Workflow Type: Common Workflow Language
Work-in-progress

Workflow for (paired) read quality control, trimming and contamination filtering based on a given reference.

Will output a merged set of read pairs, when multiple datasets are used.

Steps:

  • FastQC (read quality control)

  • fastp (read quality trimming)

  • bbduk used (rrna filtering)

  • bbmap (contamination filter)

Inputs

ID Name Description Type
identifier identifier used Identifier for this dataset used in this workflow string
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 filter rRNA Optionally remove rRNA sequences from the reads. boolean
forward_reads forward reads forward sequence file locally File[]
reverse_reads reverse reads reverse sequence file locally File[]
bbmap_reference contamination reference file bbmap reference fasta file for contamination filtering string
step CWL base step number Step number for order of steps int?

Steps

ID Name Description
fastqc FastQC Quality assessment and report of reads
fastq_merge_fwd fastq pair merge file Merge multiple paired ends of fastq files
fastq_merge_rev fastq pair merge file Merge multiple paired ends of fastq files
fastp fastp Read quality filtering and (barcode) trimming.
bbmap_contamination contamination filter (bbmap) Filters contamination sequences from reads using bbmap
bbduk_rrna 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
bbmap_files_to_folder contamination output Preparation of contamination-filter (bbduk) output files to a specific output folder. Contains fwd/rev reads stats and summary file.
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. (this output is mainly used for other workflows) File
QC_reverse_reads Filtered reverse read Filtered reverse read with fastp and (optionally) rrna filtered. (this output is mainly used for other workflows) File
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Activity

Views: 611   Downloads: 29

Created: 22nd Dec 2020 at 16:27

Last updated: 8th Jun 2021 at 08:08

Last used: 16th Oct 2021 at 20:59

help Tags
CWL
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Version History

Version 3 (latest) Created 7th Jun 2021 at 17:23 by Bart Nijsse

Changed and added some docs and labels

Version 2 Created 7th Jun 2021 at 17:14 by Bart Nijsse

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Version 1 (earliest) Created 22nd Dec 2020 at 16:27 by Bart Nijsse

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