#!/usr/bin/env cwl-runner cwlVersion: v1.0 class: Workflow requirements: - class: StepInputExpressionRequirement inputs: - id: awk_expression type: string - id: bam type: File - id: mirbase_db type: string - id: species_code type: string - id: project_directory type: string - id: ucsc_database type: string outputs: - id: mirna_adapter_report_sorted_output type: File outputSource: mirna_adapter_report_sorted/OUTPUT - id: mirna_alignment_stats_features type: Directory outputSource: mirna_alignment_stats/features - id: mirna_expression_matrix_expn_matrix_txt type: File outputSource: mirna_expression_matrix/expn_matrix_txt - id: mirna_expression_matrix_expn_matrix_norm_txt type: File outputSource: mirna_expression_matrix/expn_matrix_norm_txt - id: mirna_expression_matrix_expn_matrix_norm_log_txt type: File outputSource: mirna_expression_matrix/expn_matrix_norm_log_txt - id: mirna_expression_matrix_mimat_expn_matrix_mimat_txt type: File outputSource: mirna_expression_matrix_mimat/expn_matrix_mimat_txt - id: mirna_expression_matrix_mimat_expn_matrix_mimat_norm_txt type: File outputSource: mirna_expression_matrix_mimat/expn_matrix_mimat_norm_txt - id: mirna_expression_matrix_mimat_expn_matrix_mimat_norm_log_txt type: File outputSource: mirna_expression_matrix_mimat/expn_matrix_mimat_norm_log_txt - id: mirna_graph_libs_jpgs type: Directory outputSource: mirna_graph_libs/jpgs - id: mirna_tcga_isoforms_quant type: File outputSource: mirna_tcga/isoforms_quant - id: mirna_tcga_mirnas_quant type: File outputSource: mirna_tcga/mirnas_quant steps: - id: samtools_bamtosam run: ../../tools/samtools_view.cwl in: - id: INPUT source: bam - id: output_format valueFrom: "SAM" out: - id: OUTPUT - id: mirna_adapter_report run: ../../tools/awk.cwl in: - id: INPUT source: samtools_bamtosam/OUTPUT - id: EXPRESSION source: awk_expression - id: OUTFILE source: samtools_bamtosam/OUTPUT valueFrom: $(self.nameroot)_adapter.report out: - id: OUTPUT - id: mirna_adapter_report_sorted run: ../../tools/sort.cwl in: - id: INPUT source: mirna_adapter_report/OUTPUT - id: key valueFrom: "1n" - id: OUTFILE source: mirna_adapter_report/OUTPUT valueFrom: $(self.basename) out: - id: OUTPUT - id: mirna_annotate run: ../../tools/mirna_annotate.cwl in: - id: sam source: samtools_bamtosam/OUTPUT - id: mirbase source: mirbase_db - id: ucsc_database source: ucsc_database - id: species_code source: species_code - id: project_directory source: project_directory out: - id: output - id: mirna_alignment_stats run: ../../tools/mirna_alignment_stats.cwl in: - id: adapter_report source: mirna_adapter_report_sorted/OUTPUT - id: sam source: mirna_annotate/output - id: project_directory source: project_directory out: - id: features - id: alignment_stats_csv - id: chastity_taglengths_csv - id: crossmapped_txt - id: filtered_taglengths_csv - id: isoforms_txt - id: miRNA_txt - id: mirna_species_txt - id: softclip_taglengths_csv - id: mirna_tcga run: ../../tools/mirna_tcga.cwl in: - id: genome_version source: ucsc_database - id: mirbase_db source: mirbase_db - id: project_directory source: project_directory - id: species_code source: species_code - id: sam source: mirna_annotate/output - id: stats_miRNA_txt source: mirna_alignment_stats/miRNA_txt - id: stats_crossmapped_txt source: mirna_alignment_stats/crossmapped_txt - id: stats_isoforms_txt source: mirna_alignment_stats/isoforms_txt out: - id: isoforms_quant - id: mirnas_quant - id: mirna_expression_matrix run: ../../tools/mirna_expression_matrix.cwl in: - id: mirbase_db source: mirbase_db - id: project_directory source: project_directory - id: species_code source: species_code - id: stats_mirna_species_txt source: mirna_alignment_stats/mirna_species_txt out: - id: expn_matrix_txt - id: expn_matrix_norm_txt - id: expn_matrix_norm_log_txt - id: mirna_expression_matrix_mimat run: ../../tools/mirna_expression_matrix_mimat.cwl in: - id: mirbase_db source: mirbase_db - id: project_directory source: project_directory - id: species_code source: species_code - id: stats_crossmapped_txt source: mirna_alignment_stats/crossmapped_txt - id: stats_mirna_txt source: mirna_alignment_stats/miRNA_txt out: - id: expn_matrix_mimat_txt - id: expn_matrix_mimat_norm_txt - id: expn_matrix_mimat_norm_log_txt - id: mirna_graph_libs run: ../../tools/mirna_graph_libs.cwl in: - id: sam source: mirna_annotate/output - id: adapter_report source: mirna_adapter_report_sorted/OUTPUT - id: alignment_stats_csv source: mirna_alignment_stats/alignment_stats_csv - id: chastity_taglengths_csv source: mirna_alignment_stats/chastity_taglengths_csv - id: filtered_taglengths_csv source: mirna_alignment_stats/filtered_taglengths_csv - id: softclip_taglengths_csv source: mirna_alignment_stats/softclip_taglengths_csv out: - id: jpgs