Update metagenomic genes catalogue to 1.3

[hugolefeuvre]

Changed

• Concatenation used to be performed directly after assembly, but following steps (Prodigal and AMRFinderPlus) could take too long depending on the number of samples and their size. Concatenation is now performed later in the workflow, which speeds up the process when dealing with multiple samples, without affecting the results.

Deprecated

• The updated versions of these two tools are available only on galaxy.org
• toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.3.0 was deprecated to toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0
• toolshed.g2.bx.psu.edu/repos/iuc/coverm_contig/coverm_contig/0.8.0+galaxy0 was deprecated to toolshed.g2.bx.psu.edu/repos/iuc/coverm_contig/coverm_contig/0.7.0+galaxy0

FOR CONTRIBUTOR:

• I have read the Adding workflows guidelines
• I have added myself to the CODEOWNERS File for the workflow
• License permits unrestricted use (educational + commercial)
• Please also take note of the reviewer guidelines below to facilitate a smooth review process.

FOR REVIEWERS:

• .dockstore.yml: file is present and aligned with creator metadata in workflow. ORCID identifiers are strongly encouraged in creator metadata. The .dockstore.yml file is required to run tests
• Workflow is sufficiently generic to be used with lab data and does not hardcode sample names, reference data and can be run without reading an accompanying tutorial.
• In workflow: annotation field contains short description of what the workflow does. Should start with This workflow does/runs/performs … xyz … to generate/analyze/etc …
• In workflow: workflow inputs and outputs have human readable names (spaces are fine, no underscore, dash only where spelling dictates it), no abbreviation unless it is generally understood. Altering input or output labels requires adjusting these labels in the the workflow-tests.yml file as well
• In workflow: name field should be human readable (spaces are fine, no underscore, dash only where spelling dictates it), no abbreviation unless generally understood
• Workflow folder: prefer dash (-) over underscore (_), prefer all lowercase. Folder becomes repository in iwc-workflows organization and is included in TRS id
• Readme explains what workflow does, what are valid inputs and what outputs users can expect. If a tutorial or other resources exist they can be linked. If a similar workflow exists in IWC readme should explain differences with existing workflow and when one might prefer one workflow over another
• Changelog contains appropriate entries
• Large files (> 100 KB) are uploaded to zenodo and location urls are used in test file

[mvdbeek]

Please ask .eu to update these tools.

[mvdbeek]

which i think happens automatically in the weekend

[hugolefeuvre]

I'll check next Monday to see if the changes were actually made.

[github-actions]

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

• ❌ metagenomic-genes-catalogue.ga_0

  Execution Problem:

  • Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0 (version 0.2.0), toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy3 (version 9.5+galaxy3), toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.5+galaxy3 (version 9.5+galaxy3), toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.5+galaxy3 (version 9.5+galaxy3), toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.5+galaxy3 (version 9.5+galaxy3)","err_code":0}
    

[github-actions]

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

• ❌ metagenomic-genes-catalogue.ga_0

  Execution Problem:

  • Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0 (version 0.2.0), toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy3 (version 9.5+galaxy3), toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.5+galaxy3 (version 9.5+galaxy3), toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.5+galaxy3 (version 9.5+galaxy3), toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.5+galaxy3 (version 9.5+galaxy3)","err_code":0}
    

[hugolefeuvre]

Also I don't understand why I have this error while these tools and versions are, in fact, available on eu :
Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0 (version 0.2.0), toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy3 (version 9.5+galaxy3), toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.5+galaxy3 (version 9.5+galaxy3), toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.5+galaxy3 (version 9.5+galaxy3), toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.5+galaxy3 (version 9.5+galaxy3)","err_code":0}

[mvdbeek]

Tests run against a planemo instance bootstrapped using the repositories listed in the workflow, and you didn't update those. What's installed on a particular Galaxy server doesn't matter for the tests.

So in general you have to change the tool_id, tool_version and repository.