Add stub blocks to all local modules#368
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Tabea01 wants to merge 11 commits intonf-core:devfrom
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famosab
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May 5, 2026
famosab
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Looks good, do you plan to add stub tests somewhere to test? (ideally local modules should have tests and there you could have the stub test as well)
if you already have tests for local modules then add the stub tests now, if not then do it in the pr when you add the tests
| stub: | ||
| if (meta.single_end) { | ||
| """ | ||
| echo "" | gzip > ${meta.id}.fastq.gz |
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I know thats how its described in the docs but actually you do not even need the quotes.
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| echo "" | gzip > ${meta.id}.fastq.gz | |
| echo | gzip > ${meta.id}.fastq.gz |
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| echo "" | gzip > ${meta.id}_1.fastq.gz | ||
| echo "" | gzip > ${meta.id}_2.fastq.gz |
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| echo "" | gzip > ${meta.id}_1.fastq.gz | |
| echo "" | gzip > ${meta.id}_2.fastq.gz | |
| echo | gzip > ${meta.id}_1.fastq.gz | |
| echo | gzip > ${meta.id}_2.fastq.gz |
| stub: | ||
| if (meta.single_end) { | ||
| """ | ||
| echo "" | gzip > ${meta.id}.fastq.gz |
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| echo "" | gzip > ${meta.id}.fastq.gz | |
| echo | gzip > ${meta.id}.fastq.gz |
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| echo "" | gzip > ${meta.id}_1.fastq.gz | ||
| echo "" | gzip > ${meta.id}_2.fastq.gz |
There was a problem hiding this comment.
Suggested change
| echo "" | gzip > ${meta.id}_1.fastq.gz | |
| echo "" | gzip > ${meta.id}_2.fastq.gz | |
| echo | gzip > ${meta.id}_1.fastq.gz | |
| echo | gzip > ${meta.id}_2.fastq.gz |
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| stub: | ||
| """ | ||
| touch ${runinfo.toString().tokenize(".")[0]}.runinfo_ftp.tsv |
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do you have that info if its just a stub?
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@famosab Good point! I'll add stub test cases to each of the local modules in this PR. |
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Closes #367
What was done
stubblocks to all 6 local modules:sra_ids_to_runinfo,sra_runinfo_to_ftp,sra_fastq_ftp,aspera_cli,sra_to_samplesheet,and
multiqc_mappings_config.filter { it.size() > 0 }beforesplitCsvinworkflows/fetchngs.nfto handle empty TSV files (prevents a missing header error in stub mode)
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).