Workflow: mirzag_scan.cwl

Fetched 2020-08-14 17:13:44 GMT
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Inputs

ID Type Title Doc
input_multiple_alignments File
input_mirna File
settings_split_by String
output_file_name String
input_tree File
settings_mirza_threshold Float
settings_contextLen_U Integer
input_model_with_bls File
settings_index_after_split Integer
settings_contextLen_L Integer
input_mrna File
input_model_without_bls File

Steps

ID Runs Label Doc
filter_duplicates_from_scan
tools/filter_duplicates_from_scan.cwl (CommandLineTool)

Filter duplicates in coordinates by id, miRNA and sequence

concatenate_mirza
tools/concatenate.cwl (CommandLineTool)
split
tools/split_mirza_results.cwl (CommandLineTool)
prepare_mirnas
tools/prepare_mirnas.cwl (CommandLineTool)

Prepare miRNA fasta file for MIRZA i.e. for each miRNA sequence check if it is 21 nucleotide long and if not eliminate it. It also replaces all u or U into T. In the same time it splits miRNAs into separate files.

mirna_expressions
tools/generate_mirna_expressions.cwl (CommandLineTool)
analyze
tools/analysis.cwl (Workflow)
mirza
tools/mirza.cwl (CommandLineTool)
generate_mrna_chunks
tools/generate_mrna_chunks.cwl (CommandLineTool)

Take mRNAs and generate fragments by sliding window that can be fed into MIRZA

mirza_parser
tools/extract_data_from_mirza_output.cwl (CommandLineTool)

Take MIRZA output and arrange it in a proper way

Outputs

ID Type Label Doc
mirzag_output File
Permalink: https://w3id.org/cwl/view/git/b4a38d00a8d6e27540217ac5d590ab8a5da0a92e/mirzag_scan.cwl