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optimized resources #269

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edmundmiller
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@edmundmiller edmundmiller commented Feb 6, 2024 •
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@edmundmiller edmundmiller changed the base branch from master to dev February 6, 2024 15:44
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github-actions bot commented Feb 6, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 384a352

+| ✅ 148 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   7 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
  • 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:

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-06 15:44:18

@nf-core nf-core deleted a comment from github-actions bot Feb 6, 2024
@edmundmiller edmundmiller self-assigned this Feb 6, 2024
adamrtalbot
adamrtalbot reviewed Feb 6, 2024
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conf/test_full.config
Comment on lines +21 to +44
process {
withName: 'NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:CUSTOM_SRATOOLSNCBISETTINGS' {
cpus = { 1 * task.attempt }
memory = { 1.GB * task.attempt }
}
withName: 'NFCORE_FETCHNGS:SRA:MULTIQC_MAPPINGS_CONFIG' {
cpus = { 1 * task.attempt }
memory = { 1.GB * task.attempt }
}
withName: 'NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP' {
cpus = { 1 * task.attempt }
memory = { 1.GB * task.attempt }
}
withName: 'NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO' {
cpus = { 1 * task.attempt }
memory = { 1.GB * task.attempt }
}
withName: 'NFCORE_FETCHNGS:SRA:SRA_RUNINFO_TO_FTP' {
cpus = { 1 * task.attempt }
memory = { 1.GB * task.attempt }
}
errorStrategy = 'retry'
maxRetries = 2
}
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That seems...optimistic.

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Guess platform is an optimist 🙃

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Yes it is. Can we get some proof it works, perhaps with a big test?

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@mashehu mashehu Awaiting requested review from mashehu

@FriederikeHanssen FriederikeHanssen Awaiting requested review from FriederikeHanssen

@drpatelh drpatelh Awaiting requested review from drpatelh

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