Documentation for generate_fda_tables.cwl

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Overview

Script to create FDA-requested summary tables

Docker Requirement

python:3.7.4-slim-buster

Inputs

Name	Label	Description	Type	Secondary Files
table_file_name			string?
table_num			string
md5sum_file			File
fastqc_zips			File[]
aligned_metrics			File?
unaligned_metrics			File[]?
alignment_summary_metrics			File?
duplication_metrics			File?
insert_size_metrics			File?
hs_metrics			File?
rna_metrics			File?
flagstat			File?
unaligned_rna_table			File?
sequencing_platform			string?
sequencing_instrument			string?
sequencing_kit			string?
sequencing_type			string?
single_or_paired_end			string?
spike_in_error_rate			string?
source			string?
total_DNA			string?
reference_genome			string?
total_RNA			string?
RIN_score			string?
freq_normalization_method			string?
annotation_file			string?
sample_name			string?

Outputs

Name	Label	Description	Type	Secondary Files
table			File