Update modules to use absolute path data #249
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Changes: - Modules updated - Now use absolute paths for test data - All modules tests should work within the this repository
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First draft looks good - we might want to wait for nf-core/modules#4723 and change base path for consistency. TBC. |
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I can't seem to run this locally so can't see what's wrong. Will have to spin up a VM and try there. |
maxulysse
reviewed
Jan 12, 2024
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You deleted all of the |
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You were basically stung by this nf-core/tools#2658 |
drpatelh
reviewed
Jan 12, 2024
| @@ -3,5 +3,3 @@ includeConfig "../../modules/local/sra_fastq_ftp/nextflow.config" | |||
| includeConfig "../../modules/local/sra_ids_to_runinfo/nextflow.config" | |||
| includeConfig "../../modules/local/sra_runinfo_to_ftp/nextflow.config" | |||
| includeConfig "../../modules/local/sra_to_samplesheet/nextflow.config" | |||
| includeConfig "../../modules/nf-core/sratools/prefetch/nextflow.config" | |||
| includeConfig "../../subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config" | |||
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Don't we need this line here? Why was it deleted?
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The config files were deleted, looks like by nf-core tools. Will add them all back in.
drpatelh
reviewed
Jan 12, 2024
| { assert new File("$outputDir/fastq/DRX026011_DRR028935_1.fastq.gz").exists() }, | ||
| { assert new File("$outputDir/fastq/DRX026011_DRR028935_2.fastq.gz").exists() }, | ||
| { assert new File("$outputDir/fastq/ERX1234253_ERR1160846.fastq.gz").exists() }, | ||
| { assert new File("$outputDir/fastq/SRX10940790_SRR14593545_1.fastq.gz").exists() }, |
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Why did we change this test file?
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Sorted it properly.
drpatelh
approved these changes
Jan 14, 2024
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Changes:
To do:
PR checklist
nf-core lint).nextflow run . -profile 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).