Add content tests #169
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Add content tests #169
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mariaTsontaki
commented
Nov 1, 2025
| path("${params.outdir}/summary_tables/magmap.rRNA.counts.tsv.gz").linesGzip.findAll { l -> l.contains('orf') }, | ||
| path("${params.outdir}/summary_tables/magmap.rRNA.counts.tsv.gz").csv(sep: '\t', decompress: true, header: true).columns["tpm"].sum().round(), | ||
| path("${params.outdir}/summary_tables/magmap.tmRNA.counts.tsv.gz").linesGzip.findAll { l -> l.contains('orf') }, | ||
| path("${params.outdir}/summary_tables/magmap.tmRNA.counts.tsv.gz").csv(sep: '\t', decompress: true, header: true).columns["tpm"].sum().toBigDecimal().round(), |
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I had to add the function toBigDecimal() for round() to work in this case. sum() returns a class of Integer when there is only one row in the csv, while when there are more than 1 line, the sum() returns a class of BigDecimal, which can be used as input for round().
Here is the error I had, when I was running the test with .sum().round():
Test [e5339dde] '-profile test' groovy.lang.MissingMethodException: No signature of method: java.lang.Integer.round() is applicable for argument types: () values: []
Possible solutions: find(), find(groovy.lang.Closure), and(java.lang.Number), mod(java.lang.Number), minus(java.lang.Character), minus(java.lang.Number)
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I suppose we should add that to all.
erikrikarddaniel
approved these changes
Nov 4, 2025
| path("${params.outdir}/summary_tables/magmap.rRNA.counts.tsv.gz").linesGzip.findAll { l -> l.contains('orf') }, | ||
| path("${params.outdir}/summary_tables/magmap.rRNA.counts.tsv.gz").csv(sep: '\t', decompress: true, header: true).columns["tpm"].sum().round(), | ||
| path("${params.outdir}/summary_tables/magmap.tmRNA.counts.tsv.gz").linesGzip.findAll { l -> l.contains('orf') }, | ||
| path("${params.outdir}/summary_tables/magmap.tmRNA.counts.tsv.gz").csv(sep: '\t', decompress: true, header: true).columns["tpm"].sum().toBigDecimal().round(), |
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I suppose we should add that to all.
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Yes, let's do that! I will now merge then. |
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PR checklist
nf-core lint).nextflow run . -profile test,docker).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).