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Updating workflows/genome-assembly/quality-and-contamination-control-raw-reads from 1.1.10 to 1.1.11 #935

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Updating workflows/genome-assembly/quality-and-contamination-control-raw-reads from 1.1.10 to 1.1.11 #935

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@gxydevbot gxydevbot commented Aug 25, 2025

Hello! This is an automated update of the following workflow: workflows/genome-assembly/quality-and-contamination-control-raw-reads. I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated:

  • toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.26.0+galaxy0 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.0.1+galaxy2
  • toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.3+galaxy1 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.3+galaxy2

The workflow release number has been updated from 1.1.10 to 1.1.11.

If you want to skip this change, close this PR without deleting the branch. It will be reopened if another change is detected.
Any commit from another author than 'planemo-autoupdate' will prevent more auto-updates.
To ignore manual changes and allow autoupdates, delete the branch.

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mvdbeek commented Sep 4, 2025 

Traceback (most recent call last):
  File "/tmp/tmpa4zubutw/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 300, in prepare_job
    if job_wrapper.prepare() is False:
       ^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpa4zubutw/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1288, in prepare
    tool_evaluator.set_compute_environment(compute_environment, get_special=get_special)
  File "/tmp/tmpa4zubutw/galaxy-dev/lib/galaxy/tools/evaluation.py", line 165, in set_compute_environment
    self._validate_incoming(incoming)
  File "/tmp/tmpa4zubutw/galaxy-dev/lib/galaxy/tools/evaluation.py", line 364, in _validate_incoming
    visit_input_values(self.tool.inputs, incoming, validate_inputs)
  File "/tmp/tmpa4zubutw/galaxy-dev/lib/galaxy/tools/parameters/__init__.py", line 263, in visit_input_values
    visit_input_values(
  File "/tmp/tmpa4zubutw/galaxy-dev/lib/galaxy/tools/parameters/__init__.py", line 279, in visit_input_values
    callback_helper(
  File "/tmp/tmpa4zubutw/galaxy-dev/lib/galaxy/tools/parameters/__init__.py", line 178, in callback_helper
    new_value = callback(**args)
                ^^^^^^^^^^^^^^^^
  File "/tmp/tmpa4zubutw/galaxy-dev/lib/galaxy/tools/evaluation.py", line 361, in validate_inputs
    value = input.from_json(value, request_context, context)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpa4zubutw/galaxy-dev/lib/galaxy/tools/parameters/basic.py", line 2162, in from_json
    raise ParameterValueError("specify a dataset of the required format / build for parameter", self.name)
galaxy.tools.parameters.basic.ParameterValueError: Parameter 'input_sequences': specify a dataset of the required format / build for parameter

@gxydevbot gxydevbot changed the title Updating workflows/genome-assembly/quality-and-contamination-control-raw-reads from 1.1.10 to 1.1.11 Updating workflows/genome-assembly/quality-and-contamination-control-raw-reads from 1.1.10 to 1.1.11 Oct 7, 2025
@gxydevbot gxydevbot force-pushed the workflows/genome-assembly/quality-and-contamination-control-raw-reads branch from c8e6a35 to f358d6c Compare October 7, 2025 16:06
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gxydevbot commented Oct 7, 2025

There are new updates, they have been integrated to the PR, check the file diff.

@gxydevbot gxydevbot force-pushed the workflows/genome-assembly/quality-and-contamination-control-raw-reads branch from f358d6c to 88d1432 Compare October 20, 2025 07:27
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gxydevbot commented Oct 20, 2025

There are new updates, they have been integrated to the PR, check the file diff.

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gxydevbot commented Nov 3, 2025

There are new updates, they have been integrated to the PR, check the file diff.

@gxydevbot gxydevbot force-pushed the workflows/genome-assembly/quality-and-contamination-control-raw-reads branch from 88d1432 to dd66602 Compare November 3, 2025 05:55
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gxydevbot commented Nov 10, 2025

There are new updates, they have been integrated to the PR, check the file diff.

@gxydevbot gxydevbot force-pushed the workflows/genome-assembly/quality-and-contamination-control-raw-reads branch from dd66602 to 944565e Compare November 10, 2025 08:28
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