-
Notifications
You must be signed in to change notification settings - Fork 18
/
.gitignore
218 lines (199 loc) · 6.16 KB
/
.gitignore
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
/settings.ini
/*.log
/megSAP_tag.txt
/test/data_amplicon/*.fastq.gz
/test/data_amplicon/*.cram
/test/data_amplicon/*.cram.crai
/test/data_amplicon/*.log
/test/data_amplicon/*.qcML
/test/data_amplicon/*.vcf.gz
/test/data_amplicon/*.vcf.gz.tbi
/test/data_amplicon/*.GSvar
/test/data_amplicon/*_QCML.txt
/test/data_amplicon/*_cnvs_clincnv.tsv
/test/data_amplicon/*_lowcov.bed
/test/data_amplicon/*.igv
/test/data_amplicon/*.bedpe
/test/data_amplicon/*_ancestry.tsv
/test/data_amplicon/manta_evid/
/test/data_chrx/*.fastq.gz
/test/data_chrx/*.bam
/test/data_chrx/*.bam.bai
/test/data_chrx/*.cram
/test/data_chrx/*.cram.crai
/test/data_chrx/*.log
/test/data_chrx/*.qcML
/test/data_chrx/*.vcf.gz
/test/data_chrx/*.vcf.gz.tbi
/test/data_chrx/*.GSvar
/test/data_chrx/*_QCML.txt
/test/data_chrx/*_cnvs_clincnv.tsv
/test/data_chrx/*_cnvs_clincnv.seg
/test/data_chrx/*_mosaic_cnvs.tsv
/test/data_chrx/*_rohs.tsv
/test/data_chrx/*_lowcov.bed
/test/data_chrx/*.igv
/test/data_chrx/*.bedpe
/test/data_chrx/*_ancestry.tsv
/test/data_chrx/manta_evid/
/test/data_chrx/*_circos.png
/test/data_trio/*.GSvar
/test/data_trio/*.log
/test/data_trio/*.qcML
/test/data_trio/*.cram
/test/data_trio/*.cram.crai
/test/data_trio/*.vcf.gz
/test/data_trio/*.vcf.gz.tbi
/test/data_trio/*_special.tsv
/test/data_trio/*_upd.tsv
/test/data_trio/*_clincnv.tsv
/test/data_trio/manta_evid/
/test/data_trio/*_manta_var_structural.bedpe
/test/data_trio/*.bedpe
/test/data_multi/*.GSvar
/test/data_multi/*.log
/test/data_multi/*.qcML
/test/data_multi/*.cram
/test/data_multi/*.cram.crai
/test/data_multi/*.vcf.gz
/test/data_multi/*.vcf.gz.tbi
/test/data_multi/*_clincnv.tsv
/test/data_multi/manta_evid/
/test/data_multi/*.bedpe
/test/data_capa/*.GSvar
/test/data_capa/*.log
/test/data_capa/*_report.rtf
/test/data_capa/*_igv.xml
/test/data_capa/*_qcML.txt
/test/data_capa/*_lowcov.bed
/test/data_capa/Sample_GS150496_01/
/test/data_capa/Sample_GS150497_01/
/test/data_capa/Somatic_GS150497_01-GS150496_01/
/test/data_capa/Sample_Normal*/*_filtered.GSvar
/test/data_capa/Sample_Normal*/*_cnvs_filtered.tsv
/test/data_capa/Somatic_Tumor*/*_igv.xml
/test/data_capa/Somatic_Tumor*/*_report.rtf
/test/data_capa/Somatic_Tumor*/*.log
/test/data_capa/Somatic_Tumor*/*_cnvs_filtered.tsv
/test/data_capa/Somatic_Tumor*/*_filtered.GSvar
/test/data_rna/analyze_rna_out_se.log
/test/data_rna/analyze_rna_out_pe.log
/test/data_rna/analyze_rna_out_fu.log
/test/data_rna/paired_end/
/test/data_rna/single_end/
/test/data_rna/paired_end_fusion/
/test/data_somatic_rna/project_folder/
/test/data_somatic_rna/somatic_rna_out.log
/test/data_somatic_dna_rna/project_folder_*/
/test/data_somatic_dna_rna/results_*
/test/data_somatic_dna_rna/somatic_dna_rna_*.log
/test/data_somatic/out_*
/test/data_somatic/Sample_*/
/test/data_out/tool_test_*
/test/data_out/test_toolbase
/test/data_out/test_functions
/test/data_emed/Sample_GS160540_01/
/test/data_emed/Sample_GS160539_01/
/test/data_emed/Sample_I16R003a06_01/
/test/data_emed/Sample_I16R003a05_01/
/test/data_emed/results_emed1/
/test/data_emed/results_emed2/
/test/data_emed/*.GSvar
/test/data_emed/*.vcf.gz
/test/data_emed/*.tsv
/test/data_ivac/Sample_GS140850_02/
/test/data_ivac/Sample_GS140851_02/
/test/data_ivac/Sample_I14R010d01_01/
/test/data_ivac/Sample_I14R010d02_01/
/test/data_ivac/results_ivac1/
/test/data_ivac/results_ivac2/
/test/data_ivac/*.GSvar
/test/data_ivac/*.vcf.gz
/test/data_ivac/*.tsv
/test/data_ivac/*_qcML.txt
/test/data_trio/reanno
/test/data_multi/reanno
/test/data_chrx/*.vcf
/test/data_chrx/*.json
/test/data_cfdna/CFDNA_01/
/test/data_cfdna/CFDNA_02/
/test/data_somatic/expected_case2
/data/dbs/*/
/data/tools/*/
/data/genomes/*/
/test/data_longread/*.fastq.gz
/test/data_longread/*.bam
/test/data_longread/*.bam.bai
/test/data_longread/*.cram
/test/data_longread/*.cram.crai
/test/data_longread/*.log
/test/data_longread/*.qcML
/test/data_longread/*.vcf.gz
/test/data_longread/*.vcf.gz.tbi
/test/data_longread/*.gvcf.gz
/test/data_longread/*.gvcf.gz.tbi
/test/data_longread/*.GSvar
/test/data_longread/*_cnvs_clincnv.tsv
/test/data_longread/*_cnvs_clincnv.seg
/test/data_longread/*_mosaic_cnvs.tsv
/test/data_longread/*_rohs.tsv
/test/data_longread/*_lowcov.bed
/test/data_longread/*.igv
/test/data_longread/*.bedpe
/test/data_longread/*_ancestry.tsv
/test/data_longread/clair_temp/
/test/data_longread/*_circos.png
/test/data_longread/merge_output.vcf
/test/data_longread/*_repeats.tsv
/test/data_longread/*_repeats.vcf
/test/data_longread/repeat_expansions
/test/data_longread/*_prs.tsv
/test/data_longread/*_repeats.bed
/test/data_longread/*.bed.gz
/test/data_longread/*.bed.gz.tbi
/test/data_longread/*_phasing_track.bed
/test/data_longread/*_modkit_summary.txt
/test/data_longread/*_var_modcall.vcf
/test/data_longread/*_prs.tsv
/test/data_trio_longread/*.fastq.gz
/test/data_trio_longread/*.bam
/test/data_trio_longread/*.bam.bai
/test/data_trio_longread/*.log
/test/data_trio_longread/*.qcML
/test/data_trio_longread/*.vcf.gz
/test/data_trio_longread/*.vcf.gz.tbi
/test/data_trio_longread/*.gvcf.gz
/test/data_trio_longread/*.gvcf.gz.tbi
/test/data_trio_longread/*.GSvar
/test/data_trio_longread/*_cnvs_clincnv.tsv
/test/data_trio_longread/*_cnvs_clincnv_cut.tsv
/test/data_trio_longread/*_cnvs_clincnv.seg
/test/data_trio_longread/*_mosaic_cnvs.tsv
/test/data_trio_longread/*_rohs.tsv
/test/data_trio_longread/*_lowcov.bed
/test/data_trio_longread/*.igv
/test/data_trio_longread/*.bedpe
/test/data_trio_longread/trio_upd.tsv
/test/data_trio_longread/*_phasing_track.bed
/test/data_trio_longread/*.csi
/test/data_multi_longread/*.fastq.gz
/test/data_multi_longread/*.bam
/test/data_multi_longread/*.bam.bai
/test/data_multi_longread/*.log
/test/data_multi_longread/*.qcML
/test/data_multi_longread/*.vcf.gz
/test/data_multi_longread/*.vcf.gz.tbi
/test/data_multi_longread/*.gvcf.gz
/test/data_multi_longread/*.gvcf.gz.tbi
/test/data_multi_longread/*.GSvar
/test/data_multi_longread/*_cnvs_clincnv.tsv
/test/data_multi_longread/*_cnvs_clincnv_cut.tsv
/test/data_multi_longread/*_cnvs_clincnv.seg
/test/data_multi_longread/*_mosaic_cnvs.tsv
/test/data_multi_longread/*_rohs.tsv
/test/data_multi_longread/*_lowcov.bed
/test/data_multi_longread/*.igv
/test/data_multi_longread/*.bedpe
/test/data_multi_longread/*_ancestry.tsv
/test/data_multi_longread/*.csi
/.idea