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

Version History

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

Changed and added some docs and labels


Open master b53352c

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

No revision comments

Frozen master 186752d

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

Added/updated 1 files


Frozen master 341f38d
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Views: 1441   Downloads: 38

Created: 22nd Dec 2020 at 16:27

Last updated: 8th Jun 2021 at 08:08

Last used: 26th Jun 2022 at 03:45

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