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        "yaml": "{\nname: \"RnaSeq-Fatsp-Hisat2-Htseq-Deseq.json\",\ndocker_name: \"rnaseq-fatsp-hisat2-htseq-deseq.json\",\ndescription: \"Rnaseq differential expression \",\nversion: \"0.0.1\",\nauthor: \"MBB\",\noptions: [\n    {\n    name: \"results_dir\",\n    type: \"output_dir\",\n    value: \"\/Results\",\n    label: \"Results directory: \",\n    volumes:  [Results: \"\/Results\"]\n    },\n],\nsteps_in: [\n{ step_name: \"indexing\", tool_name: \"hisat2_index\", rule_name: \"hisat2_index\",\n    params: [\n        #{ input_name: genome_fasta, origin_command: raw_contigs, origin_name: contigs, origin_step: input}, # This input will be read from the params file (see documentation)\n    ]\n},\n{ step_name: \"quality\", tool_name: \"fastp\", rule_name: \"fastp_PE\",\n    params: [\n        { input_name: read, origin_command: raw_reads, origin_name: read, origin_step: input},\n        { input_name: read2, origin_command: raw_reads, origin_name: read2, origin_step: input},\n    ]\n},\n{ step_name: \"quality_2\", tool_name: \"fastqc\", rule_name: \"fastqc_PE\",\n    params: [\n        { input_name: read, origin_command: fastp_PE, origin_name: read_preprocessed, origin_step: quality},\n        { input_name: read2, origin_command: fastp_PE, origin_name: read2_preprocessed, origin_step: quality},\n    ]\n},\n{ step_name: \"mapping\", tool_name: \"hisat2\", rule_name: \"hisat2_PE\",\n    params: [\n        { input_name: read, origin_command: fastp_PE, origin_name: read_preprocessed, origin_step: quality},\n        { input_name: read2, origin_command: fastp_PE, origin_name: read_preprocessed, origin_step: quality},\n        { input_name: index, origin_command: hisat2_index, origin_name: index, origin_step: indexing},\n    ]\n},\n{ step_name: \"quantification\", tool_name: \"htseq_count\", rule_name: \"htseq_count\",\n    params: [\n        { input_name: bam, origin_command: hisat2_PE, origin_name: bam, origin_step: mapping},\n        { input_name: gff_file, origin_command: raw_gff3, origin_name: gff3, origin_step: input},\n    ]\n},\n{ step_name: \"differential_expression\", tool_name: \"deseq2\", rule_name: \"deseq2\",\n    params: [\n        { input_name: counts, origin_command: htseq_count, origin_name: stats, origin_step: quantification},\n        { input_name: popmap_file, origin_command: raw_popmap, origin_name: popmap, origin_step: input},\n    ]\n},\n],\nsteps: [\n    { title: \"indexing\", name: \"indexing\", tools: [hisat2_index], default: \"hisat2_index\" },\n    { title: \"quality\", name: \"quality\", tools: [fastp], default: \"fastp\" },\n    { title: \"quality_2\", name: \"quality_2\", tools: [fastqc], default: \"fastqc\" },\n    { title: \"mapping\", name: \"mapping\", tools: [hisat2], default: \"hisat2\" },\n    { title: \"quantification\", name: \"quantification\", tools: [htseq_count], default: \"htseq_count\" },\n    { title: \"differential_expression\", name: \"differential_expression\", tools: [deseq2], default: \"deseq2\" },\n],\ninput: [\"raw_contigs\",\"raw_reads\",\"raw_gff3\",\"raw_popmap\",],\nparams_equals: [\n\n]\n}\n"
    }
]