|
2 | 2 | "name": "nf-core/rnaseq", |
3 | 3 | "homePage": "https://github.com/nf-core/rnaseq", |
4 | 4 | "repos": { |
5 | | - "nf-core/modules": { |
6 | | - "git_url": "https://github.com/nf-core/modules.git", |
| 5 | + "https://github.com/nf-core/modules.git": { |
7 | 6 | "modules": { |
8 | | - "bbmap/bbsplit": { |
9 | | - "branch": "master", |
10 | | - "git_sha": "848ee9a215d02d80be033bfa60881700f2bd914c" |
11 | | - }, |
12 | | - "cat/fastq": { |
13 | | - "branch": "master", |
14 | | - "git_sha": "e9bc33485e420b51cfbed3cf63ac7463cd5739d3" |
15 | | - }, |
16 | | - "custom/dumpsoftwareversions": { |
17 | | - "branch": "master", |
18 | | - "git_sha": "82501fe6d0d12614db67751d30af98d16e63dc59" |
19 | | - }, |
20 | | - "custom/getchromsizes": { |
21 | | - "branch": "master", |
22 | | - "git_sha": "213403187932dbbdd936a04474cc8cd8abae7a08" |
23 | | - }, |
24 | | - "fastqc": { |
25 | | - "branch": "master", |
26 | | - "git_sha": "49b18b1639f4f7104187058866a8fab33332bdfe" |
27 | | - }, |
28 | | - "gffread": { |
29 | | - "branch": "master", |
30 | | - "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" |
31 | | - }, |
32 | | - "gunzip": { |
33 | | - "branch": "master", |
34 | | - "git_sha": "90aef30f432332bdf0ce9f4b9004aa5d5c4960bb" |
35 | | - }, |
36 | | - "hisat2/align": { |
37 | | - "branch": "master", |
38 | | - "git_sha": "4eed099a12a7d586ce830a662a33a9df5bd67a24" |
39 | | - }, |
40 | | - "hisat2/build": { |
41 | | - "branch": "master", |
42 | | - "git_sha": "4eed099a12a7d586ce830a662a33a9df5bd67a24" |
43 | | - }, |
44 | | - "hisat2/extractsplicesites": { |
45 | | - "branch": "master", |
46 | | - "git_sha": "4eed099a12a7d586ce830a662a33a9df5bd67a24" |
47 | | - }, |
48 | | - "picard/markduplicates": { |
49 | | - "branch": "master", |
50 | | - "git_sha": "682f789f93070bd047868300dd018faf3d434e7c" |
51 | | - }, |
52 | | - "preseq/lcextrap": { |
53 | | - "branch": "master", |
54 | | - "git_sha": "90aef30f432332bdf0ce9f4b9004aa5d5c4960bb" |
55 | | - }, |
56 | | - "qualimap/rnaseq": { |
57 | | - "branch": "master", |
58 | | - "git_sha": "82501fe6d0d12614db67751d30af98d16e63dc59" |
59 | | - }, |
60 | | - "rsem/calculateexpression": { |
61 | | - "branch": "master", |
62 | | - "git_sha": "1b5d3f5ac2ae61ee35dece20a2aeb8018b6438ce" |
63 | | - }, |
64 | | - "rsem/preparereference": { |
65 | | - "branch": "master", |
66 | | - "git_sha": "1b5d3f5ac2ae61ee35dece20a2aeb8018b6438ce" |
67 | | - }, |
68 | | - "rseqc/bamstat": { |
69 | | - "branch": "master", |
70 | | - "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" |
71 | | - }, |
72 | | - "rseqc/inferexperiment": { |
73 | | - "branch": "master", |
74 | | - "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" |
75 | | - }, |
76 | | - "rseqc/innerdistance": { |
77 | | - "branch": "master", |
78 | | - "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" |
79 | | - }, |
80 | | - "rseqc/junctionannotation": { |
81 | | - "branch": "master", |
82 | | - "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" |
83 | | - }, |
84 | | - "rseqc/junctionsaturation": { |
85 | | - "branch": "master", |
86 | | - "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" |
87 | | - }, |
88 | | - "rseqc/readdistribution": { |
89 | | - "branch": "master", |
90 | | - "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" |
91 | | - }, |
92 | | - "rseqc/readduplication": { |
93 | | - "branch": "master", |
94 | | - "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" |
95 | | - }, |
96 | | - "rseqc/tin": { |
97 | | - "branch": "master", |
98 | | - "git_sha": "4dbc166a7c30e963511fb5c9870fbcaa158a53a9" |
99 | | - }, |
100 | | - "salmon/index": { |
101 | | - "branch": "master", |
102 | | - "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" |
103 | | - }, |
104 | | - "salmon/quant": { |
105 | | - "branch": "master", |
106 | | - "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" |
107 | | - }, |
108 | | - "samtools/flagstat": { |
109 | | - "branch": "master", |
110 | | - "git_sha": "bbb99cb8d679555cc01c98766de7869f83283545" |
111 | | - }, |
112 | | - "samtools/idxstats": { |
113 | | - "branch": "master", |
114 | | - "git_sha": "f0a86eaf5bf6ca73c5571193edd00c25bfa308f5" |
115 | | - }, |
116 | | - "samtools/index": { |
117 | | - "branch": "master", |
118 | | - "git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773" |
119 | | - }, |
120 | | - "samtools/sort": { |
121 | | - "branch": "master", |
122 | | - "git_sha": "d5d785b3d8b422cda9c6d84a23f629a8e9ff8cd8" |
123 | | - }, |
124 | | - "samtools/stats": { |
125 | | - "branch": "master", |
126 | | - "git_sha": "f4eab7945952dc4934224309701a49913ea05ae6" |
127 | | - }, |
128 | | - "sortmerna": { |
129 | | - "branch": "master", |
130 | | - "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046" |
131 | | - }, |
132 | | - "star/align": { |
133 | | - "branch": "master", |
134 | | - "git_sha": "cd22a76c78b09f7837a5a75642774a4bf48c92ba" |
135 | | - }, |
136 | | - "star/genomegenerate": { |
137 | | - "branch": "master", |
138 | | - "git_sha": "cd22a76c78b09f7837a5a75642774a4bf48c92ba" |
139 | | - }, |
140 | | - "stringtie/stringtie": { |
141 | | - "branch": "master", |
142 | | - "git_sha": "47cc7a77bfa10c0aa6e6c393d09e895a85d1583e" |
143 | | - }, |
144 | | - "subread/featurecounts": { |
145 | | - "branch": "master", |
146 | | - "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" |
147 | | - }, |
148 | | - "trimgalore": { |
149 | | - "branch": "master", |
150 | | - "git_sha": "bfbdc4f79bb26bc698d30b74abd081db8af77f4d" |
151 | | - }, |
152 | | - "ucsc/bedclip": { |
153 | | - "branch": "master", |
154 | | - "git_sha": "233fa70811a03a4cecb2ece483b5c8396e2cee1d" |
155 | | - }, |
156 | | - "ucsc/bedgraphtobigwig": { |
157 | | - "branch": "master", |
158 | | - "git_sha": "90aef30f432332bdf0ce9f4b9004aa5d5c4960bb" |
159 | | - }, |
160 | | - "umitools/dedup": { |
161 | | - "branch": "master", |
162 | | - "git_sha": "9d489648a7425fa18d8bed18935442c104d8733c" |
163 | | - }, |
164 | | - "umitools/extract": { |
165 | | - "branch": "master", |
166 | | - "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" |
167 | | - }, |
168 | | - "untar": { |
169 | | - "branch": "master", |
170 | | - "git_sha": "b63b9f752dc8e43fc70b0491aad5e0a270ab0e10" |
| 7 | + "nf-core": { |
| 8 | + "bbmap/bbsplit": { |
| 9 | + "branch": "master", |
| 10 | + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" |
| 11 | + }, |
| 12 | + "cat/fastq": { |
| 13 | + "branch": "master", |
| 14 | + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" |
| 15 | + }, |
| 16 | + "custom/dumpsoftwareversions": { |
| 17 | + "branch": "master", |
| 18 | + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" |
| 19 | + }, |
| 20 | + "custom/getchromsizes": { |
| 21 | + "branch": "master", |
| 22 | + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", |
| 23 | + "patch": "modules/nf-core/custom/getchromsizes/custom-getchromsizes.diff" |
| 24 | + }, |
| 25 | + "fastqc": { |
| 26 | + "branch": "master", |
| 27 | + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" |
| 28 | + }, |
| 29 | + "gffread": { |
| 30 | + "branch": "master", |
| 31 | + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" |
| 32 | + }, |
| 33 | + "gunzip": { |
| 34 | + "branch": "master", |
| 35 | + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" |
| 36 | + }, |
| 37 | + "hisat2/align": { |
| 38 | + "branch": "master", |
| 39 | + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" |
| 40 | + }, |
| 41 | + "hisat2/build": { |
| 42 | + "branch": "master", |
| 43 | + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" |
| 44 | + }, |
| 45 | + "hisat2/extractsplicesites": { |
| 46 | + "branch": "master", |
| 47 | + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" |
| 48 | + }, |
| 49 | + "picard/markduplicates": { |
| 50 | + "branch": "master", |
| 51 | + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" |
| 52 | + }, |
| 53 | + "preseq/lcextrap": { |
| 54 | + "branch": "master", |
| 55 | + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" |
| 56 | + }, |
| 57 | + "qualimap/rnaseq": { |
| 58 | + "branch": "master", |
| 59 | + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" |
| 60 | + }, |
| 61 | + "rsem/calculateexpression": { |
| 62 | + "branch": "master", |
| 63 | + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" |
| 64 | + }, |
| 65 | + "rsem/preparereference": { |
| 66 | + "branch": "master", |
| 67 | + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" |
| 68 | + }, |
| 69 | + "rseqc/bamstat": { |
| 70 | + "branch": "master", |
| 71 | + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" |
| 72 | + }, |
| 73 | + "rseqc/inferexperiment": { |
| 74 | + "branch": "master", |
| 75 | + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" |
| 76 | + }, |
| 77 | + "rseqc/innerdistance": { |
| 78 | + "branch": "master", |
| 79 | + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" |
| 80 | + }, |
| 81 | + "rseqc/junctionannotation": { |
| 82 | + "branch": "master", |
| 83 | + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" |
| 84 | + }, |
| 85 | + "rseqc/junctionsaturation": { |
| 86 | + "branch": "master", |
| 87 | + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" |
| 88 | + }, |
| 89 | + "rseqc/readdistribution": { |
| 90 | + "branch": "master", |
| 91 | + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" |
| 92 | + }, |
| 93 | + "rseqc/readduplication": { |
| 94 | + "branch": "master", |
| 95 | + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" |
| 96 | + }, |
| 97 | + "rseqc/tin": { |
| 98 | + "branch": "master", |
| 99 | + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" |
| 100 | + }, |
| 101 | + "salmon/index": { |
| 102 | + "branch": "master", |
| 103 | + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" |
| 104 | + }, |
| 105 | + "salmon/quant": { |
| 106 | + "branch": "master", |
| 107 | + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" |
| 108 | + }, |
| 109 | + "samtools/flagstat": { |
| 110 | + "branch": "master", |
| 111 | + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" |
| 112 | + }, |
| 113 | + "samtools/idxstats": { |
| 114 | + "branch": "master", |
| 115 | + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" |
| 116 | + }, |
| 117 | + "samtools/index": { |
| 118 | + "branch": "master", |
| 119 | + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" |
| 120 | + }, |
| 121 | + "samtools/sort": { |
| 122 | + "branch": "master", |
| 123 | + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" |
| 124 | + }, |
| 125 | + "samtools/stats": { |
| 126 | + "branch": "master", |
| 127 | + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" |
| 128 | + }, |
| 129 | + "sortmerna": { |
| 130 | + "branch": "master", |
| 131 | + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" |
| 132 | + }, |
| 133 | + "star/align": { |
| 134 | + "branch": "master", |
| 135 | + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" |
| 136 | + }, |
| 137 | + "star/genomegenerate": { |
| 138 | + "branch": "master", |
| 139 | + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" |
| 140 | + }, |
| 141 | + "stringtie/stringtie": { |
| 142 | + "branch": "master", |
| 143 | + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" |
| 144 | + }, |
| 145 | + "subread/featurecounts": { |
| 146 | + "branch": "master", |
| 147 | + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" |
| 148 | + }, |
| 149 | + "trimgalore": { |
| 150 | + "branch": "master", |
| 151 | + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" |
| 152 | + }, |
| 153 | + "ucsc/bedclip": { |
| 154 | + "branch": "master", |
| 155 | + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" |
| 156 | + }, |
| 157 | + "ucsc/bedgraphtobigwig": { |
| 158 | + "branch": "master", |
| 159 | + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" |
| 160 | + }, |
| 161 | + "umitools/dedup": { |
| 162 | + "branch": "master", |
| 163 | + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" |
| 164 | + }, |
| 165 | + "umitools/extract": { |
| 166 | + "branch": "master", |
| 167 | + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" |
| 168 | + }, |
| 169 | + "untar": { |
| 170 | + "branch": "master", |
| 171 | + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" |
| 172 | + } |
171 | 173 | } |
172 | 174 | } |
173 | 175 | } |
|
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