shrimp.json

{
  "define":
    {
      "QUERY":"query.csfasta",
      "GENOME":"genome.fasta",
      "MAPPER":"./rmapper-cs",
      "MOPTIONS":"-M fast -M 50bp",
      "SPLIT":"./split_fasta",
      "SEQ_PER_SPLIT":10000,
      "TOTAL_SEQ":7620000
    },
  "rules":
    [
      
      {
        "command":"./split_fasta 10000 query.csfasta",
        "inputs":
          [
            "query.csfasta",
            "./split_fasta"
          ],
        "outputs":
          [
            "query.csfasta.0",
            "query.csfasta.1",
            "query.csfasta.2",
            "query.csfasta.3",
            "query.csfasta.4",
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output.98 output.99 output.100 output.101 output.102 output.103 output.104 output.105 output.106 output.107 output.108 output.109 output.110 output.111 output.112 output.113 output.114 output.115 output.116 output.117 output.118 output.119 output.120 output.121 output.122 output.123 output.124 output.125 output.126 output.127 output.128 output.129 output.130 output.131 output.132 output.133 output.134 output.135 output.136 output.137 output.138 output.139 output.140 output.141 output.142 output.143 output.144 output.145 output.146 output.147 output.148 output.149 output.150 output.151 output.152 output.153 output.154 output.155 output.156 output.157 output.158 output.159 output.160 output.161 output.162 output.163 output.164 output.165 output.166 output.167 output.168 output.169 output.170 output.171 output.172 output.173 output.174 output.175 output.176 output.177 output.178 output.179 output.180 output.181 output.182 output.183 output.184 output.185 output.186 output.187 output.188 output.189 output.190 output.191 output.192 output.193 output.194 output.195 output.196 output.197 output.198 output.199 output.200 output.201 output.202 output.203 output.204 output.205 output.206 output.207 output.208 output.209 output.210 output.211 output.212 output.213 output.214 output.215 output.216 output.217 output.218 output.219 output.220 output.221 output.222 output.223 output.224 output.225 output.226 output.227 output.228 output.229 output.230 output.231 output.232 output.233 output.234 output.235 output.236 output.237 output.238 output.239 output.240 output.241 output.242 output.243 output.244 output.245 output.246 output.247 output.248 output.249 output.250 output.251 output.252 output.253 output.254 output.255 output.256 output.257 output.258 output.259 output.260 output.261 output.262 output.263 output.264 output.265 output.266 output.267 output.268 output.269 output.270 output.271 output.272 output.273 output.274 output.275 output.276 output.277 output.278 output.279 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