nf-core-aMeta/modules.json at dev · NBISweden/nf-core-aMeta · 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
{
    "name": "NBISweden/nf-core-aMeta",
    "homePage": "https://github.com/NBISweden/nf-core-aMeta",
    "repos": {
        "https://github.com/nf-core/modules.git": {
            "modules": {
                "nf-core": {
                    "bowtie2/align": {
                        "branch": "master",
                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                        "installed_by": ["fastq_align_bowtie2", "modules"],
                        "patch": "modules/nf-core/bowtie2/align/bowtie2-align.diff"
                    },
                    "bowtie2/build": {
                        "branch": "master",
                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                        "installed_by": ["modules"]
                    },
                    "cutadapt": {
                        "branch": "master",
                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                        "installed_by": ["modules"],
                        "patch": "modules/nf-core/cutadapt/cutadapt.diff"
                    },
                    "fastqc": {
                        "branch": "master",
                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                        "installed_by": ["modules"]
                    },
                    "krakenuniq/build": {
                        "branch": "master",
                        "git_sha": "e069fcf0b37ce455ebc845c1d278219ffc065c37",
                        "installed_by": ["modules"]
                    },
                    "krakenuniq/preloadedkrakenuniq": {
                        "branch": "master",
                        "git_sha": "65d35c30a46419599cfd1b2b183e6f17af6889f6",
                        "installed_by": ["modules"]
                    },
                    "krona/ktimporttaxonomy": {
                        "branch": "master",
                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                        "installed_by": ["modules"]
                    },
                    "krona/ktupdatetaxonomy": {
                        "branch": "master",
                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                        "installed_by": ["modules"],
                        "patch": "modules/nf-core/krona/ktupdatetaxonomy/krona-ktupdatetaxonomy.diff"
                    },
                    "malt/build": {
                        "branch": "master",
                        "git_sha": "70a5a677f10ea745e43e0f6c4bb15a2fb3cc7892",
                        "installed_by": ["modules"],
                        "patch": "modules/nf-core/malt/build/malt-build.diff"
                    },
                    "malt/run": {
                        "branch": "master",
                        "git_sha": "70a5a677f10ea745e43e0f6c4bb15a2fb3cc7892",
                        "installed_by": ["modules"],
                        "patch": "modules/nf-core/malt/run/malt-run.diff"
                    },
                    "maltextract": {
                        "branch": "master",
                        "git_sha": "6ad84060025a8d683485d07e16a8d1e45f71ed63",
                        "installed_by": ["modules"],
                        "patch": "modules/nf-core/maltextract/maltextract.diff"
                    },
                    "mapdamage2": {
                        "branch": "master",
                        "git_sha": "f7121ee60aeb28828852d5b5ff35661a7ea000b5",
                        "installed_by": ["modules"]
                    },
                    "multiqc": {
                        "branch": "master",
                        "git_sha": "98403d15b0e50edae1f3fec5eae5e24982f1fade",
                        "installed_by": ["modules"]
                    },
                    "samtools/faidx": {
                        "branch": "master",
                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                        "installed_by": ["modules"]
                    },
                    "samtools/flagstat": {
                        "branch": "master",
                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                        "installed_by": ["bam_stats_samtools"]
                    },
                    "samtools/idxstats": {
                        "branch": "master",
                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                        "installed_by": ["bam_stats_samtools"]
                    },
                    "samtools/index": {
                        "branch": "master",
                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                        "installed_by": ["bam_sort_stats_samtools"]
                    },
                    "samtools/sort": {
                        "branch": "master",
                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                        "installed_by": ["bam_sort_stats_samtools"]
                    },
                    "samtools/stats": {
                        "branch": "master",
                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                        "installed_by": ["bam_stats_samtools"]
                    },
                    "samtools/view": {
                        "branch": "master",
                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                        "installed_by": ["modules"]
                    }
                }
            },
            "subworkflows": {
                "nf-core": {
                    "bam_sort_stats_samtools": {
                        "branch": "master",
                        "git_sha": "156feda0cb6589cd29c04902004fa3b53bc00205",
                        "installed_by": ["fastq_align_bowtie2"]
                    },
                    "bam_stats_samtools": {
                        "branch": "master",
                        "git_sha": "156feda0cb6589cd29c04902004fa3b53bc00205",
                        "installed_by": ["bam_sort_stats_samtools"]
                    },
                    "fastq_align_bowtie2": {
                        "branch": "master",
                        "git_sha": "a30aa3fd25cc48b7612d53b749e9fcd879433f91",
                        "installed_by": ["subworkflows"]
                    },
                    "utils_nextflow_pipeline": {
                        "branch": "master",
                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                        "installed_by": ["subworkflows"]
                    },
                    "utils_nfcore_pipeline": {
                        "branch": "master",
                        "git_sha": "a3fb7351b1fdb2b1de282b765816bbea190e86a8",
                        "installed_by": ["subworkflows"]
                    },
                    "utils_nfschema_plugin": {
                        "branch": "master",
                        "git_sha": "fdc08b8b1ae74f56686ce21f7ea11ad11990ce57",
                        "installed_by": ["subworkflows"]
                    }
                }
            }
        }
    }
}