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Revert sratools fasterqdump version #261

Merged
merged 4 commits into from
Jan 31, 2024
Merged

Revert sratools fasterqdump version #261

merged 4 commits into from
Jan 31, 2024

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drpatelh
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Partial fix for #221

Reverting the version for sratools/fasterqdump from 3.0.8 -> 2.11.0 because a number of users have reported having issues when they have a . (dot) anywhere in their path. We can update this version when the fix has been pushed upstream (see ncbi/sra-tools#865)

In the meantime, anyone wanting to use more recent support for ngc files can use v3.0.8 via a custom config file passed to the pipeline:

process {
    withName: 'SRATOOLS_FASTERQDUMP' {
        container = 'quay.io/biocontainers/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:2f4a4c900edd6801ff0068c2b3048b4459d119eb-0'
    }
}

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github-actions bot commented Jan 30, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit f932649

+| ✅ 147 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   6 tests had warnings |!
-| ❌   1 tests failed       |-

❌ Test failures:

  • files_unchanged - assets/sendmail_template.txt does not match the template

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • files_exist - File not found: lib/WorkflowFetchngs.groovy
  • 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

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_exist - File is ignored: lib/NfcoreTemplate.groovy
  • files_exist - File is ignored: lib/Utils.groovy
  • files_exist - File is ignored: lib/WorkflowMain.groovy
  • files_unchanged - File does not exist: lib/NfcoreTemplate.groovy
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/fetchngs/fetchngs/.github/workflows/awstest.yml
  • multiqc_config - 'assets/multiqc_config.yml' not found

✅ Tests passed:

Run details

  • nf-core/tools version 2.12
  • Run at 2024-01-31 12:19:58

@drpatelh drpatelh mentioned this pull request Jan 30, 2024
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adamrtalbot
adamrtalbot approved these changes Jan 31, 2024
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Out, damned spot!

@drpatelh drpatelh merged commit 7f0a645 into nf-core:dev Jan 31, 2024
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