-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathmodules.json
220 lines (220 loc) · 10.3 KB
/
modules.json
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
{
"name": "BrentLab/callvariants",
"homePage": "https://github.com/BrentLab/callvariants",
"repos": {
"https://github.com/nf-core/modules.git": {
"modules": {
"nf-core": {
"bcftools/stats": {
"branch": "master",
"git_sha": "e2693a7e2d773b92e0649b25880ee22fe82bb79d",
"installed_by": ["modules"]
},
"bwa/index": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"bwamem2/index": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"bwamem2/mem": {
"branch": "master",
"git_sha": "0460d316170f75f323111b4a2c0a2989f0c32013",
"installed_by": ["modules"]
},
"cat/fastq": {
"branch": "master",
"git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
"installed_by": ["modules"]
},
"cnvpytor/histogram": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"],
"patch": "modules/nf-core/cnvpytor/histogram/cnvpytor-histogram.diff"
},
"cnvpytor/importreaddepth": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"cnvpytor/partition": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"],
"patch": "modules/nf-core/cnvpytor/partition/cnvpytor-partition.diff"
},
"cnvpytor/view": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"],
"patch": "modules/nf-core/cnvpytor/view/cnvpytor-view.diff"
},
"custom/dumpsoftwareversions": {
"branch": "master",
"git_sha": "76cc4938c1f6ea5c7d83fed1eeffc146787f9543",
"installed_by": ["modules"]
},
"fastqc": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"installed_by": ["fastq_fastqc_umitools_trimgalore", "modules"]
},
"freebayes": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"gatk4/createsequencedictionary": {
"branch": "master",
"git_sha": "541811d779026c5d395925895fa5ed35e7216cc0",
"installed_by": ["modules"]
},
"gatk4/intervallisttobed": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"gatk4/markduplicates": {
"branch": "master",
"git_sha": "0a261469640941da2488e1a5aa023b64db837c70",
"installed_by": ["modules"]
},
"gatk4/mergevcfs": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"gunzip": {
"branch": "master",
"git_sha": "e06548bfa36ee31869b81041879dd6b3a83b1d57",
"installed_by": ["modules"]
},
"multiqc": {
"branch": "master",
"git_sha": "f2d63bd5b68925f98f572eed70993d205cc694b7",
"installed_by": ["modules"]
},
"picard/addorreplacereadgroups": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"picard/markduplicates": {
"branch": "master",
"git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
"installed_by": ["modules"]
},
"picard/sortvcf": {
"branch": "master",
"git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
"installed_by": ["modules"]
},
"samtools/faidx": {
"branch": "master",
"git_sha": "fd742419940e01ba1c5ecb172c3e32ec840662fe",
"installed_by": ["modules"]
},
"samtools/fastq": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"samtools/flagstat": {
"branch": "master",
"git_sha": "570ec5bcfe19c49e16c9ca35a7a116563af6cc1c",
"installed_by": ["modules", "bam_stats_samtools"]
},
"samtools/idxstats": {
"branch": "master",
"git_sha": "e662ab16e0c11f1e62983e21de9871f59371a639",
"installed_by": ["modules", "bam_stats_samtools"]
},
"samtools/index": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules", "bam_sort_stats_samtools"]
},
"samtools/merge": {
"branch": "master",
"git_sha": "0460d316170f75f323111b4a2c0a2989f0c32013",
"installed_by": ["modules"]
},
"samtools/sort": {
"branch": "master",
"git_sha": "a0f7be95788366c1923171e358da7d049eb440f9",
"installed_by": ["bam_sort_stats_samtools", "modules"]
},
"samtools/stats": {
"branch": "master",
"git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
"installed_by": ["modules", "bam_stats_samtools"]
},
"samtools/view": {
"branch": "master",
"git_sha": "3ffae3598260a99e8db3207dead9f73f87f90d1f",
"installed_by": ["modules"]
},
"snpeff/snpeff": {
"branch": "master",
"git_sha": "4d584d5cf6ed5f7363a51cdb4b3eb25398e9e537",
"installed_by": ["modules"],
"patch": "modules/nf-core/snpeff/snpeff/snpeff-snpeff.diff"
},
"tabix/bgziptabix": {
"branch": "master",
"git_sha": "591b71642820933dcb3c954c934b397bd00d8e5e",
"installed_by": ["modules"]
},
"tiddit/cov": {
"branch": "master",
"git_sha": "1c90a501d102b800c27697f5ef39a6e217ab1915",
"installed_by": ["modules"]
},
"tiddit/sv": {
"branch": "master",
"git_sha": "1c90a501d102b800c27697f5ef39a6e217ab1915",
"installed_by": ["modules"]
},
"trimgalore": {
"branch": "master",
"git_sha": "d2c5e76f291379f3dd403e48e46ed7e6ba5da744",
"installed_by": ["fastq_fastqc_umitools_trimgalore"]
},
"umitools/extract": {
"branch": "master",
"git_sha": "d2c5e76f291379f3dd403e48e46ed7e6ba5da744",
"installed_by": ["fastq_fastqc_umitools_trimgalore"]
},
"vcftools": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
}
}
},
"subworkflows": {
"nf-core": {
"bam_sort_stats_samtools": {
"branch": "master",
"git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
"installed_by": ["subworkflows"]
},
"bam_stats_samtools": {
"branch": "master",
"git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
"installed_by": ["subworkflows", "bam_sort_stats_samtools"]
},
"fastq_fastqc_umitools_trimgalore": {
"branch": "master",
"git_sha": "cb6defa0834eda9d6d3f967e981c819fc3e257bf",
"installed_by": ["subworkflows"]
}
}
}
}
}
}