Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Fastp - Format_source to ensure WF usability and remove non-sanger input formats #6499

Open
wants to merge 2 commits into
base: main
Choose a base branch
from

Conversation

RZ9082
Copy link
Contributor

@RZ9082 RZ9082 commented Oct 30, 2024

FOR CONTRIBUTOR:

  • I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
  • License permits unrestricted use (educational + commercial)
  • This PR adds a new tool or tool collection
  • This PR updates an existing tool or tool collection
  • This PR does something else (explain below)
  • Removed non-sanger input formats as wished.
  • Back to using format_source to ensure WF usability. However 'paired' and 'paired_collection' use format_source="in1" or format_source="in2" which is not affecting functionality, but it is still wrong!('paired_collection' should use format_source="paired_input['forward']" or format_source="paired_input['reverse']"). I still didn't figure out how to solve that rather than creating distinct outputs for each 'paired' and 'paired_collection, Any Ideas, before I do this?

@mvdbeek, @wm75 Could you review this please?

@RZ9082 RZ9082 changed the title Format_source to ensure WF usability and remove non-sanger input formats Fastp - Format_source to ensure WF usability and remove non-sanger input formats Oct 30, 2024
tools/fastp/fastp.xml Outdated Show resolved Hide resolved
@@ -379,10 +335,10 @@ $read_mod_options.base_correction_options.correction
</inputs>

<outputs>
<data name="out1" format="auto" label="${tool.name} on ${on_string}: Read 1 output">
<data name="out1" format_source="in1" label="${tool.name} on ${on_string}: Read 1 output">
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Does fastp compress the output if the input is compressed ?
I would assume all output is uncompressed ?

Suggested change
<data name="out1" format_source="in1" label="${tool.name} on ${on_string}: Read 1 output">
<data name="out1" format="fastqsanger" label="${tool.name} on ${on_string}: Read 1 output">

Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

The tool itself produces a compressed output if the output name has the ext .gz regardless whether the input is compressed or not.
Actually i had it this way at the beginning, but changed to format_source to be able to connect the output to fastqsanger.gz inputs..

Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants