sarek/tests/test_sentieon_aligner_bwamem.yml at 56c191642abdfea36d76a86ae41acbd328739a93 · nf-core/sarek · GitHub

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
- name: Run sentieon bwamem
  command: nextflow run main.nf -profile test_cache,software_license --sentieon_extension --aligner sentieon-bwamem --save_reference --outdir results
  tags:
    - aligner
    - sentieon/bwamem
    - preprocessing
  files:
    - path: results/csv/markduplicates.csv
      md5sum: 0d6120bb99e92f6810343270711ca53e
    - path: results/csv/markduplicates_no_table.csv
      md5sum: 2a2d3d4842befd4def39156463859ee3
    - path: results/csv/recalibrated.csv
      md5sum: 2d29d9e53894dcce96a1b5beb6ef3312
    - path: results/multiqc
    - path: results/preprocessing/markduplicates/test/test.md.cram
    # binary changes md5sums on reruns
    - path: results/preprocessing/markduplicates/test/test.md.cram.crai
    # binary changes md5sums on reruns
    - path: results/preprocessing/recal_table/test/test.recal.table
    # binary changes md5sums on reruns
    - path: results/preprocessing/recalibrated/test/test.recal.cram
    # binary changes md5sums on reruns
    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
    # binary changes md5sums on reruns
    - path: results/reference/bwa/genome.amb
      md5sum: 1891c1de381b3a96d4e72f590fde20c1
    - path: results/reference/bwa/genome.ann
      md5sum: 2df4aa2d7580639fa0fcdbcad5e2e969
    - path: results/reference/bwa/genome.bwt
      md5sum: 815eded87e4cb6b0f1daab5c4d6e30af
    - path: results/reference/bwa/genome.pac
      md5sum: 8569fbdb2c98c6fb16dfa73d8eacb070
    - path: results/reference/bwa/genome.sa
      md5sum: e7cff62b919448a3a3d0fe4aaf427594
    - path: results/reference/dbsnp/dbsnp_146.hg38.vcf.gz.tbi
    # conda changes md5sums for test
    - path: results/reference/dict/genome.dict
      md5sum: 2433fe2ba31257337bf4c4bd4cb8da15
    - path: results/reference/fai/genome.fasta.fai
      md5sum: 3520cd30e1b100e55f578db9c855f685
    - path: results/reference/intervals/chr22_1-40001.bed
      md5sum: 87a15eb9c2ff20ccd5cd8735a28708f7
    - path: results/reference/intervals/chr22_1-40001.bed.gz
      md5sum: d3341fa28986c40b24fcc10a079dbb80
    - path: results/reference/intervals/genome.bed
      md5sum: a87dc7d20ebca626f65cc16ff6c97a3e
    - path: results/reference/known_indels/mills_and_1000G.indels.vcf.gz.tbi
    # conda changes md5sums for test
    - path: results/reports/fastqc/test-test_L1
    - path: results/reports/markduplicates/test/test.md.cram.metrics
      contains: ["test	17094	1534	168	1046782	12429	197	0	0.635998", "1.0	0.999991	1171"]
    - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
      md5sum: b61e1acee11a6ddf7ce3232a5948a6a0
    - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
      md5sum: 1a382f98d488d2ae3df83a0d87caafc1
    - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
      md5sum: 9afbcd5e44b62b3947e47af850a66188
    - path: results/reports/mosdepth/test/test.md.regions.bed.gz
      md5sum: 3bd6a6f7127394802d9a7c7d559072ee
    - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
      md5sum: 72ae14370dfdaab906e50d0552c90119
    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
      md5sum: b61e1acee11a6ddf7ce3232a5948a6a0
    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
      md5sum: 1a382f98d488d2ae3df83a0d87caafc1
    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
      md5sum: 9afbcd5e44b62b3947e47af850a66188
    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
      md5sum: 3bd6a6f7127394802d9a7c7d559072ee
    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
      md5sum: 72ae14370dfdaab906e50d0552c90119
    - path: results/reports/samtools/test/test.md.cram.stats
    # conda changes md5sums for test
    - path: results/reports/samtools/test/test.recal.cram.stats
    # conda changes md5sums for test
- name: Build only index with sentieon bwa
  command: nextflow run main.nf -profile test_cache,software_license --sentieon_extension --aligner sentieon-bwamem --build_only_index --outdir results
  tags:
    - aligner
    - build_only_index
    - sentieon/bwamem
  files:
    - path: results/multiqc
    - path: results/reference/bwa/genome.amb
      md5sum: 1891c1de381b3a96d4e72f590fde20c1
    - path: results/reference/bwa/genome.ann
      md5sum: 2df4aa2d7580639fa0fcdbcad5e2e969
    - path: results/reference/bwa/genome.bwt
      md5sum: 815eded87e4cb6b0f1daab5c4d6e30af
    - path: results/reference/bwa/genome.pac
      md5sum: 8569fbdb2c98c6fb16dfa73d8eacb070
    - path: results/reference/bwa/genome.sa
      md5sum: e7cff62b919448a3a3d0fe4aaf427594
    - path: results/reference/dbsnp/dbsnp_146.hg38.vcf.gz.tbi
    # conda changes md5sums for test
    - path: results/reference/dict/genome.dict
      md5sum: 2433fe2ba31257337bf4c4bd4cb8da15
    - path: results/reference/fai/genome.fasta.fai
      md5sum: 3520cd30e1b100e55f578db9c855f685
    - path: results/reference/intervals/chr22_1-40001.bed
      md5sum: 87a15eb9c2ff20ccd5cd8735a28708f7
    - path: results/reference/intervals/chr22_1-40001.bed.gz
      md5sum: d3341fa28986c40b24fcc10a079dbb80
    - path: results/reference/intervals/genome.bed
      md5sum: a87dc7d20ebca626f65cc16ff6c97a3e
    - path: results/reference/known_indels/mills_and_1000G.indels.vcf.gz.tbi
    # conda changes md5sums for test
- name: Run sentieon bwamem save bam
  command: nextflow run main.nf -profile test_cache,software_license --sentieon_extension --aligner sentieon-bwamem --save_mapped --save_output_as_bam --outdir results
  tags:
    - aligner
    - sentieon/bwamem
    - save_output_as_bam
    - preprocessing
  files:
    - path: results/csv/markduplicates.csv
      md5sum: 6004ab16b63012e336f6251396a983c5
    - path: results/csv/markduplicates_no_table.csv
      md5sum: 8a145eca178cfd02403d60122b9d3960
    - path: results/csv/recalibrated.csv
      md5sum: 2dfbcaaeaaf4937c51c5c310f1c77614
    - path: results/multiqc
    - path: results/preprocessing/mapped/test/test.sorted.bam
    - path: results/preprocessing/mapped/test/test.sorted.bam.bai
    - path: results/preprocessing/markduplicates/test/test.md.bam
    # binary changes md5sums on reruns
    - path: results/preprocessing/markduplicates/test/test.md.bam.bai
    # binary changes md5sums on reruns
    - path: results/preprocessing/recal_table/test/test.recal.table
    # binary changes md5sums on reruns
    - path: results/preprocessing/recalibrated/test/test.recal.bam
    # binary changes md5sums on reruns
    - path: results/preprocessing/recalibrated/test/test.recal.bam.bai
    # binary changes md5sums on reruns
    - path: results/reports/fastqc/test-test_L1
    - path: results/reports/markduplicates/test/test.md.cram.metrics
      contains: ["test	17094	1534	168	1046782	12429	197	0	0.635998", "1.0	0.999991	1171"]
    - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
      md5sum: b61e1acee11a6ddf7ce3232a5948a6a0
    - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
      md5sum: 1a382f98d488d2ae3df83a0d87caafc1
    - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
      md5sum: 9afbcd5e44b62b3947e47af850a66188
    - path: results/reports/mosdepth/test/test.md.regions.bed.gz
      md5sum: 3bd6a6f7127394802d9a7c7d559072ee
    - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
      md5sum: 72ae14370dfdaab906e50d0552c90119
    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
      md5sum: b61e1acee11a6ddf7ce3232a5948a6a0
    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
      md5sum: 1a382f98d488d2ae3df83a0d87caafc1
    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
      md5sum: 9afbcd5e44b62b3947e47af850a66188
    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
      md5sum: 3bd6a6f7127394802d9a7c7d559072ee
    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
      md5sum: 72ae14370dfdaab906e50d0552c90119
    - path: results/reports/samtools/test/test.md.cram.stats
    # conda changes md5sums for test
    - path: results/reports/samtools/test/test.recal.cram.stats
    # conda changes md5sums for test
- name: Run sentieon bwamem save cram
  command: nextflow run main.nf -profile test_cache,software_license --sentieon_extension --aligner sentieon-bwamem --save_mapped --outdir results
  tags:
    - aligner
    - sentieon/bwamem
    - save_output_as_cram
    - preprocessing
  files:
    - path: results/csv/markduplicates.csv
      md5sum: 0d6120bb99e92f6810343270711ca53e
    - path: results/csv/markduplicates_no_table.csv
      md5sum: 2a2d3d4842befd4def39156463859ee3
    - path: results/csv/recalibrated.csv
      md5sum: 2d29d9e53894dcce96a1b5beb6ef3312
    - path: results/multiqc
    - path: results/preprocessing/mapped/test/test.sorted.cram
    - path: results/preprocessing/mapped/test/test.sorted.cram.crai
    - path: results/preprocessing/markduplicates/test/test.md.cram
    # binary changes md5sums on reruns
    - path: results/preprocessing/markduplicates/test/test.md.cram.crai
    # binary changes md5sums on reruns
    - path: results/preprocessing/recal_table/test/test.recal.table
    # binary changes md5sums on reruns
    - path: results/preprocessing/recalibrated/test/test.recal.cram
    # binary changes md5sums on reruns
    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
    # binary changes md5sums on reruns
    - path: results/reports/fastqc/test-test_L1
    - path: results/reports/markduplicates/test/test.md.cram.metrics
      contains: ["test	17094	1534	168	1046782	12429	197	0	0.635998", "1.0	0.999991	1171"]
    - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
      md5sum: b61e1acee11a6ddf7ce3232a5948a6a0
    - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
      md5sum: 1a382f98d488d2ae3df83a0d87caafc1
    - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
      md5sum: 9afbcd5e44b62b3947e47af850a66188
    - path: results/reports/mosdepth/test/test.md.regions.bed.gz
      md5sum: 3bd6a6f7127394802d9a7c7d559072ee
    - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
      md5sum: 72ae14370dfdaab906e50d0552c90119
    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
      md5sum: b61e1acee11a6ddf7ce3232a5948a6a0
    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
      md5sum: 1a382f98d488d2ae3df83a0d87caafc1
    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
      md5sum: 9afbcd5e44b62b3947e47af850a66188
    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
      md5sum: 3bd6a6f7127394802d9a7c7d559072ee
    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
      md5sum: 72ae14370dfdaab906e50d0552c90119
    - path: results/reports/samtools/test/test.md.cram.stats
    # conda changes md5sums for test
    - path: results/reports/samtools/test/test.recal.cram.stats
    # conda changes md5sums for test