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Revert to using FTP for default downloads over Aspera #277

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merged 2 commits into from
Feb 19, 2024
Merged

Revert to using FTP for default downloads over Aspera #277

merged 2 commits into from
Feb 19, 2024

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drpatelh
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@drpatelh drpatelh commented Feb 18, 2024 •
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Since making Aspera the default download method on the dev branch we have observed some flakiness in the Github Actions CI/CD and an issue with using Singularity. Maybe it was a bit premature to make it the default without real-world testing. We did test Aspera on public Clouds via Seqera Platform and it worked out of the box but I am going to revert back to making FTP the default download method until we can collect and fix any issues.

  • Rename --force_ftp_download to --force_aspera_download
  • Update tests where required

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github-actions bot commented Feb 18, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 047f81f

+| ✅ 149 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   6 tests had warnings |!

❗ 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
  • nextflow_config - Config manifest.version should end in dev: 1.12.0

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-18 12:36:56

@drpatelh drpatelh mentioned this pull request Feb 18, 2024
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drpatelh commented Feb 18, 2024 •
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Now that we have 3 methods to download data, I'm wondering whether we remove both --force_ftp_download and --force_aspera_download, and replace it with a single --download_method parameter that can be either ftp, sratools or aspera.

maxulysse
maxulysse reviewed Feb 19, 2024
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workflows/sra/main.nf
Comment on lines +87 to +88
aspera: download_method == 'aspera'
return [ meta, meta.fastq_aspera.tokenize(';').take(2) ]
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You know me and my alphabetical order, but not blocking...

@drpatelh drpatelh merged commit f557990 into nf-core:dev Feb 19, 2024
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@drpatelh drpatelh mentioned this pull request Feb 19, 2024
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@maxulysse maxulysse maxulysse approved these changes

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