Pathogen-Detection-Nanopore-Pre-Processing-collection
Version 1

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Workflow Type: Galaxy

Galaxy workflow

SEEK ID: https://dev.workflowhub.eu/workflows/913?version=1

Inputs

ID Name Description Type
Collection of all samples #main/Collection of all samples Nanopore reads of each sample are all in a single fastq or fastq.gz file
  • array containing
    • File

Steps

ID Name Description
1 Porechop Preprocessing (Trimming) toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4
2 NanoPlot Quality Check Before Preprocessing toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1
3 FastQC Quality Check Before Preprocessing toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0
4 fastp Preprocessing toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0
5 NanoPlot Nanoplot Quality Check After Preprocessing toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1
6 Kraken2 toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1
7 FastQC Quality Check After Preprocessing toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0
8 Filter failed datasets __FILTER_FAILED_DATASETS__
9 Filter failed datasets __FILTER_FAILED_DATASETS__
10 MultiQC Quality Control Before and After Preprocessing toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0
11 Krakentools: Extract Kraken Reads By ID toolshed.g2.bx.psu.edu/repos/iuc/krakentools_extract_kraken_reads/krakentools_extract_kraken_reads/1.2+galaxy1

Outputs

ID Name Description Type
FastQC Quality Check After Preprocessing HTML file #main/FastQC Quality Check After Preprocessing HTML file n/a
  • File
FastQC Quality Check After Preprocessing Text file #main/FastQC Quality Check After Preprocessing Text file n/a
  • File
FastQC Quality Check Before Preprocessing HTML file #main/FastQC Quality Check Before Preprocessing HTML file n/a
  • File
FastQC Quality Check Before Preprocessing Text file #main/FastQC Quality Check Before Preprocessing Text file n/a
  • File
Kraken2 with Kalamri database Report #main/Kraken2 with Kalamri database Report n/a
  • File
Kraken2 with Kalamri database output #main/Kraken2 with Kalamri database output n/a
  • File
MultiQC HTML report Before and After Preprocessing #main/MultiQC HTML report Before and After Preprocessing n/a
  • File
MultiQC Stats Before and After Preprocessing #main/MultiQC Stats Before and After Preprocessing n/a
  • File
Nanoplot QC on Reads After Preprocessing HTML Report #main/Nanoplot QC on Reads After Preprocessing HTML Report n/a
  • File
Nanoplot QC on Reads Before Preprocessing HTML Report #main/Nanoplot QC on Reads Before Preprocessing HTML Report n/a
  • File
Nanoplot on Reads After Preprocessing Histogram Read Length #main/Nanoplot on Reads After Preprocessing Histogram Read Length n/a
  • File
Nanoplot on Reads After Preprocessing Log Transformed Histogram Read Length #main/Nanoplot on Reads After Preprocessing Log Transformed Histogram Read Length n/a
  • File
Nanoplot on Reads After Preprocessing NanoStats #main/Nanoplot on Reads After Preprocessing NanoStats n/a
  • File
Nanoplot on Reads After Preprocessing NanoStats post filtering #main/Nanoplot on Reads After Preprocessing NanoStats post filtering n/a
  • File
Nanoplot on Reads Before Preprocessing Histogram Read Length #main/Nanoplot on Reads Before Preprocessing Histogram Read Length n/a
  • File
Nanoplot on Reads Before Preprocessing Log Transformed Histogram Read Length #main/Nanoplot on Reads Before Preprocessing Log Transformed Histogram Read Length n/a
  • File
Nanoplot on Reads Before Preprocessing NanoStats #main/Nanoplot on Reads Before Preprocessing NanoStats n/a
  • File
Nanoplot on Reads Before Preprocessing NanoStats post filtering #main/Nanoplot on Reads Before Preprocessing NanoStats post filtering n/a
  • File
Nanopore Processed Sequenced Reads #main/Nanopore Processed Sequenced Reads n/a
  • File
Nanopore sequenced reads processed with Fastp #main/Nanopore sequenced reads processed with Fastp n/a
  • File
Nanopore sequenced reads processed with Fastp HTML Report #main/Nanopore sequenced reads processed with Fastp HTML Report n/a
  • File
Porechop output Trimmed Reads #main/Porechop output Trimmed Reads n/a
  • File
Successful Kraken2 with Kalamari Tabular Report output #main/Successful Kraken2 with Kalamari Tabular Report output n/a
  • File
Successful Kraken2 with Kalamari Tabular output #main/Successful Kraken2 with Kalamari Tabular output n/a
  • File

Version History

1 (earliest) Created 22nd Apr 2024 at 11:04 by Helena Rasche

Added/updated 3 files


Open master 0b7ba62
help Creators and Submitter
Creators
  • Bérénice Batut
  • Engy Nasr
Submitter
Tools
NanoPlot
FastQC
fastp
kraken2
MultiQC
License
MIT License
Activity

Views: 29

Created: 22nd Apr 2024 at 11:04

Last updated: 22nd Apr 2024 at 11:04

help Attributions

None

Total size: 42.1 KB
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