-
Notifications
You must be signed in to change notification settings - Fork 149
/
modules.json
237 lines (237 loc) · 11.2 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
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
{
"name": "nf-core/chipseq",
"homePage": "https://github.com/nf-core/chipseq",
"repos": {
"https://github.com/nf-core/modules.git": {
"modules": {
"nf-core": {
"bowtie2/align": {
"branch": "master",
"git_sha": "9bfc81874554e87740bcb3e5e07acf0a153c9ecb",
"installed_by": ["fastq_align_bowtie2", "modules"]
},
"bowtie2/build": {
"branch": "master",
"git_sha": "1fea64f5132a813ec97c1c6d3a74e0aee7142b6d",
"installed_by": ["modules"]
},
"bwa/index": {
"branch": "master",
"git_sha": "e0ff65e1fb313677de09f5f477ae3da30ce19b7b",
"installed_by": ["modules"]
},
"bwa/mem": {
"branch": "master",
"git_sha": "2201e21b09213f083832ac58e33353d410a6fde7",
"installed_by": ["fastq_align_bwa", "modules"]
},
"chromap/chromap": {
"branch": "master",
"git_sha": "8438ab16df8334b8e15526cef7e8eda7f218ea20",
"installed_by": ["fastq_align_chromap", "modules"],
"patch": "modules/nf-core/chromap/chromap/chromap-chromap.diff"
},
"chromap/index": {
"branch": "master",
"git_sha": "8438ab16df8334b8e15526cef7e8eda7f218ea20",
"installed_by": ["modules"]
},
"custom/getchromsizes": {
"branch": "master",
"git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7",
"installed_by": ["modules"]
},
"deeptools/computematrix": {
"branch": "master",
"git_sha": "dd51244ab3b1e4a30ddeb93ba3c6ef3ce1f02ef8",
"installed_by": ["modules"]
},
"deeptools/plotfingerprint": {
"branch": "master",
"git_sha": "dd51244ab3b1e4a30ddeb93ba3c6ef3ce1f02ef8",
"installed_by": ["modules"]
},
"deeptools/plotheatmap": {
"branch": "master",
"git_sha": "dd51244ab3b1e4a30ddeb93ba3c6ef3ce1f02ef8",
"installed_by": ["modules"]
},
"deeptools/plotprofile": {
"branch": "master",
"git_sha": "dd51244ab3b1e4a30ddeb93ba3c6ef3ce1f02ef8",
"installed_by": ["modules"]
},
"fastqc": {
"branch": "master",
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
"installed_by": ["fastq_fastqc_umitools_trimgalore", "modules"]
},
"gffread": {
"branch": "master",
"git_sha": "6c996d7fbe0816dcbb68ce587ad5f873313682a1",
"installed_by": ["modules"]
},
"gunzip": {
"branch": "master",
"git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
"installed_by": ["modules"]
},
"homer/annotatepeaks": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"]
},
"khmer/uniquekmers": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"]
},
"macs3/callpeak": {
"branch": "master",
"git_sha": "3a3f471ed42f640115b2661edee5b258e6a254c1",
"installed_by": ["modules"]
},
"multiqc": {
"branch": "master",
"git_sha": "b80f5fd12ff7c43938f424dd76392a2704fa2396",
"installed_by": ["modules"]
},
"phantompeakqualtools": {
"branch": "master",
"git_sha": "ec48f56f6e1571e23800aaaba41cceda13408e02",
"installed_by": ["modules"]
},
"picard/collectmultiplemetrics": {
"branch": "master",
"git_sha": "0dee12b56ccecc416d6f7a1ccd85fd571eab3307",
"installed_by": ["modules"]
},
"picard/markduplicates": {
"branch": "master",
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
"installed_by": ["bam_markduplicates_picard", "modules"]
},
"picard/mergesamfiles": {
"branch": "master",
"git_sha": "0dee12b56ccecc416d6f7a1ccd85fd571eab3307",
"installed_by": ["modules"]
},
"preseq/lcextrap": {
"branch": "master",
"git_sha": "2c6b1144ed58b6184ad58fc4e6b6a90219b4bf4f",
"installed_by": ["modules"]
},
"samtools/flagstat": {
"branch": "master",
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
"installed_by": ["bam_stats_samtools", "modules"]
},
"samtools/idxstats": {
"branch": "master",
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
"installed_by": ["bam_stats_samtools", "modules"]
},
"samtools/index": {
"branch": "master",
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
"installed_by": ["bam_markduplicates_picard", "bam_sort_stats_samtools", "modules"]
},
"samtools/sort": {
"branch": "master",
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
"installed_by": ["bam_sort_stats_samtools", "modules"]
},
"samtools/stats": {
"branch": "master",
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
"installed_by": ["bam_stats_samtools", "modules"]
},
"subread/featurecounts": {
"branch": "master",
"git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1",
"installed_by": ["modules"]
},
"trimgalore": {
"branch": "master",
"git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1",
"installed_by": ["fastq_fastqc_umitools_trimgalore", "modules"]
},
"ucsc/bedgraphtobigwig": {
"branch": "master",
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
"installed_by": ["modules"]
},
"umitools/extract": {
"branch": "master",
"git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1",
"installed_by": ["fastq_fastqc_umitools_trimgalore"]
},
"untar": {
"branch": "master",
"git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
"installed_by": ["modules"]
},
"untarfiles": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"]
}
}
},
"subworkflows": {
"nf-core": {
"bam_markduplicates_picard": {
"branch": "master",
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
"installed_by": ["subworkflows"]
},
"bam_sort_stats_samtools": {
"branch": "master",
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
"installed_by": ["fastq_align_bowtie2", "fastq_align_bwa", "fastq_align_chromap"]
},
"bam_stats_samtools": {
"branch": "master",
"git_sha": "0eacd714effe5aac1c1de26593873960b3346cab",
"installed_by": ["bam_markduplicates_picard", "bam_sort_stats_samtools"]
},
"fastq_align_bowtie2": {
"branch": "master",
"git_sha": "0eacd714effe5aac1c1de26593873960b3346cab",
"installed_by": ["subworkflows"]
},
"fastq_align_bwa": {
"branch": "master",
"git_sha": "e0ff65e1fb313677de09f5f477ae3da30ce19b7b",
"installed_by": ["subworkflows"]
},
"fastq_align_chromap": {
"branch": "master",
"git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
"installed_by": ["subworkflows"]
},
"fastq_fastqc_umitools_trimgalore": {
"branch": "master",
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
"installed_by": ["subworkflows"]
},
"utils_nextflow_pipeline": {
"branch": "master",
"git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
"installed_by": ["subworkflows"]
},
"utils_nfcore_pipeline": {
"branch": "master",
"git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
"installed_by": ["subworkflows"]
},
"utils_nfvalidation_plugin": {
"branch": "master",
"git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
"installed_by": ["subworkflows"]
}
}
}
}
}
}