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Add AWS Megatest #130

Merged
merged 1 commit into from
Feb 14, 2024
Merged

Add AWS Megatest #130

merged 1 commit into from
Feb 14, 2024

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edmundmiller
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@edmundmiller edmundmiller commented Feb 10, 2024 •
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Closes #66

@edmundmiller edmundmiller requested review from maxulysse and a team February 10, 2024 13:55
@edmundmiller edmundmiller self-assigned this Feb 10, 2024
@edmundmiller edmundmiller added this to the v2.2.0 milestone Feb 10, 2024
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github-actions bot commented Feb 10, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 93ddcbd

+| ✅ 168 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 2.1.1
  • pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file
  • pipeline_todos - TODO string in WorkflowNascent.groovy: Optionally add in-text citation tools to this list.
  • 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_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/email_template.html

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-14 18:22:24

FriederikeHanssen
FriederikeHanssen reviewed Feb 10, 2024
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assets/samplesheet_full.csv
Comment on lines +2 to +12
GM_0h,ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR211/ERR2114683/GM0h.fastq.gz,
GM_30min,ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR211/ERR2114684/GM30min.fastq.gz,
GM_1h,ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR211/ERR2114685/GM1h.fastq.gz,
GM_2h,ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR211/ERR2114686/GM2h.fastq.gz,
GM_4h,ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR211/ERR2114687/GM4h.fastq.gz,
GM_6h,ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR211/ERR2114688/GM6h.fastq.gz,
GM_9h,ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR211/ERR2114689/GM9h.fastq.gz,
GM_12h,ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR211/ERR2114690/GM12h.fastq.gz,
GM_18h,ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR211/ERR2114691/GM18h.fastq.gz,
GM_48h,ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR211/ERR2114693/GM48h.fastq.gz,
GM_72h,ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR211/ERR2114694/GM72h.fastq.gz,
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if download is an issue we can also move this data to the megatest bucket.

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Oh good point I hadn't thought of that... Might be more expensive due to the slow download, but it should just be the head node...

FriederikeHanssen
FriederikeHanssen approved these changes Feb 10, 2024
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🚀

@edmundmiller
test(#66): Add AWS Mega Test
93ddcbd 
skip-checks: true
@edmundmiller edmundmiller merged commit fbf44d4 into dev Feb 14, 2024
2 checks passed
@edmundmiller edmundmiller deleted the full_test branch February 14, 2024 18:21
@edmundmiller edmundmiller linked an issue Mar 7, 2024 that may be closed by this pull request
test_full profile is broken #108
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

@maxulysse maxulysse Awaiting requested review from maxulysse

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test_full profile is broken
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