data/demo_data/demo.bam --ref ${CI_PROJECT_NAME}/data/demo_data/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa.gz --sample_name demo --sex XX --bam_min_coverage 0.00001 --annotation false --clair3_model_path ${CI_PROJECT_NAME}/data/r1041_e82_400bps_sup_g615"
- if: $MATRIX_NAME == "str-infersex"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -qO ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-str/demo_data.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/ && wget -qO ${CI_PROJECT_NAME}/data/r1041_e82_400bps_sup_g615.tar.gz https://cdn.oxfordnanoportal.com/software/analysis/models/clair3/r1041_e82_400bps_sup_g615.tar.gz && tar -xvf ${CI_PROJECT_NAME}/data/r1041_e82_400bps_sup_g615.tar.gz -C ${CI_PROJECT_NAME}/data"
NF_PROCESS_FILES: "modules/local/wf-human-str.nf"
NF_IGNORE_PROCESSES: "get_coverage,getVersions,getParams,failedQCReport,makeAlignmentReport"
NF_WORKFLOW_OPTS: "--snp false --sv false --mod false --cnv false --str --bam ${CI_PROJECT_NAME}/data/demo_data/demo.bam --ref ${CI_PROJECT_NAME}/data/demo_data/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa.gz --sample_name demo --bam_min_coverage 0.00001 --annotation false --clair3_model_path ${CI_PROJECT_NAME}/data/r1041_e82_400bps_sup_g615"
- if: $MATRIX_NAME == "run_all_no_report"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -qO ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-str/demo_data.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/ && wget -qO ${CI_PROJECT_NAME}/data/r1041_e82_400bps_sup_g615.tar.gz https://cdn.oxfordnanoportal.com/software/analysis/models/clair3/r1041_e82_400bps_sup_g615.tar.gz && tar -xvf ${CI_PROJECT_NAME}/data/r1041_e82_400bps_sup_g615.tar.gz -C ${CI_PROJECT_NAME}/data"
NF_PROCESS_FILES: "modules/local/wf-human-str.nf"
NF_IGNORE_PROCESSES: "get_coverage,getVersions,getParams,failedQCReport,makeAlignmentReport,make_report"
NF_WORKFLOW_OPTS: "--snp --sv --cnv --str --phased --output_report false --bam ${CI_PROJECT_NAME}/data/demo_data/demo.bam --ref ${CI_PROJECT_NAME}/data/demo_data/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa.gz --sample_name demo --bam_min_coverage 0 --annotation false --clair3_model_path ${CI_PROJECT_NAME}/data/r1041_e82_400bps_sup_g615"
- if: $MATRIX_NAME == "wf-human-phase_all"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-variation/snp_demo.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "modules/local/wf-human-sv.nf modules/local/wf-human-snp.nf"
NF_IGNORE_PROCESSES: "get_coverage,getVersions,getParams,failedQCReport,makeAlignmentReport,hap,phase_contig,post_clair_phase_contig,bed_filter,phase_gvcf"
NF_WORKFLOW_OPTS: "--mod false --cnv false --str false --sv --snp --phased --bam ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bam --bed ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bed --ref ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.fasta --sample_name demo --sex XX --bam_min_coverage 0.00001 --annotation false --override_basecaller_cfg dna_r10.4.1_e8.2_400bps_hac_prom"
- if: $MATRIX_NAME == "wf-human-phase_all_lp"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-variation/snp_demo.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "modules/local/wf-human-sv.nf modules/local/wf-human-snp.nf"
NF_IGNORE_PROCESSES: "get_coverage,getVersions,getParams,failedQCReport,makeAlignmentReport,hap,phase_contig,post_clair_phase_contig,bed_filter,phase_gvcf"
NF_WORKFLOW_OPTS: "--mod false --cnv false --str false --sv --snp --phased --use_longphase true --bam ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bam --bed ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bed --ref ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.fasta --sample_name demo --sex XX --bam_min_coverage 0.00001 --annotation false --override_basecaller_cfg dna_r10.4.1_e8.2_400bps_hac_prom"
- if: $MATRIX_NAME == "wf-human-snp_GVCF_unphased"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-variation/snp_demo.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "modules/local/wf-human-snp.nf"
NF_IGNORE_PROCESSES: "get_coverage,getVersions,getParams,failedQCReport,makeAlignmentReport,hap,phase_contig,post_clair_phase_contig,bed_filter,phase_gvcf,cat_haplotagged_contigs,post_clair_contig_haplotag,refine_with_sv"
NF_WORKFLOW_OPTS: "--mod false --cnv false --str false --sv false --snp --phased false --GVCF --use_longphase false --bam ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bam --bed ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bed --ref ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.fasta --sample_name demo --sex XX --bam_min_coverage 0.00001 --annotation false --override_basecaller_cfg dna_r10.4.1_e8.2_400bps_hac_prom"
- if: $MATRIX_NAME == "wf-human-snp_GVCF_phased"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-variation/snp_demo.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "modules/local/wf-human-snp.nf"
NF_IGNORE_PROCESSES: "get_coverage,getVersions,getParams,failedQCReport,makeAlignmentReport,hap,phase_contig,post_clair_phase_contig,bed_filter,phase_gvcf,refine_with_sv"
NF_WORKFLOW_OPTS: "--mod false --cnv false --str false --sv false --snp --phased true --GVCF --use_longphase false --bam ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bam --bed ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bed --ref ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.fasta --sample_name demo --sex XX --bam_min_coverage 0.00001 --annotation false --override_basecaller_cfg dna_r10.4.1_e8.2_400bps_hac_prom"
- if: $MATRIX_NAME == "wf-human-snp-gene-summary"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/snp_demo_new/snp_demo.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "modules/local/wf-human-snp.nf"
NF_IGNORE_PROCESSES: "phase_gvcf,hap,phase_contig_haplotag,cat_haplotagged_contigs,phase_contig,getGenome,get_coverage,getVersions,getParams,failedQCReport,refine_with_sv,makeAlignmentReport"
NF_WORKFLOW_OPTS: "--snp --sv false --mod false --cnv false --str false --bam ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bam --bed ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20_with_gene.bed --ref ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.fasta --phased --bam_min_coverage 0.00001 --output_gene_summary --annotation false --override_basecaller_cfg dna_r10.4.1_e8.2_400bps_hac_prom"
aws-run:
stage: test
artifacts:
when: always
paths:
- ${CI_PROJECT_NAME}
- .nextflow.log
exclude:
- ${CI_PROJECT_NAME}/**/*.bam
- ${CI_PROJECT_NAME}/**/*.cram
- ${CI_PROJECT_NAME}/**/*.fa
- ${CI_PROJECT_NAME}/**/*.fna
- ${CI_PROJECT_NAME}/**/*.fasta
- ${CI_PROJECT_NAME}/**/ref_cache/**
variables:
CWG_AWS_ENV_NAME: "stack"
# Define a 1D job matrix to inject a variable named MATRIX_NAME into
# the CI environment, we can use the value of MATRIX_NAME to determine
# which options to apply as part of the rules block below
# NOTE There is a slightly cleaner way to define this matrix to include
# the variables, but it is broken when using long strings! See CW-756
parallel:
matrix:
- MATRIX_NAME: [
"wf-human-cnv-ubam-to-bam",
"wf-human-cnv-downsample",
"wf-human-cnv-skip-downsample",
]
rules:
# NOTE As we're overriding the rules block for the included docker-run
# we must redefine this CI_COMMIT_BRANCH rule to prevent docker-run
# being incorrectly scheduled for "detached merge request pipelines" etc.
- if: ($CI_COMMIT_BRANCH == null || $CI_COMMIT_BRANCH == "dev-template")
when: never
- if: $MATRIX_NAME == "wf-human-cnv-downsample"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/snp_demo/snp_demo.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "modules/local/wf-human-cnv-qdnaseq.nf"
NF_IGNORE_PROCESSES: "get_coverage,getVersions,getParams,failedQCReport,makeAlignmentReport"
NF_WORKFLOW_OPTS: "--snp false --sv false --mod false --cnv --use_qdnaseq --str false --bam ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bam --bed ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bed --ref ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.fasta --bin_size 500 --bam_min_coverage 0.00001 --downsample_coverage --downsample_coverage_target 20"
- if: $MATRIX_NAME == "wf-human-cnv-skip-downsample"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/snp_demo/snp_demo.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "modules/local/wf-human-cnv-qdnaseq.nf"
NF_IGNORE_PROCESSES: "get_coverage,getVersions,getParams,failedQCReport,makeAlignmentReport"
NF_WORKFLOW_OPTS: "--snp false --sv false --mod false --cnv --use_qdnaseq --str false --bam ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bam --bed ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bed --ref ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.fasta --bin_size 500 --bam_min_coverage 0.00001 --downsample_coverage --downsample_coverage_target 1000"
- if: $MATRIX_NAME == "wf-human-cnv-ubam-to-bam"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-cnv/demo_data.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "modules/local/wf-human-cnv-qdnaseq.nf"
NF_IGNORE_PROCESSES: "get_coverage,getVersions,getParams,failedQCReport,makeAlignmentReport"
NF_WORKFLOW_OPTS: "--snp false --sv false --mod false --cnv --use_qdnaseq --str false --bam ${CI_PROJECT_NAME}/data/demo_data/test.ubam --ref ${CI_PROJECT_NAME}/data/demo_data/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz --bin_size 500 --bam_min_coverage 0.00001"
macos-run:
# Let's avoid those ARM64 runners for now
tags:
- macos
- x86