Workflow: mirna_profiling.cwl

Fetched 2019-07-23 16:40:42 GMT
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Inputs

ID Type Title Doc
project_directory String
species_code String
awk_expression String
ucsc_database String
mirbase_db String
bam File

Steps

ID Runs Label Doc
samtools_bamtosam
../../tools/samtools_view.cwl (CommandLineTool)
mirna_alignment_stats
../../tools/mirna_alignment_stats.cwl (CommandLineTool)
mirna_adapter_report
../../tools/awk.cwl (CommandLineTool)
mirna_expression_matrix_mimat
../../tools/mirna_expression_matrix_mimat.cwl (CommandLineTool)
mirna_graph_libs
../../tools/mirna_graph_libs.cwl (CommandLineTool)
mirna_annotate
../../tools/mirna_annotate.cwl (CommandLineTool)
mirna_tcga
../../tools/mirna_tcga.cwl (CommandLineTool)
mirna_expression_matrix
../../tools/mirna_expression_matrix.cwl (CommandLineTool)
mirna_adapter_report_sorted
../../tools/sort.cwl (CommandLineTool)

Outputs

ID Type Label Doc
mirna_graph_libs_jpgs Directory
mirna_expression_matrix_expn_matrix_txt File
mirna_expression_matrix_mimat_expn_matrix_mimat_norm_log_txt File
mirna_tcga_mirnas_quant File
mirna_expression_matrix_mimat_expn_matrix_mimat_txt File
mirna_alignment_stats_features Directory
mirna_expression_matrix_expn_matrix_norm_log_txt File
mirna_expression_matrix_mimat_expn_matrix_mimat_norm_txt File
mirna_tcga_isoforms_quant File
mirna_expression_matrix_expn_matrix_norm_txt File
mirna_adapter_report_sorted_output File
Permalink: https://w3id.org/cwl/view/git/17823fcd036d134df803fbf76e23b0bc5eabedfd/workflows/mirnaseq/mirna_profiling.cwl