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Merged
merged 15 commits into from
Jul 15, 2025
Merged

Default pipeline nf-test #619

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06ba53d
Update snapshot for default test
sofstam Jun 11, 2025
1e16981
Added changelog
sofstam Jun 11, 2025
2ebfad0
Add bbduk to ignore and update snap
sofstam Jun 12, 2025
1aa4846
Fix linting
sofstam Jun 12, 2025
e9d21bc
Update snap
sofstam Jun 17, 2025
b6a2bf8
Updata snaps
sofstam Jun 17, 2025
ef59959
Update snaps
sofstam Jun 17, 2025
54e1383
Update snapshots
sofstam Jun 17, 2025
585266d
Remove NFT
sofstam Jun 18, 2025
2c22d47
Update snapshot
sofstam Jun 19, 2025
7fcac39
Remove two lines
sofstam Jul 3, 2025
de45de9
Add more files to ignore
sofstam Jul 3, 2025
221cd08
Ignore more files
sofstam Jul 4, 2025
7d64b29
Add more files for the test to pass
sofstam Jul 4, 2025
4b373b7
Ignore files
sofstam Jul 4, 2025
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2 changes: 0 additions & 2 deletions .github/actions/nf-test/action.yml
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Expand Up @@ -59,8 +59,6 @@ runs:
- name: Run nf-test
shell: bash
env:
NFT_DIFF: ${{ env.NFT_DIFF }}
NFT_DIFF_ARGS: ${{ env.NFT_DIFF_ARGS }}
NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
run: |
nf-test test \
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2 changes: 0 additions & 2 deletions .github/workflows/nf-test.yml
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Expand Up @@ -99,8 +99,6 @@ jobs:
- name: Run nf-test
uses: ./.github/actions/nf-test
env:
NFT_DIFF: ${{ env.NFT_DIFF }}
NFT_DIFF_ARGS: ${{ env.NFT_DIFF_ARGS }}
NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
with:
profile: ${{ matrix.profile }}
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Added`

- [#619](https://github.com/nf-core/taxprofiler/pull/619) Added default pipeline nf-test (added by @sofstam)
- [#615](https://github.com/nf-core/taxprofiler/pull/615) Updated to nf-core pipeline template v3.3.1 (added by @sofstam)
- [#614](https://github.com/nf-core/taxprofiler/pull/614) Updated module `krakenuniq/preloadedkrakenuniq` to fix preload mechanism. The RAM chunk size can now be customised on a per-database basis. (added by @muniheart with help from / ❤️ to @jfy133)
- [#600](https://github.com/nf-core/taxprofiler/pull/600) Added metaphlan to multiqc report (❤️ to @harper357 for reporting and added by @sofstam)
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20 changes: 20 additions & 0 deletions tests/.nftignore
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Expand Up @@ -4,7 +4,27 @@ multiqc/multiqc_data/multiqc.log
multiqc/multiqc_data/multiqc_data.json
multiqc/multiqc_data/multiqc_sources.txt
multiqc/multiqc_data/multiqc_software_versions.txt
multiqc/multiqc_data/*.txt
multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png}
multiqc/multiqc_report.html
fastqc/*_fastqc.{html,zip}
fastqc/*/*fastqc.zip
pipeline_info/*.{html,json,txt,yml}
bbduk/*.log
nonpareil/*.{npa,npc,npl,npo,png,json,png,tsv,txt,pdf,csv}
bracken/*combined_reports.txt
centrifuge/*/*.mapped.fastq.gz
centrifuge/*/*results.txt
centrifuge/*/*.unmapped.fastq.gz
diamond/*/*.{tsv,log,txt}
fastp/*.{html,zip,json,log}
kaiju/*/*.tsv
kaiju/*.txt
krona/*.html
ganon/*/*.log
kraken2/*/*.fastq.gz
metaphlan/*/*.{biom,txt}
porechop_abi/*.log
samtools/*.bam.bai
samtools/*.unmapped.bam
taxpasta/*.tsv
1 change: 1 addition & 0 deletions tests/default.nf.test
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Expand Up @@ -3,6 +3,7 @@ nextflow_pipeline {
name "Test pipeline"
script "../main.nf"
tag "pipeline"
profile "test"

test("-profile test") {

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