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-596.0999999999999 ] } ], "version": 2 }, "yaml": "{\r\nname: \"JAMP\",\r\ndocker_name: \"JAMP\",\r\ndescription: \"\",\r\nversion: \"0.0.1\",\r\nauthor: \"MBB\",\r\noptions: [\r\n {\r\n name: \"results_dir\",\r\n type: \"output_dir\",\r\n value: \"\/Results\",\r\n label: \"Results directory: \",\r\n volumes: [Results: \"\/Results\"]\r\n },\r\n],\r\nsteps_in: [\r\n{ step_name: \"VSEARCH_3\", tool_name: \"VSEARCH_mergepairs\", rule_name: \"VSEARCH_mergepairs\",\r\n params: [\r\n { input_name: read_dir, origin_command: raw_read_dir, origin_name: read_dir, origin_step: input},\r\n ]\r\n},\r\n{ step_name: \"VSEARCH_2\", tool_name: \"VSEARCH_filter\", rule_name: \"VSEARCH_filter\",\r\n params: [\r\n { input_name: read_dir, origin_command: VSEARCH_mergepairs, origin_name: mergepairs_done, origin_step: VSEARCH_3},\r\n ]\r\n},\r\n{ step_name: \"VSEARCH\", tool_name: \"VSEARCH_derep\", rule_name: \"VSEARCH_derep\",\r\n params: [\r\n { input_name: fasta_dir, origin_command: VSEARCH_filter, origin_name: filter_done, origin_step: VSEARCH_2},\r\n ]\r\n},\r\n{ step_name: \"format_conversion\", tool_name: \"fastamerge\", rule_name: \"fastamerge\",\r\n params: [\r\n { input_name: fasta_dir, origin_command: VSEARCH_derep, origin_name: derepfasta_dir, origin_step: VSEARCH},\r\n ]\r\n},\r\n{ step_name: \"VSEARCH_4\", tool_name: \"VSEARCH_derep_fastafile\", rule_name: \"VSEARCH_derep_fastafile\",\r\n params: [\r\n { input_name: fasta, origin_command: fastamerge, origin_name: fasta, origin_step: format_conversion},\r\n ]\r\n},\r\n{ step_name: \"VSEARCH_5\", tool_name: \"VSEARCH_unoise\", rule_name: \"VSEARCH_unoise\",\r\n params: [\r\n { input_name: fasta, origin_command: VSEARCH_derep_fastafile, origin_name: derepfasta, origin_step: VSEARCH_4},\r\n { input_name: otutab, origin_command: VSEARCH_derep_fastafile, origin_name: otutab, origin_step: VSEARCH_4},\r\n ]\r\n},\r\n{ step_name: \"VSEARCH_6\", tool_name: \"VSEARCH_clustering\", rule_name: \"VSEARCH_clustering\",\r\n params: [\r\n { input_name: fasta, origin_command: VSEARCH_unoise, origin_name: centroids, origin_step: VSEARCH_5},\r\n { input_name: otutab, origin_command: VSEARCH_unoise, origin_name: otutab, origin_step: VSEARCH_5},\r\n ]\r\n},\r\n{ step_name: \"metabarcoding_2\", tool_name: \"lulu\", rule_name: \"lulu\",\r\n params: [\r\n { input_name: abundance_file, origin_command: VSEARCH_clustering, origin_name: otutab, origin_step: VSEARCH_6},\r\n { input_name: sequence_file, origin_command: VSEARCH_clustering, origin_name: centroids, origin_step: VSEARCH_6},\r\n ]\r\n},\r\n{ step_name: \"phylogenetics\", tool_name: \"mafft\", rule_name: \"mafft\",\r\n params: [\r\n { input_name: fasta, origin_command: VSEARCH_clustering, origin_name: centroids, origin_step: VSEARCH_6},\r\n ]\r\n},\r\n{ step_name: \"phylogenetics_2\", tool_name: \"raxml_ng\", rule_name: \"raxml_ng\",\r\n params: [\r\n { input_name: aligned_seqs, origin_command: mafft, origin_name: aligned_fasta, origin_step: phylogenetics},\r\n ]\r\n},\r\n{ step_name: \"metabarcoding\", tool_name: \"dada2_assign_taxonomy\", rule_name: \"dada2_assign_taxonomy\",\r\n params: [\r\n { input_name: seqs, origin_command: VSEARCH_clustering, origin_name: centroids, origin_step: VSEARCH_6},\r\n { input_name: abundance, origin_command: lulu, origin_name: curated_table, origin_step: metabarcoding_2},\r\n ]\r\n},\r\n],\r\nsteps: [\r\n { title: \"VSEARCH_3\", name: \"VSEARCH_3\", tools: [VSEARCH_mergepairs], default: \"VSEARCH_mergepairs\" },\r\n { title: \"VSEARCH_2\", name: \"VSEARCH_2\", tools: [VSEARCH_filter], default: \"VSEARCH_filter\" },\r\n { title: \"VSEARCH\", name: \"VSEARCH\", tools: [VSEARCH_derep], default: \"VSEARCH_derep\" },\r\n { title: \"format_conversion\", name: \"format_conversion\", tools: [fastamerge], default: \"fastamerge\" },\r\n { title: \"VSEARCH_4\", name: \"VSEARCH_4\", tools: [VSEARCH_derep_fastafile], default: \"VSEARCH_derep_fastafile\" },\r\n { title: \"VSEARCH_5\", name: \"VSEARCH_5\", tools: [VSEARCH_unoise], default: \"VSEARCH_unoise\" },\r\n { title: \"VSEARCH_6\", name: \"VSEARCH_6\", tools: [VSEARCH_clustering], default: \"VSEARCH_clustering\" },\r\n { title: \"metabarcoding_2\", name: \"metabarcoding_2\", tools: [lulu], default: \"lulu\" },\r\n { title: \"phylogenetics\", name: \"phylogenetics\", tools: [mafft], default: \"mafft\" },\r\n { title: \"phylogenetics_2\", name: \"phylogenetics_2\", tools: [raxml_ng], default: \"raxml_ng\" },\r\n { title: \"metabarcoding\", name: \"metabarcoding\", tools: [dada2_assign_taxonomy], default: \"dada2_assign_taxonomy\" },\r\n],\r\ninput: [\"raw_read_dir\",],\r\nparams_equals: [\r\n { remove: phylogenetics_2__raxml_ng_aligned_seqs},\r\n\r\n]\r\n}\r\n" } ]