Checking expected species and contamination in bacterial isolate
Version 1

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Workflow Type: Galaxy

Galaxy workflow

SEEK ID: https://dev.workflowhub.eu/workflows/971?version=1

Inputs

ID Name Description Type
forward_reads #main/forward_reads forward_reads
  • File
reverse_reads #main/reverse_reads reverse_reads
  • File

Steps

ID Name Description
2 Kraken2 toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1
3 Bracken toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.9+galaxy0
4 Recentrifuge toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.12.1+galaxy0

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
kraken_report_reads #main/kraken_report_reads n/a
  • File
kraken_report_tabular #main/kraken_report_tabular 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

Version History

3 (earliest) Created 22nd Apr 2024 at 11:12 by Helena Rasche

Added/updated 3 files


Open master 30c9567
help Creators and Submitter
Creators
  • Pierre MARIN
  • Bérénice Batut
Submitter
Tools
kraken2
Bracken
Recentrifuge
License
GNU General Public License v3.0 or later
Activity

Views: 27

Created: 22nd Apr 2024 at 11:12

Last updated: 22nd Apr 2024 at 11:12

help Tags
help Attributions

None

Total size: 17.9 KB
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