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        "yaml": "{\nname: \"BWT2-Pic-MarkDup-GatkRealign-BCFmpileup\",\ndocker_name: \"bwt2-pic-markdup-gatkrealign-bcfmpileup\",\ndescription: \"SNP calling\",\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: \"gatk_prepare_fasta\", rule_name: \"gatk_prepare_fasta\",\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: \"mapping\", tool_name: \"bowtie2\", rule_name: \"bowtie2_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        { input_name: index, origin_command: raw_bowtie2_index, origin_name: bowtie2_index, origin_step: input},\n    ]\n},\n{ step_name: \"bam_correction\", tool_name: \"Picard_MarkDuplicates\", rule_name: \"Picard_MarkDuplicates\",\n    params: [\n        { input_name: bam_in, origin_command: bowtie2_PE, origin_name: bam, origin_step: mapping},\n    ]\n},\n{ step_name: \"bam_correction_2\", tool_name: \"gatk_IndelRealigner\", rule_name: \"gatk_IndelRealigner\",\n    params: [\n        { input_name: bam, origin_command: Picard_MarkDuplicates, origin_name: sorted_bam, origin_step: bam_correction},\n        { input_name: genome_fasta, origin_command: gatk_prepare_fasta, origin_name: fasta, origin_step: indexing},\n        { input_name: fasta_index, origin_command: gatk_prepare_fasta, origin_name: index, origin_step: indexing},\n        { input_name: sequence_dict, origin_command: gatk_prepare_fasta, origin_name: fadict, origin_step: indexing},\n    ]\n},\n{ step_name: \"format_conversion\", tool_name: \"bams2Dir\", rule_name: \"bams2Dir\",\n    params: [\n        { input_name: bam, origin_command: gatk_IndelRealigner, origin_name: sorted_bam, origin_step: bam_correction_2},\n    ]\n},\n{ step_name: \"variant_calling\", tool_name: \"bcftools_mpileup_and_call_onbam_dir\", rule_name: \"bcftools_mpileup_and_call_onbam_dir\",\n    params: [\n        { input_name: bamDir, origin_command: bams2Dir, origin_name: bamDir, origin_step: format_conversion},\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: \"vcf_postprocess\", tool_name: \"multiSamplesvcfparser\", rule_name: \"multiSamplesvcfparser\",\n    params: [\n        { input_name: vcf, origin_command: bcftools_mpileup_and_call_onbam_dir, origin_name: vcf, origin_step: variant_calling},\n    ]\n},\n],\nsteps: [\n    { title: \"indexing\", name: \"indexing\", tools: [gatk_prepare_fasta], default: \"gatk_prepare_fasta\" },\n    { title: \"mapping\", name: \"mapping\", tools: [bowtie2], default: \"bowtie2\" },\n    { title: \"bam_correction\", name: \"bam_correction\", tools: [Picard_MarkDuplicates], default: \"Picard_MarkDuplicates\" },\n    { title: \"bam_correction_2\", name: \"bam_correction_2\", tools: [gatk_IndelRealigner], default: \"gatk_IndelRealigner\" },\n    { title: \"format_conversion\", name: \"format_conversion\", tools: [bams2Dir], default: \"bams2Dir\" },\n    { title: \"variant_calling\", name: \"variant_calling\", tools: [bcftools_mpileup_and_call_onbam_dir], default: \"bcftools_mpileup_and_call_onbam_dir\" },\n    { title: \"vcf_postprocess\", name: \"vcf_postprocess\", tools: [multiSamplesvcfparser], default: \"multiSamplesvcfparser\" },\n],\ninput: [\"raw_contigs\",\"raw_reads\",\"raw_bowtie2_index\",],\nparams_equals: [\n        { param_A: \"variant_calling__bcftools_mpileup_and_call_onbam_dir_genome_fasta\", param_B:   \"indexing__gatk_prepare_fasta_genome_fasta\"},\n\n]\n}\n"
    }
]