Read quality control and trimming
Version 1

Work-in-progress

Workflow for read quality control and trimming.

Steps:

- FastQC (read quality control)

- fastp (read quality trimming)

- bbduk used for rrna filtering

Inputs

ID Name Description Type
threads number of threads number of threads to use for computational processes int?
memory maximum memory usage in megabytes maximum memory usage in megabytes int?
filter_rrna n/a n/a boolean
forward_reads forward reads forward sequence file locally File
reverse_reads reverse reads reverse sequence file locally File
step CWL base step number Step number for order of steps int?

Steps

ID Name Description
fastqc FastQC Quality assessment and report of reads
fastp fastp Read quality filtering and (barcode) trimming.
bbduk rrna filter (bbduk) Filters rrna sequences from reads using bbduk
fastqc_files_to_folder FastQC output Preparation of FastQC output files to a specific output folder
filtered_files_to_folder fastp output Preparation of fastp output files to a specific output folder
bbduk_files_to_folder fastp output Preparation of rrna-filter (bbduk) output files to a specific output folder. Contains fwd/rev reads stats and summary file.

Outputs

ID Name Description Type
files_to_folder_fastqc FASTQC Quality reporting by FASTQC Directory
files_to_folder_filtered Filtered reads folder Output folder with filtered reads, stats and reports. Directory
QC_forward_reads Filtered forward read Filtered forward read with fastp and (optionally) rrna filtered. File
QC_reverse_reads Filtered reverse read Filtered reverse read with fastp and (optionally) rrna filtered. File
help Creators and Submitter
License
Activity

Views: 67   Downloads: 8

Created: 22nd Dec 2020 at 16:27

Last updated: 22nd Dec 2020 at 16:28

Last used: 17th Jan 2021 at 20:30

help Tags
CWL
help Attributions

None

Related items

Powered by
(v.1.11.master)
Copyright © 2008 - 2020 The University of Manchester and HITS gGmbH