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pipeline.json
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pipeline.json
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{
"nodes":[
{"name":"validate_map_and_barcodes", "group":"validate", "value":"1", "desc":"Takes mapping file and barcodes and makes sure all is correctly formatted"},
{"name":"duk_contam", "group":"remove_contam", "value":"1", "desc":"Remove contaminants using kmer matching software"},
{"name":"duk_phix", "group":"remove_contam", "value":"1", "desc":"NA"},
{"name":"split_barcodes", "group":"split_barcodes", "value":"1", "desc":"NA"},
{"name":"remove_unpaired", "group":"split_barcodes", "value":"1", "desc":"NA"},
{"name":"split_pairs", "group":"split_barcodes", "value":"4", "desc":"NA"},
{"name":"generate_qscore_reads1", "group":"qscores", "value":"1", "desc":"NA"},
{"name":"generate_qscore_reads2", "group":"qscores", "value":"1", "desc":"NA"},
{"name":"generate_qscore_graph_paired", "group":"qscores", "value":"1", "desc":"NA"},
{"name":"cut_reads1", "group":"qc", "value":"1", "desc":"NA"},
{"name":"cut_reads2", "group":"qc", "value":"1", "desc":"NA"},
{"name":"flash", "group":"qc", "value":"4", "desc":"Assemble overlapping paired end reads"},
{"name":"itags_qc", "group":"qc", "value":"1", "desc":"Remove low quality sequences"},
{"name":"qscore_sheet_assembled_qced", "group":"qc", "value":"1", "desc":"NA"},
{"name":"qscore_graph_assembled_qced", "group":"qc", "value":"1", "desc":"NA"},
{"name":"generate_clusters", "group":"generate_clusters", "value":"6", "desc":"Cluster sequences at 100% id, followed by clustering at 99% id, followed by chimera removal, followed by clustering at 97% id"},
{"name":"classify", "group":"classify", "value":"1", "desc":"Classify OTUs using the RDP classifier software with a Greengenes training set"},
{"name":"generate_otu_table", "group":"generate_otu_table", "value":"1", "desc":"NA"},
{"name":"filter_otu_table", "group":"filter_otu_table", "value":"1", "desc":"NA"},
{"name":"split_otu_table", "group":"filter_otu_table", "value":"1", "desc":"NA"},
{"name":"convert_otu_table_to_biom_target_organisms", "group":"filter_otu_table", "value":"1", "desc":"NA"},
{"name":"rarefy_otu_table_target_organisms", "group":"filter_otu_table", "value":"1", "desc":"NA"},
{"name":"normalize_otu_table_target_organisms", "group":"filter_otu_table", "value":"1", "desc":"NA"},
{"name":"convert_otu_table_to_biom_everything", "group":"filter_otu_table", "value":"1", "desc":"NA"},
{"name":"normalize_otu_table_all_organisms", "group":"filter_otu_table", "value":"1", "desc":"Normalize using edgeR"},
{"name":"normalize_otu_table_all_organisms", "group":"filter_otu_table", "value":"1", "desc":"Normalize using edgeR"},
{"name":"tax_summary_qc_absolute_raw_L2", "group":"summarize_taxonomy_qc", "value":"1", "desc":"NA"},
{"name":"tax_summary_qc_relative_raw_L2", "group":"summarize_taxonomy_qc", "value":"1", "desc":"NA"},
{"name":"tax_summary_qc_absolute_normalized_L2", "group":"summarize_taxonomy_qc", "value":"1", "desc":"NA"},
{"name":"tax_summary_qc_relative_normalized_L2", "group":"summarize_taxonomy_qc", "value":"1", "desc":"NA"},
{"name":"tax_summary_qc_absolute_all_L2", "group":"summarize_taxonomy_qc", "value":"1", "desc":"NA"},
{"name":"tax_summary_qc_relative_all_L2", "group":"summarize_taxonomy_qc", "value":"1", "desc":"NA"},
{"name":"plot_taxa_single_relative_phylum", "group":"summarize_taxonomy_qc", "value":"1", "desc":"NA"},
{"name":"plot_taxa_single_absolute_phylum", "group":"summarize_taxonomy_qc", "value":"1", "desc":"NA"},
{"name":"plot_taxa_single_relative_phylum", "group":"summarize_taxonomy_qc", "value":"1", "desc":"NA"},
{"name":"plot_taxa_single_absolute_phylum", "group":"summarize_taxonomy_qc", "value":"1", "desc":"NA"},
{"name":"plot_taxa_single_relative_phylum_all", "group":"summarize_taxonomy_qc", "value":"1", "desc":"NA"},
{"name":"plot_taxa_single_absolute_phylum_all", "group":"summarize_taxonomy_qc", "value":"1", "desc":"NA"},
{"name":"filter_otu_table_norm", "group":"prepare_tables_for_diversity", "value":"1", "desc":"NA"},
{"name":"filter_otu_table_rar", "group":"prepare_tables_for_diversity", "value":"1", "desc":"NA"},
{"name":"convert_otu_table_to_biom_norm", "group":"prepare_tables_for_diversity", "value":"1", "desc":"NA"},
{"name":"convert_otu_table_to_biom_rarefied", "group":"prepare_tables_for_diversity", "value":"1", "desc":"NA"},
{"name":"filter_for_pynast", "group":"align", "value":"1", "desc":"NA"},
{"name":"pynast", "group":"align", "value":"1", "desc":"NA"},
{"name":"filter_pynast_alignment", "group":"align", "value":"1", "desc":"NA"},
{"name":"fasttree", "group":"align", "value":"1", "desc":"NA"},
{"name":"tax_summary_absolute_L1", "group":"summarize_taxonomy", "value":"1", "desc":"NA"},
{"name":"tax_summary_absolute_L2", "group":"summarize_taxonomy", "value":"1", "desc":"NA"},
{"name":"tax_summary_absolute_L3", "group":"summarize_taxonomy", "value":"1", "desc":"NA"},
{"name":"tax_summary_absolute_L4", "group":"summarize_taxonomy", "value":"1", "desc":"NA"},
{"name":"tax_summary_absolute_L5", "group":"summarize_taxonomy", "value":"1", "desc":"NA"},
{"name":"tax_summary_absolute_L6", "group":"summarize_taxonomy", "value":"1", "desc":"NA"},
{"name":"tax_summary_relative_L1", "group":"summarize_taxonomy", "value":"1", "desc":"NA"},
{"name":"tax_summary_relative_L2", "group":"summarize_taxonomy", "value":"1", "desc":"NA"},
{"name":"tax_summary_relative_L3", "group":"summarize_taxonomy", "value":"1", "desc":"NA"},
{"name":"tax_summary_relative_L4", "group":"summarize_taxonomy", "value":"1", "desc":"NA"},
{"name":"tax_summary_relative_L5", "group":"summarize_taxonomy", "value":"1", "desc":"NA"},
{"name":"tax_summary_relative_L6", "group":"summarize_taxonomy", "value":"1", "desc":"NA"},
{"name":"plot_taxa_single_relative_L1", "group":"summarize_taxonomy", "value":"1", "desc":"NA"},
{"name":"plot_taxa_single_absolute_L1", "group":"summarize_taxonomy", "value":"1", "desc":"NA"},
{"name":"plot_taxa_single_relative_L1", "group":"summarize_taxonomy", "value":"1", "desc":"NA"},
{"name":"plot_taxa_single_absolute_L1", "group":"summarize_taxonomy", "value":"1", "desc":"NA"},
{"name":"plot_taxa_single_relative_L2", "group":"summarize_taxonomy", "value":"1", "desc":"NA"},
{"name":"plot_taxa_single_absolute_L2", "group":"summarize_taxonomy", "value":"1", "desc":"NA"},
{"name":"plot_taxa_single_relative_L2", "group":"summarize_taxonomy", "value":"1", "desc":"NA"},
{"name":"plot_taxa_single_absolute_L2", "group":"summarize_taxonomy", "value":"1", "desc":"NA"},
{"name":"plot_taxa_single_relative_L3", "group":"summarize_taxonomy", "value":"1", "desc":"NA"},
{"name":"plot_taxa_single_absolute_L3", "group":"summarize_taxonomy", "value":"1", "desc":"NA"},
{"name":"plot_taxa_single_relative_L3", "group":"summarize_taxonomy", "value":"1", "desc":"NA"},
{"name":"plot_taxa_single_absolute_L3", "group":"summarize_taxonomy", "value":"1", "desc":"NA"},
{"name":"plot_taxa_single_relative_L4", "group":"summarize_taxonomy", "value":"1", "desc":"NA"},
{"name":"plot_taxa_single_absolute_L4", "group":"summarize_taxonomy", "value":"1", "desc":"NA"},
{"name":"plot_taxa_single_relative_L4", "group":"summarize_taxonomy", "value":"1", "desc":"NA"},
{"name":"plot_taxa_single_absolute_L4", "group":"summarize_taxonomy", "value":"1", "desc":"NA"},
{"name":"plot_taxa_single_relative_L5", "group":"summarize_taxonomy", "value":"1", "desc":"NA"},
{"name":"plot_taxa_single_absolute_L5", "group":"summarize_taxonomy", "value":"1", "desc":"NA"},
{"name":"plot_taxa_single_relative_L5", "group":"summarize_taxonomy", "value":"1", "desc":"NA"},
{"name":"plot_taxa_single_absolute_L5", "group":"summarize_taxonomy", "value":"1", "desc":"NA"},
{"name":"plot_taxa_single_relative_L6", "group":"summarize_taxonomy", "value":"1", "desc":"NA"},
{"name":"plot_taxa_single_absolute_L6", "group":"summarize_taxonomy", "value":"1", "desc":"NA"},
{"name":"plot_taxa_single_relative_L6", "group":"summarize_taxonomy", "value":"1", "desc":"NA"},
{"name":"plot_taxa_single_absolute_L6", "group":"summarize_taxonomy", "value":"1", "desc":"NA"},
{"name":"beta_diversity_unifrac_unweighted", "group":"beta_diversity", "value":"1", "desc":"NA"},
{"name":"beta_diversity_unifrac_weighted", "group":"beta_diversity", "value":"1", "desc":"NA"},
{"name":"beta_diversity_bray_curtis", "group":"beta_diversity", "value":"1", "desc":"NA"},
{"name":"compare_categories_1", "group":"beta_diversity", "value":"1", "desc":"NA"},
{"name":"compare_categories_2", "group":"beta_diversity", "value":"1", "desc":"NA"},
{"name":"compare_categories_3", "group":"beta_diversity", "value":"1", "desc":"NA"},
{"name":"beta_diversity_unifrac_unweighted_PCA", "group":"beta_diversity", "value":"1", "desc":"NA"},
{"name":"beta_diversity_unifrac_weighted_PCA", "group":"beta_diversity", "value":"1", "desc":"NA"},
{"name":"beta_diversity_bray_curtis_PCA", "group":"beta_diversity", "value":"1", "desc":"NA"},
{"name":"beta_diversity_unweighted_unifrac_2d_plot", "group":"beta_diversity", "value":"1", "desc":"NA"},
{"name":"beta_diversity_weighted_unifrac_2d_plot", "group":"beta_diversity", "value":"1", "desc":"NA"},
{"name":"beta_diversity_bray_curtis_2d_plot", "group":"beta_diversity", "value":"1", "desc":"NA"},
{"name":"beta_diversity_unweighted_unifrac_3d_plot", "group":"beta_diversity", "value":"1", "desc":"NA"},
{"name":"beta_diversity_weighted_unifrac_3d_plot", "group":"beta_diversity", "value":"1", "desc":"NA"},
{"name":"beta_diversity_bray_curtis_3d_plot", "group":"beta_diversity", "value":"1", "desc":"NA"},
{"name":"unweighted_unifrac_pca_plots", "group":"beta_diversity", "value":"1", "desc":"NA"},
{"name":"weighted_unifrac_pca_plots", "group":"beta_diversity", "value":"1", "desc":"NA"},
{"name":"bray_curtis_pca_plots", "group":"beta_diversity", "value":"1", "desc":"NA"},
{"name":"multiple_rarefaction", "group":"alpha_diversity", "value":"4", "desc":"NA"},
{"name":"alpha_diversity", "group":"alpha_diversity", "value":"1", "desc":"NA"},
{"name":"collate_alpha", "group":"alpha_diversity", "value":"1", "desc":"NA"},
{"name":"rarefaction_plots", "group":"alpha_diversity", "value":"1", "desc":"NA"},
{"name":"upgma_clustering_unweighted_unifrac", "group":"upgma_clustering", "value":"1", "desc":"NA"},
{"name":"upgma_clustering_weighted_unifrac", "group":"upgma_clustering", "value":"1", "desc":"NA"},
{"name":"upgma_clustering_bray_curtis", "group":"upgma_clustering", "value":"1", "desc":"NA"},
{"name":"otu_heatmap_20", "group":"heatmap", "value":"1", "desc":"NA"},
{"name":"otu_heatmap_40", "group":"heatmap", "value":"1", "desc":"NA"},
{"name":"otu_heatmap_60", "group":"heatmap", "value":"1", "desc":"NA"},
{"name":"otu_heatmap_80", "group":"heatmap", "value":"1", "desc":"NA"},
{"name":"otu_heatmap_100", "group":"heatmap", "value":"1", "desc":"NA"},
{"name":"blast", "group":"blast", "value":"16", "desc":"BLASTn all OTUs against NCBI's nt DB"},
{"name":"count_report", "group":"deliverables", "value":"1", "desc":"NA"},
{"name":"deliverables_complete", "group":"deliverables", "value":"1", "desc":"NA"}
],
"links":[
{"source":0, "source_name":"validate_map_and_barcodes", "target":1, "target_name":"duk_contam"},
{"source":1, "source_name":"duk_contam", "target":2, "target_name":"duk_phix"},
{"source":2, "source_name":"duk_phix", "target":3, "target_name":"split_barcodes"},
{"source":3, "source_name":"split_barcodes", "target":4, "target_name":"remove_unpaired"},
{"source":4, "source_name":"remove_unpaired", "target":5, "target_name":"split_pairs"},
{"source":5, "source_name":"split_pairs", "target":6, "target_name":"generate_qscore_reads1"},
{"source":5, "source_name":"split_pairs", "target":7, "target_name":"generate_qscore_reads2"},
{"source":7, "source_name":"generate_qscore_reads2", "target":8, "target_name":"generate_qscore_graph_paired"},
{"source":6, "source_name":"generate_qscore_reads1", "target":8, "target_name":"generate_qscore_graph_paired"},
{"source":5, "source_name":"split_pairs", "target":9, "target_name":"cut_reads1"},
{"source":5, "source_name":"split_pairs", "target":10, "target_name":"cut_reads2"},
{"source":10, "source_name":"cut_reads2", "target":11, "target_name":"flash"},
{"source":9, "source_name":"cut_reads1", "target":11, "target_name":"flash"},
{"source":11, "source_name":"flash", "target":12, "target_name":"itags_qc"},
{"source":12, "source_name":"itags_qc", "target":13, "target_name":"qscore_sheet_assembled_qced"},
{"source":13, "source_name":"qscore_sheet_assembled_qced", "target":14, "target_name":"qscore_graph_assembled_qced"},
{"source":12, "source_name":"itags_qc", "target":15, "target_name":"generate_clusters"},
{"source":15, "source_name":"generate_clusters", "target":16, "target_name":"classify"},
{"source":16, "source_name":"classify", "target":17, "target_name":"generate_otu_table"},
{"source":15, "source_name":"generate_clusters", "target":17, "target_name":"generate_otu_table"},
{"source":17, "source_name":"generate_otu_table", "target":18, "target_name":"filter_otu_table"},
{"source":18, "source_name":"filter_otu_table", "target":19, "target_name":"split_otu_table"},
{"source":19, "source_name":"split_otu_table", "target":20, "target_name":"convert_otu_table_to_biom_target_organisms"},
{"source":20, "source_name":"convert_otu_table_to_biom_target_organisms", "target":21, "target_name":"rarefy_otu_table_target_organisms"},
{"source":19, "source_name":"split_otu_table", "target":22, "target_name":"normalize_otu_table_target_organisms"},
{"source":18, "source_name":"filter_otu_table", "target":23, "target_name":"convert_otu_table_to_biom_everything"},
{"source":23, "source_name":"convert_otu_table_to_biom_everything", "target":24, "target_name":"normalize_otu_table_all_organisms"},
{"source":18, "source_name":"filter_otu_table", "target":25, "target_name":"normalize_otu_table_all_organisms"},
{"source":20, "source_name":"convert_otu_table_to_biom_target_organisms", "target":26, "target_name":"tax_summary_qc_absolute_raw_L2"},
{"source":20, "source_name":"convert_otu_table_to_biom_target_organisms", "target":27, "target_name":"tax_summary_qc_relative_raw_L2"},
{"source":22, "source_name":"normalize_otu_table_target_organisms", "target":28, "target_name":"tax_summary_qc_absolute_normalized_L2"},
{"source":22, "source_name":"normalize_otu_table_target_organisms", "target":29, "target_name":"tax_summary_qc_relative_normalized_L2"},
{"source":23, "source_name":"convert_otu_table_to_biom_everything", "target":30, "target_name":"tax_summary_qc_absolute_all_L2"},
{"source":23, "source_name":"convert_otu_table_to_biom_everything", "target":31, "target_name":"tax_summary_qc_relative_all_L2"},
{"source":27, "source_name":"tax_summary_qc_relative_raw_L2", "target":32, "target_name":"plot_taxa_single_relative_phylum"},
{"source":26, "source_name":"tax_summary_qc_absolute_raw_L2", "target":33, "target_name":"plot_taxa_single_absolute_phylum"},
{"source":29, "source_name":"tax_summary_qc_relative_normalized_L2", "target":34, "target_name":"plot_taxa_single_relative_phylum"},
{"source":28, "source_name":"tax_summary_qc_absolute_normalized_L2", "target":35, "target_name":"plot_taxa_single_absolute_phylum"},
{"source":31, "source_name":"tax_summary_qc_relative_all_L2", "target":36, "target_name":"plot_taxa_single_relative_phylum_all"},
{"source":30, "source_name":"tax_summary_qc_absolute_all_L2", "target":37, "target_name":"plot_taxa_single_absolute_phylum_all"},
{"source":22, "source_name":"normalize_otu_table_target_organisms", "target":38, "target_name":"filter_otu_table_norm"},
{"source":21, "source_name":"rarefy_otu_table_target_organisms", "target":39, "target_name":"filter_otu_table_rar"},
{"source":38, "source_name":"filter_otu_table_norm", "target":40, "target_name":"convert_otu_table_to_biom_norm"},
{"source":39, "source_name":"filter_otu_table_rar", "target":41, "target_name":"convert_otu_table_to_biom_rarefied"},
{"source":38, "source_name":"filter_otu_table_norm", "target":42, "target_name":"filter_for_pynast"},
{"source":15, "source_name":"generate_clusters", "target":42, "target_name":"filter_for_pynast"},
{"source":42, "source_name":"filter_for_pynast", "target":43, "target_name":"pynast"},
{"source":43, "source_name":"pynast", "target":44, "target_name":"filter_pynast_alignment"},
{"source":44, "source_name":"filter_pynast_alignment", "target":45, "target_name":"fasttree"},
{"source":40, "source_name":"convert_otu_table_to_biom_norm", "target":46, "target_name":"tax_summary_absolute_L1"},
{"source":40, "source_name":"convert_otu_table_to_biom_norm", "target":47, "target_name":"tax_summary_absolute_L2"},
{"source":40, "source_name":"convert_otu_table_to_biom_norm", "target":48, "target_name":"tax_summary_absolute_L3"},
{"source":40, "source_name":"convert_otu_table_to_biom_norm", "target":49, "target_name":"tax_summary_absolute_L4"},
{"source":40, "source_name":"convert_otu_table_to_biom_norm", "target":50, "target_name":"tax_summary_absolute_L5"},
{"source":40, "source_name":"convert_otu_table_to_biom_norm", "target":51, "target_name":"tax_summary_absolute_L6"},
{"source":40, "source_name":"convert_otu_table_to_biom_norm", "target":52, "target_name":"tax_summary_relative_L1"},
{"source":40, "source_name":"convert_otu_table_to_biom_norm", "target":53, "target_name":"tax_summary_relative_L2"},
{"source":40, "source_name":"convert_otu_table_to_biom_norm", "target":54, "target_name":"tax_summary_relative_L3"},
{"source":40, "source_name":"convert_otu_table_to_biom_norm", "target":55, "target_name":"tax_summary_relative_L4"},
{"source":40, "source_name":"convert_otu_table_to_biom_norm", "target":56, "target_name":"tax_summary_relative_L5"},
{"source":40, "source_name":"convert_otu_table_to_biom_norm", "target":57, "target_name":"tax_summary_relative_L6"},
{"source":52, "source_name":"tax_summary_relative_L1", "target":58, "target_name":"plot_taxa_single_relative_L1"},
{"source":46, "source_name":"tax_summary_absolute_L1", "target":59, "target_name":"plot_taxa_single_absolute_L1"},
{"source":52, "source_name":"tax_summary_relative_L1", "target":60, "target_name":"plot_taxa_single_relative_L1"},
{"source":46, "source_name":"tax_summary_absolute_L1", "target":61, "target_name":"plot_taxa_single_absolute_L1"},
{"source":53, "source_name":"tax_summary_relative_L2", "target":62, "target_name":"plot_taxa_single_relative_L2"},
{"source":47, "source_name":"tax_summary_absolute_L2", "target":63, "target_name":"plot_taxa_single_absolute_L2"},
{"source":53, "source_name":"tax_summary_relative_L2", "target":64, "target_name":"plot_taxa_single_relative_L2"},
{"source":47, "source_name":"tax_summary_absolute_L2", "target":65, "target_name":"plot_taxa_single_absolute_L2"},
{"source":54, "source_name":"tax_summary_relative_L3", "target":66, "target_name":"plot_taxa_single_relative_L3"},
{"source":48, "source_name":"tax_summary_absolute_L3", "target":67, "target_name":"plot_taxa_single_absolute_L3"},
{"source":54, "source_name":"tax_summary_relative_L3", "target":68, "target_name":"plot_taxa_single_relative_L3"},
{"source":48, "source_name":"tax_summary_absolute_L3", "target":69, "target_name":"plot_taxa_single_absolute_L3"},
{"source":55, "source_name":"tax_summary_relative_L4", "target":70, "target_name":"plot_taxa_single_relative_L4"},
{"source":49, "source_name":"tax_summary_absolute_L4", "target":71, "target_name":"plot_taxa_single_absolute_L4"},
{"source":55, "source_name":"tax_summary_relative_L4", "target":72, "target_name":"plot_taxa_single_relative_L4"},
{"source":49, "source_name":"tax_summary_absolute_L4", "target":73, "target_name":"plot_taxa_single_absolute_L4"},
{"source":56, "source_name":"tax_summary_relative_L5", "target":74, "target_name":"plot_taxa_single_relative_L5"},
{"source":50, "source_name":"tax_summary_absolute_L5", "target":75, "target_name":"plot_taxa_single_absolute_L5"},
{"source":56, "source_name":"tax_summary_relative_L5", "target":76, "target_name":"plot_taxa_single_relative_L5"},
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