mgnify-amplicon-pipeline-v5-quality-control-single-end/main

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Workflow Type: Galaxy

Quality control subworkflow for single-end reads.

SEEK ID: https://workflowhub.eu/workflows/1271?version=1

Inputs

ID Name Description Type
Ambiguity filtering - Maximal N percentage threshold to conserve sequences #main/Ambiguity filtering - Maximal N percentage threshold to conserve sequences Maximal N percentage threshold to conserve sequences.
  • int
Length filtering - Minimum size #main/Length filtering - Minimum size Minimum sequence length.
  • int
Single-end reads #main/Single-end reads Single-end reads collection.
  • array containing
    • File
Trimmomatic - LEADING #main/Trimmomatic - LEADING Cut bases off the start of a read, if below a threshold quality.
  • int
Trimmomatic - MINLEN #main/Trimmomatic - MINLEN Minimum length of reads to be kept.
  • int
Trimmomatic - SLIDING WINDOW - Average quality required #main/Trimmomatic - SLIDING WINDOW - Average quality required Average quality required.
  • int
Trimmomatic - SLIDING WINDOW - Number of bases to average across #main/Trimmomatic - SLIDING WINDOW - Number of bases to average across Number of bases to average across.
  • int
Trimmomatic - TRAILING #main/Trimmomatic - TRAILING Cut bases off the end of a read, if below a threshold quality.
  • int

Steps

ID Name Description
8 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1
9 Trimming toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.39+galaxy2
10 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1
11 Length filtering toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5+galaxy2
12 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1
13 Ambiguity filtering toolshed.g2.bx.psu.edu/repos/iuc/prinseq/prinseq/0.20.4+galaxy2
14 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1
15 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1
16 FASTQ to FASTA toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.1.5+galaxy2
17 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1
18 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1
19 FASTA Width toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.1+galaxy2
20 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1
21 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy0

Outputs

ID Name Description Type
Single-end MultiQC report #main/Single-end MultiQC report n/a
  • File
Single-end MultiQC statistics #main/Single-end MultiQC statistics n/a
  • File
Single-end post quality control FASTA files #main/Single-end post quality control FASTA files n/a
  • File

Version History

v0.3 (latest) Created 26th Mar 2025 at 09:52 by WorkflowHub Bot

Updated to v0.3


Frozen v0.3 8f4e89d

v0.2 Created 25th Feb 2025 at 03:01 by WorkflowHub Bot

Updated to v0.2


Frozen v0.2 104158b

v0.1 (earliest) Created 4th Feb 2025 at 03:02 by WorkflowHub Bot

Updated to v0.1


Frozen v0.1 49128b7
help Creators and Submitter
Creators
Additional credit

MGnify - EMBL

Submitter
Tools
FastQC
Trimmomatic
PRINSEQ
FASTX-Toolkit
MultiQC
License
Apache License 2.0 (Apache-2.0)
Activity

Views: 3694   Downloads: 17002   Runs: 1

Created: 4th Feb 2025 at 03:02

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