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run_estimate

description

[DEPRECATED] Given a gene expression file, run the ESTIMATE software package

outputs

{'estimate_file': 'The results file of the ESTIMATE software package'}

deprecated

true

Inputs

Required

• _runtime (Any, required)
• gene_expression_file (File, required): A 2 column headered TSV file with 'Gene name' in the first column and gene expression values (as floats) in the second column. Can be generated with the calc_tpm task.

Defaults

• disk_size_gb (Int, default=10): Disk space to allocate for task, specified in GB
• max_retries (Int, default=1): Number of times to retry in case of failure
• memory_gb (Int, default=4): RAM to allocate for task, specified in GB
• outfile_name (String, default=basename(gene_expression_file,".TPM.txt") + ".ESTIMATE.gct"): Name of the ESTIMATE output file

Outputs

• estimate_file (File)