{ "id": 2, "steps": [ {"name": "sol2bfq", "function": "sol2bfq", "params": [{"name": "INPUT", "data_locator": null}], "max_nodes": 1}, {"name": "MAQ map", "function": "maq-map", "params": [{"name": "REFERENCEFILE", "value": "ref.bfa"}, {"name": "INPUT", "subpath": null, "from_step": 0}, {"name": "REFERENCE", "data_locator": null}, {"name": "MAQ_DEB", "data_locator": null}], "max_nodes": 2}, {"name": "MAQ merge", "function": "maq-merge", "params": [{"name": "REFERENCEFILE", "value": "ref.bfa"}, {"name": "REFERENCE", "data_locator": null}, {"name": "INPUT", "subpath": null, "from_step": 1}, {"name": "MAQ_DEB", "data_locator": null}], "max_nodes": 1}, {"name": "MAQ mapview", "function": "maq-mapview", "params": [{"name": "INPUT", "subpath": null, "from_step": 2}, {"name": "MAQ_DEB", "data_locator": null}], "max_nodes": 1}, {"name": "MAQ assemble", "function": "maq-assemble", "params": [{"name": "REFERENCEFILE", "value": "ref.bfa"}, {"name": "INPUT", "subpath": null, "from_step": 2}, {"name": "REFERENCE", "data_locator": null}, {"name": "MAQ_DEB", "data_locator": null}], "max_nodes": 1}, {"name": "MAQ cns2x", "function": "maq-cns2x", "params": [{"name": "INPUT", "subpath": null, "from_step": 4}, {"name": "MAQ_DEB", "data_locator": null}], "max_nodes": 1}, {"name": "SNP Filter", "function": "maq-snpfilter", "params": [{"name": "INPUT", "subpath": null, "from_step": 5}, {"name": "SNPFILTER_ARGS", "value": null}, {"name": "MAQ_DEB", "data_locator": null}], "max_nodes": 1}, {"name": "SNP Translate", "function": "awz-stream", "params": [{"name": "FUNCTION", "value": "mrs-maq-snptranslate"}, {"name": "INPUT", "subpath": null, "from_step": 6}, {"name": "OUTPUTNAME", "value": "cns.translated.snp.txt"}], "max_nodes": 1}, {"name": "SNP Detail", "function": "filefilter", "params": [{"name": "SNPCALL_MIN_STARTS", "value": null}, {"name": "INPUT", "subpath": null, "from_step": 3}, {"name": "SNPREFERENCE", "subpath": "/cns.translated.snp.txt", "from_step": 7}, {"name": "MINCONSENSUSQUALITY", "value": null}, {"name": "COMMAND", "value": "mrs-reftranslate|mrs-maq-alnfilter"}, {"name": "WANT_SNPS", "value": "1"}, {"name": "OUTPUTNAME", "value": "snplist.txt"}, {"name": "SNPCALL_MIN_COVER", "value": null}], "max_nodes": 1}, {"name": "snp2gff", "function": "filefilter", "params": [{"name": "OUTPUTNAME", "value": "snp.gff"}, {"name": "COMMAND", "value": "mrs-snp2gff"}, {"name": "INPUT", "subpath": null, "from_step": 8}], "max_nodes": 1} ] }