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#!/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
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