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Move out multiQC and versions #189

Merged
merged 5 commits into from
Aug 24, 2023
Merged

Move out multiQC and versions #189

merged 5 commits into from
Aug 24, 2023

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maxulysse
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github-actions bot commented Aug 24, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 7f6439c

+| ✅ 134 tests passed       |+
#| ❔  13 tests were ignored |#
!| ❗   7 tests had warnings |!

❗ Test warnings:

  • 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: 1.10.1
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
  • schema_description - No description provided in schema for parameter: dbgap_key

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-08-24 16:47:42

maxulysse
maxulysse commented Aug 24, 2023
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maxulysse
maxulysse commented Aug 24, 2023
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adamrtalbot
adamrtalbot approved these changes Aug 24, 2023
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It's basically fine, just spotted one or two things.

We should tidy

fetchngs/main.nf

Lines 49 to 67 in 5dab8d0

// Auto-detect input id type
def input_type = ''
if (WorkflowMain.isSraId(ch_input)) {
input_type = 'sra'
} else if (WorkflowMain.isSynapseId(ch_input)) {
input_type = 'synapse'
} else {
exit 1, 'Ids provided via --input not recognised please make sure they are either SRA / ENA / GEO / DDBJ or Synapse ids!'
}
if (params.input_type == input_type) {
if (params.input_type == 'sra') {
include { SRA } from './workflows/sra'
} else if (params.input_type == 'synapse') {
include { SYNAPSE } from './workflows/synapse'
}
} else {
exit 1, "Ids auto-detected as ${input_type}. Please provide '--input_type ${input_type}' as a parameter to the pipeline!"
}
in a separate PR

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maxulysse and others added 2 commits August 24, 2023 18:43
@maxulysse @adamrtalbot
Apply suggestions from code review
aff72b7 
Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
@maxulysse
fix syntax
7f6439c
@maxulysse maxulysse merged commit 54e7d7d into nf-core:refactor Aug 24, 2023
23 checks passed
@maxulysse maxulysse deleted the move_things branch August 24, 2023 17:45
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@maxulysse @adamrtalbot