preprocessing/modules.json at main · nf-cmgg/preprocessing · 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
{
    "name": "nf-cmgg/preprocessing",
    "homePage": "https://github.com/nf-cmgg/preprocessing",
    "repos": {
        "https://github.com/nf-core/modules.git": {
            "modules": {
                "nf-core": {
                    "bclconvert": {
                        "branch": "master",
                        "git_sha": "21e4662ae927fdbc5fc04eec9bde38b0689d4954",
                        "installed_by": ["modules"]
                    },
                    "biobambam/bamsormadup": {
                        "branch": "master",
                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                        "installed_by": ["modules"],
                        "patch": "modules/nf-core/biobambam/bamsormadup/biobambam-bamsormadup.diff"
                    },
                    "bowtie2/align": {
                        "branch": "master",
                        "git_sha": "a0961c41021561ac7cf139f86bd7812a2f99e994",
                        "installed_by": ["fastq_align_dna", "modules"],
                        "patch": "modules/nf-core/bowtie2/align/bowtie2-align.diff"
                    },
                    "bwa/mem": {
                        "branch": "master",
                        "git_sha": "2fb127c8fd13de0adaa676df7169131e45c0b114",
                        "installed_by": ["fastq_align_dna"],
                        "patch": "modules/nf-core/bwa/mem/bwa-mem.diff"
                    },
                    "bwamem2/mem": {
                        "branch": "master",
                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                        "installed_by": ["fastq_align_dna"],
                        "patch": "modules/nf-core/bwamem2/mem/bwamem2-mem.diff"
                    },
                    "dragmap/align": {
                        "branch": "master",
                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                        "installed_by": ["fastq_align_dna"],
                        "patch": "modules/nf-core/dragmap/align/dragmap-align.diff"
                    },
                    "falco": {
                        "branch": "master",
                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                        "installed_by": ["modules"]
                    },
                    "fastp": {
                        "branch": "master",
                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                        "installed_by": ["modules"]
                    },
                    "gnu/sort": {
                        "branch": "master",
                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                        "installed_by": ["modules"]
                    },
                    "md5sum": {
                        "branch": "master",
                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                        "installed_by": ["modules"]
                    },
                    "mosdepth": {
                        "branch": "master",
                        "git_sha": "999b9db1d6b8bdc591e1168e183f4cc87d6606f9",
                        "installed_by": ["modules"],
                        "patch": "modules/nf-core/mosdepth/mosdepth.diff"
                    },
                    "multiqc": {
                        "branch": "master",
                        "git_sha": "008f9d3e61209bf995edac3ba531f54e269e1215",
                        "installed_by": ["modules"]
                    },
                    "multiqcsav": {
                        "branch": "master",
                        "git_sha": "008f9d3e61209bf995edac3ba531f54e269e1215",
                        "installed_by": ["modules"]
                    },
                    "picard/collecthsmetrics": {
                        "branch": "master",
                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                        "installed_by": ["modules"],
                        "patch": "modules/nf-core/picard/collecthsmetrics/picard-collecthsmetrics.diff"
                    },
                    "picard/collectmultiplemetrics": {
                        "branch": "master",
                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                        "installed_by": ["modules"],
                        "patch": "modules/nf-core/picard/collectmultiplemetrics/picard-collectmultiplemetrics.diff"
                    },
                    "picard/collectwgsmetrics": {
                        "branch": "master",
                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                        "installed_by": ["modules"],
                        "patch": "modules/nf-core/picard/collectwgsmetrics/picard-collectwgsmetrics.diff"
                    },
                    "samtools/convert": {
                        "branch": "master",
                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                        "installed_by": ["modules"],
                        "patch": "modules/nf-core/samtools/convert/samtools-convert.diff"
                    },
                    "samtools/coverage": {
                        "branch": "master",
                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                        "installed_by": ["modules"],
                        "patch": "modules/nf-core/samtools/coverage/samtools-coverage.diff"
                    },
                    "samtools/flagstat": {
                        "branch": "master",
                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                        "installed_by": ["modules"]
                    },
                    "samtools/idxstats": {
                        "branch": "master",
                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                        "installed_by": ["modules"]
                    },
                    "samtools/sormadup": {
                        "branch": "master",
                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                        "installed_by": ["modules"],
                        "patch": "modules/nf-core/samtools/sormadup/samtools-sormadup.diff"
                    },
                    "samtools/sort": {
                        "branch": "master",
                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                        "installed_by": ["modules"],
                        "patch": "modules/nf-core/samtools/sort/samtools-sort.diff"
                    },
                    "samtools/stats": {
                        "branch": "master",
                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                        "installed_by": ["modules"],
                        "patch": "modules/nf-core/samtools/stats/samtools-stats.diff"
                    },
                    "snapaligner/align": {
                        "branch": "master",
                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                        "installed_by": ["fastq_align_dna", "modules"],
                        "patch": "modules/nf-core/snapaligner/align/snapaligner-align.diff"
                    },
                    "star/align": {
                        "branch": "master",
                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                        "installed_by": ["modules"],
                        "patch": "modules/nf-core/star/align/star-align.diff"
                    },
                    "strobealign": {
                        "branch": "master",
                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                        "installed_by": ["fastq_align_dna", "modules"],
                        "patch": "modules/nf-core/strobealign/strobealign.diff"
                    }
                }
            },
            "subworkflows": {
                "nf-core": {
                    "fastq_align_dna": {
                        "branch": "master",
                        "git_sha": "a0961c41021561ac7cf139f86bd7812a2f99e994",
                        "installed_by": ["subworkflows"],
                        "patch": "subworkflows/nf-core/fastq_align_dna/fastq_align_dna.diff"
                    },
                    "utils_nextflow_pipeline": {
                        "branch": "master",
                        "git_sha": "1a545fcbd762911c21a64ced3dbef99b2b51ac75",
                        "installed_by": ["subworkflows"]
                    },
                    "utils_nfcore_pipeline": {
                        "branch": "master",
                        "git_sha": "a3fb7351b1fdb2b1de282b765816bbea190e86a8",
                        "installed_by": ["subworkflows"]
                    },
                    "utils_nfschema_plugin": {
                        "branch": "master",
                        "git_sha": "ce3424257de288c0ca25f097a68d3a289da23f12",
                        "installed_by": ["subworkflows"]
                    }
                }
            }
        }
    }
}