Fixing the failing tests in Release 1.0.1 #42
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mashehu
reviewed
Mar 27, 2024
| @@ -69,4 +69,4 @@ jobs: | |||
| env: | |||
| NXF_SINGULARITY_CACHEDIR: ./ | |||
| NXF_SINGULARITY_HOME_MOUNT: true | |||
| run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results | |||
| run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results --input https://raw.githubusercontent.com/nf-core/test-datasets/readsimulator/samplesheet/test_samplesheet.csv | |||
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why don't you provide the input in the test config? easier to keep it in sync
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The problem is that I did provide the input in the test config. I've put it in conf/test.config. So maybe this is a case of a misleading error message because PR #41 has a failing test with the error "Missing required parameter: --input"
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Maybe I should remove the -stub option instead. This discussion on Slack makes it seem like the -stub option could be the issue.
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I've removed the download_pipeline.yml changes from this PR. Now the PR is just adding the extra input parameter that the insilicoseq module is expecting. |
sateeshperi
approved these changes
Apr 11, 2024
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PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).