{
 "name": "MetLab Pipeline",
 "description": "",
 "input":{
   "reads":"file",
   "paired reads":"file",
   "reference":"file",
   "kraken_db":"./local_apps/kraken_db",
   "vFam":"./local_apps/vFam-A_2014.hmm",
   "vFam_annotation":"./local_apps/annotationFiles_2014"
 },
 "output":{},
 "version":"0.2.0",
 "groups": [
   {
     "name":"Data filtering",
     "optional":true,
     "commands": [
       {
         "name":"prinseq-lite",
         "command":"<prinseq-lite.pl> -fastq <reads> [-fastq2 <paired reads>] -min_qual_mean %(min_qual)s -ns_max_p %(ns_max)s -derep %(derep)s -trim_qual_right %(trim_qual_right)s -out_format %(format)s -out_good %(out_good)s -out_bad %(out_bad)s [-graph_data %(graph_data)s]",
         "in": ["reads", "[paired reads]"],
         "out": {
           "reads":"{<paired reads> <out_good>_1.fastq <out_good>.fastq}",
           "paired reads":"{<paired reads> <out_good>_2.fastq ''}"
         },
         "options": {
           "derep":1,
           "min_qual":20,
           "format":3,
           "trim_qual_right":20,
           "ns_max":20,
           "graph_data":null,
           "out_good":"filtered_data",
           "out_bad":"discarded_data"
         }
       }
     ]
   },
   {
     "name":"Reference mapping",
     "optional":true,
     "commands": [
       {
         "name":"bowtie2-build",
         "command":"<bowtie2-build> <reference> ref_index",
         "in": ["reference"],
         "out": {},
         "options": {}
       },
       {
         "name":"bowtie2",
         "command":"<bowtie2> -x ref_index {<paired reads> '-1 <reads>' '-U <reads>'} [-2 <paired reads>] -S host_mapping.sam",
         "in": ["reference", "reads", "[paired reads]"],
         "out": {},
         "options": {}
       },
       {
         "name":"samtools view",
         "command":"<samtools> view -b -f 4 -o unmapped.bam host_mapping.sam",
         "in": [],
         "out": {}
       },
       {
         "name":"samtools bam2fq",
         "command":"<samtools> bam2fq -O unmapped.bam >unmapped.fastq",
         "in": [],
         "out": {
           "reads":"unmapped.fastq",
           "paired reads":null
         }
       }
     ]
   },
   {
     "name":"Assembly",
     "optional":true,
     "commands": [
       {
         "name":"Spades",
         "command":"<spades.py> --careful {<paired reads> '-1 <reads> -2 <paired reads>' '-s <reads>'} -o <assembly>",
         "in": ["reads", "[paired reads]"],
         "out": {"reads":"./<assembly>/contigs.fasta"},
         "options": {
           "assembly":"spades_assembly"
         }
       }
     ]
   },
   {
     "name":"Taxonomic classification",
     "optional":false,
     "commands": [
       {
         "name":"to fasta",
         "command":"<to_fasta.py> <reads> -o unmapped.fasta",
         "in": [],
         "out": {"reads":"unmapped.fasta"},
         "options": {}
       },
       {
         "name":"kraken",
         "command":"<kraken> --preload --db <kraken_db> --output kraken_results.txt --classified %(classified)s --unclassified kraken_unclassified.fasta <reads>",
         "in": ["reads"],
         "out": {"reads":"kraken_unclassified.fasta"},
         "options": {
           "classified":"kraken_classified.fasta"
         }
       },
       {
         "name":"kraken-report",
         "command":"<kraken-report> --db <kraken_db> kraken_results.txt >kraken_report.txt",
         "in": [],
         "out": {},
         "options": {}
       },
       {
         "name":"kraken to krona",
         "command":"<kraken_to_krona.py> kraken_report.txt",
         "in": [],
         "out": {},
         "options": {}
       },
       {
         "name":"krona plot",
         "command":"<ktImportText> -o kraken_krona.html <reads> kraken_report.krona.in",
         "in": [],
         "out": {},
         "options": {}
       },
       {
         "name":"FragGeneScan",
         "command":"<run_FragGeneScan.pl> -genome=<reads> -out=frag_gene_scan.out -complete=0 -train=%(train_file)s",
         "in": [],
         "out": {},
         "options": {
           "train_file":"illumina_5"
         }
       },
       {
         "name":"HMMsearch",
         "command":"<hmmsearch> -o hmmsearch.out --tblout hmmsearch_vFamA_table.hs --incE 0.01 <vFam> frag_gene_scan.out.faa",
         "in": [],
         "out": {},
         "options": {}
       },
       {
         "name":"HMMsearch parse",
         "command":"<vFam_HmmSearch_parse.py> -t hmmsearch_vFamA_table.hs -a <vFam_annotation> -e 0.1 -o hmmsearch-parsed.txt -k hmmsearch.krona.in",
         "in": [],
         "out": {},
         "options": {}
       },
       {
         "name":"hmmsearch krona plot",
         "command":"<ktImportText> -o hmmsearch_krona.html <reads> hmmsearch.krona.in",
         "in": [],
         "out": {},
         "options": {}
       }
     ]
   }
  ]
}