Add tests#29
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Added this to integrate CI, but can also remove if it's annoying to keep getting errors every time we push a commit.
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Tests executed properly. For some reason the test run in the second image was processing more slowly yesterday. Not sure if that was due to some other jobs on the cluster taking up resources. The test had no problem executing, though.
| .fromPath("${params.readsdir}/${params.filepattern}", checkIfExists: true) | ||
| .map { file -> | ||
| def sample = file.baseName // ERR3405856.fastq -> ERR3405856 | ||
| def sample = file.baseName.replaceFirst(/(\.fastq|\.fq)$/, '') // ERR3405856.fastq -> ERR3405856 |
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Added this because just baseName was just removing .gz when the filename ended with fastq.gz.
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OK, so the tests work locally, but #30 is still open? |
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Yes, I created this issue because I think it will be hard to fully use CI with Github unless we create a docker environment that can be used on the Github servers. Last time we chatted you said that may be out of scope, but we can definitely revisit. |
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It's definitely doable, but yes, out of scope. |
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