Update learnmsa module to work with compressed files. #5276
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Hm, weird, on local this works at least using singularity... will have a look tomorrow |
| assertAll( | ||
| { assert process.success }, | ||
| { assert path(process.out.alignment.get(0).get(1)).getTextGzip().contains(">sample1") }, | ||
| { assert snapshot(process.out.versions).match("versions1") } |
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why does have the 1 in it?
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To get the output file from the meta + file-output channel, if you mean the .get(1).
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Ah nvm, for the snapshot name of the versions snapshot it's because since v 0.8.4 nf-test throws an error when overwriting a snapshot with the same name – compare [0].
This was causing the CI to fail despite the test passing locally (where I have nf-test v 0.8.3 installed).
[0] askimed/nf-test@d2508b2#diff-fd31905853152ac935c5509db52bb497033040fa8cb2523810950c3595ba450aR31-R37
luisas
approved these changes
Mar 22, 2024
Co-authored-by: Luisa Santus <[email protected]>
jvfe
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Mar 26, 2024
* master: (47 commits) Update genomescope2 module and add nf-tests (#5399) PLINK/GWAS additional output (#5387) Plink linkage disequilibrium additional output (#5388) new module: Plink epistasis analysis (#5386) Add module for TaxonKit name2taxid (#4778) Update-cellranger-modules (#5016) Update: GTDBTK/CLASSIFYWF (migrate to nf-test and only execute mv when dirs actually present) (#5390) Added MetaPlAn subworkflow (#5356) port `vcftools` to nf-test (#5375) Update modules: rgi (#5383) Update condaforge/mambaforge Docker tag to v24 (#5381) Update gecco + migrate to nf-test (#5372) Update learnmsa module to work with compressed files. (#5276) New module: kraken2/build (#5212) Update kalign module to work with compressed files. (#5277) port `ensemblvep/download` to nf-test (#5373) port `manta-germline` to nf-test (#5362) port `tiddit-sv` to nf-test and add `--threads` (#5371) Decoupler module (#5317) fix optional cram support in modules and migrate to nf-test (#5329) ...
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Add the compression handling introduced to MSA modules in #4754 to learnmsa (forgot learnmsa and kalign it in that PR).