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Merge fix: "use wget instead of curl #229" #241

Merged
merged 11 commits into from
Jan 4, 2024
Merged

Merge fix: "use wget instead of curl #229" #241

merged 11 commits into from
Jan 4, 2024

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nicolae06
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@nicolae06 nicolae06 commented Dec 13, 2023 •
edited by drpatelh
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Closes #169

@nicolae06
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Hi @drpatelh , I tried to redo PR #229 and fix the merge. Could you take a look? Thank you!

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github-actions bot commented Dec 19, 2023 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 9c3a086

+| ✅ 131 tests passed       |+
#| ❔  18 tests were ignored |#
!| ❗   6 tests had warnings |!
-| ❌   3 tests failed       |-

❌ Test failures:

  • files_unchanged - .github/CONTRIBUTING.md does not match the template
  • files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 1.11.0
  • 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 meta.yml: #Add a description of the subworkflow and list keywords
  • pipeline_todos - TODO string in meta.yml: #Add a list of the modules and/or subworkflows used in the subworkflow
  • pipeline_todos - TODO string in meta.yml: #List all of the channels used as input with a description and their structure
  • pipeline_todos - TODO string in meta.yml: #List all of the channels used as output with a descriptions and their structure

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: assets/multiqc_config.yml
  • files_exist - File is ignored: conf/igenomes.config
  • 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/WorkflowFetchngs.groovy
  • files_exist - File is ignored: lib/WorkflowMain.groovy
  • files_exist - File is ignored: lib/nfcore_external_java_deps.jar
  • files_unchanged - File ignored due to lint config: .gitattributes
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File does not exist: lib/nfcore_external_java_deps.jar
  • files_unchanged - File ignored due to lint config: 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 2.11.1
  • Run at 2024-01-04 14:49:10

@maxulysse
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I see no reasons not to switch from curl to wget

@maxulysse
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@nicolae06 I updated the CHANGELOG, so you'll need to git pull before doing any changes.

Since you changed a process, the corresponding tests are now failing.
Can you try to run nf-test with the following command:

nf-test test --tag sra_fastq_ftp --profile "test,docker" --updateSnapshot and commit the newly changed snapshot file.

@nicolae06
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Hi @maxulysse, I executed your command, but I removed the arguments as I encountered errors while attempting to run the test. The errors indicated that '--retry 5 --continue-at - --max-time 1200' are not recognized by wget. I checked the 'man wget' command, but these flags were not listed there.

@drpatelh drpatelh added this to the 1.12.0 milestone Jan 3, 2024
@drpatelh drpatelh mentioned this pull request Jan 3, 2024
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@suhrig
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suhrig commented Jan 3, 2024

Thanks @nicolae06 for taking care of this! And apologies that I didn't manage.

drpatelh
drpatelh reviewed Jan 4, 2024
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@drpatelh drpatelh mentioned this pull request Jan 4, 2024
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@drpatelh
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drpatelh commented Jan 4, 2024

Thanks @nicolae06 ! The failing tests should be fixed when we merge in the template updates in #242

drpatelh
drpatelh approved these changes Jan 4, 2024
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@drpatelh drpatelh merged commit a6f7d52 into nf-core:dev Jan 4, 2024
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@drpatelh drpatelh mentioned this pull request Jan 17, 2024
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@nicolae06 @maxulysse @suhrig @drpatelh