quality-and-contamination-control-raw-reads/main
v1.1.10

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Workflow Type: Galaxy

Short paired-end read analysis to provide quality analysis, read cleaning and taxonomy assignation directly from raw reads

SEEK ID: https://workflowhub.eu/workflows/1881?version=1

Inputs

ID Name Description Type
Input sequence reads (forward) #main/Input sequence reads (forward) Should be the forward strand of the paired end reads.
  • File
Input sequence reads (reverse) #main/Input sequence reads (reverse) Should be the reverse strand of the paired end reads.
  • File
Select a NCBI taxonomy database #main/Select a NCBI taxonomy database Select the ncbi taxonomy database for Recentrifuge.
  • string
Select a taxonomy database #main/Select a taxonomy database Select the database to use for assigning taxonomies for Kraken2 and Bracken.
  • string

Steps

ID Name Description
4 zip_collections __ZIP_COLLECTION__
5 fastp_trimming_step fastp_triming, quality analaysis and read cleaning toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.26.0+galaxy0
6 unzip_collections __UNZIP_COLLECTION__
7 kraken_taxonomy_assignation kraken_taxonomy_assignation toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.3+galaxy1
8 bracken_abundance_estimation bracken_abundance_estimation toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/3.1+galaxy0
9 recentrifuge_taxonomy_visualization recentrifuge_taxonomy_visualization toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.16.1+galaxy0
10 ToolDistillator ToolDistillator extracts results from tools and creates a JSON file for each tool toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/1.0.0+galaxy1
11 ToolDistillator summarize ToolDistillator summarize groups all JSON file into a unique JSON file toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/1.0.0+galaxy1

Outputs

ID Name Description Type
bracken_kraken_report #main/bracken_kraken_report n/a
  • File
bracken_report_tsv #main/bracken_report_tsv n/a
  • File
fastp_report_html #main/fastp_report_html n/a
  • File
fastp_report_json #main/fastp_report_json n/a
  • File
fastp_trim_coll #main/fastp_trim_coll n/a
  • File
fastp_trimmed_R1 #main/fastp_trimmed_R1 n/a
  • File
fastp_trimmed_R2 #main/fastp_trimmed_R2 n/a
  • File
kraken_report #main/kraken_report n/a
  • File
kraken_report_tabular #main/kraken_report_tabular n/a
  • File
paired_coll #main/paired_coll n/a
  • File
recentrifuge_data_tabular #main/recentrifuge_data_tabular n/a
  • File
recentrifuge_logfile #main/recentrifuge_logfile n/a
  • File
recentrifuge_report_html #main/recentrifuge_report_html n/a
  • File
recentrifuge_stats_tabular #main/recentrifuge_stats_tabular n/a
  • File
tooldistillator_results_control #main/tooldistillator_results_control n/a
  • File
tooldistillator_summarize_control #main/tooldistillator_summarize_control n/a
  • File

Version History

v1.1.10 (earliest) Created 22nd Aug 2025 at 03:01 by WorkflowHub Bot

Updated to v1.1.10


Frozen v1.1.10 e979f3b
help Creators and Submitter
Creators
Additional credit

abromics-consortium

Submitter
Tools
fastp
kraken2
Bracken
Recentrifuge
ToolDistillator
License
GNU General Public License v3.0 or later (GPL-3.0-or-later)
Activity

Views: 602   Downloads: 1320   Runs: 0

Created: 22nd Aug 2025 at 03:01

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