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Fix "Argument list too long" issue #119

Merged
merged 4 commits into from
Sep 29, 2023
Merged

Fix "Argument list too long" issue #119

merged 4 commits into from
Sep 29, 2023

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JoseEspinosa
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Fixes #108

Since the previous fix did not work, as reported on this slack thread, the code is changed now to run using a for loop. This should avoid getting the "Argument list too long" without modifying the ulimit size.

PR checklist

  • This comment contains a description of changes (with reason).
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • CHANGELOG.md is updated.

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github-actions bot commented Sep 29, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 6d71c38

+| ✅ 150 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗  11 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: lib/WorkflowProteinfold.groovy
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • pipeline_todos - TODO string in WorkflowAlphafold2.groovy: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in check_samplesheet.py: Update the script to check the samplesheet
  • pipeline_todos - TODO string in check_samplesheet.py: Update the check_samplesheet function
  • pipeline_todos - TODO string in check_samplesheet.py: Update the column names for the input samplesheet
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • multiqc_config - multiqc_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-09-29 09:27:24

@JoseEspinosa JoseEspinosa merged commit 37ff17f into nf-core:dev Sep 29, 2023
9 checks passed
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@luisas luisas luisas approved these changes

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@JoseEspinosa @luisas