Merge pull request nf-core#619 from nf-core/default_nftest

Default pipeline nf-test

Author: sofstam

.github/actions/nf-test/action.yml

@@ -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 \

.github/workflows/nf-test.yml

@@ -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 }}

CHANGELOG.md

@@ -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)

tests/.nftignore

@@ -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

tests/default.nf.test

@@ -3,6 +3,7 @@ nextflow_pipeline {
     name "Test pipeline"
     script "../main.nf"
     tag "pipeline"
+    profile "test"
 
     test("-profile test") {