New module: xengsort/classify

[LeonHornich]

Added new module xengsort/classify for classifying reads using a existing index file.

Notes:

• apart from versions_xengsort, all output files are declared optional. This is due to the optional parameters --filter and --count. When specifying those a different set of files is produced.
• in the nf-tests i only check for file creation since i got md5sum for empty file found error otherwise. I am assuming this is due to the minimum and small nature of the testing data

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[SPPearce]

Are all your output files unstable? That doesn't seem great for the tool...
Can you use sanitizeOutput from nft-utils please.

[SPPearce]

Why are all the output files unstable?

[LeonHornich]

Sorry for the auto ping on all the people, not intended. In the process of pushing some changes something went wrong and i had to reset. The current commit should be fine with what i want it to be.

*have been removed from the review list

[LeonHornich]

@SPPearce i looked into it a bit more. When i just run:

... i get empty files.

My understanding is that due to the small nature of the test data, some of the output files host, graft, both, neither, ambiguous stay empty and this causes the error.

[SPPearce]

If some of the files are empty, then yes that makes sense as to why you need to mark them as unstable. But are ANY of the files non-empty?

[LeonHornich]

Alright, finally got to look into this again. I checked where the test reads are being written to:

0 reads  .nf-test/tests/48f34874e238eb6d9d9dfbaf43e01ff9/work/cd/9563c52ff3c8f9b0bf6dbefbcf85c1/test-ambiguous.1.fq.gz
     0 reads  .nf-test/tests/48f34874e238eb6d9d9dfbaf43e01ff9/work/cd/9563c52ff3c8f9b0bf6dbefbcf85c1/test-ambiguous.2.fq.gz
     0 reads  .nf-test/tests/48f34874e238eb6d9d9dfbaf43e01ff9/work/cd/9563c52ff3c8f9b0bf6dbefbcf85c1/test-both.1.fq.gz
     0 reads  .nf-test/tests/48f34874e238eb6d9d9dfbaf43e01ff9/work/cd/9563c52ff3c8f9b0bf6dbefbcf85c1/test-both.2.fq.gz
     0 reads  .nf-test/tests/48f34874e238eb6d9d9dfbaf43e01ff9/work/cd/9563c52ff3c8f9b0bf6dbefbcf85c1/test-graft.1.fq.gz
     0 reads  .nf-test/tests/48f34874e238eb6d9d9dfbaf43e01ff9/work/cd/9563c52ff3c8f9b0bf6dbefbcf85c1/test-graft.2.fq.gz
     0 reads  .nf-test/tests/48f34874e238eb6d9d9dfbaf43e01ff9/work/cd/9563c52ff3c8f9b0bf6dbefbcf85c1/test-host.1.fq.gz
     0 reads  .nf-test/tests/48f34874e238eb6d9d9dfbaf43e01ff9/work/cd/9563c52ff3c8f9b0bf6dbefbcf85c1/test-host.2.fq.gz
     0 reads  .nf-test/tests/48f34874e238eb6d9d9dfbaf43e01ff9/work/cd/9563c52ff3c8f9b0bf6dbefbcf85c1/test-neither.1.fq.gz
     0 reads  .nf-test/tests/48f34874e238eb6d9d9dfbaf43e01ff9/work/cd/9563c52ff3c8f9b0bf6dbefbcf85c1/test-neither.2.fq.gz
     0 reads  .nf-test/tests/63ca06643019f3f6d133a0b3c84102b3/work/dd/b0adac5c921857896747e68b2616fb/test-ambiguous.fq.gz
     0 reads  .nf-test/tests/63ca06643019f3f6d133a0b3c84102b3/work/dd/b0adac5c921857896747e68b2616fb/test-both.fq.gz
   100 reads  .nf-test/tests/63ca06643019f3f6d133a0b3c84102b3/work/dd/b0adac5c921857896747e68b2616fb/test-graft.fq.gz
     0 reads  .nf-test/tests/63ca06643019f3f6d133a0b3c84102b3/work/dd/b0adac5c921857896747e68b2616fb/test-host.fq.gz
     0 reads  .nf-test/tests/63ca06643019f3f6d133a0b3c84102b3/work/dd/b0adac5c921857896747e68b2616fb/test-neither.fq.gz
     0 reads  .nf-test/tests/63ca06643019f3f6d133a0b3c84102b3/work/dd/b0adac5c921857896747e68b2616fb/test-sites.fq.gz
     0 reads  .nf-test/tests/c4fc34643a2860da654ec49f35bec2d9/work/1f/f805be6a762bd19fa3b0187db5a186/test-ambiguous.1.fq.gz
     0 reads  .nf-test/tests/c4fc34643a2860da654ec49f35bec2d9/work/1f/f805be6a762bd19fa3b0187db5a186/test-ambiguous.2.fq.gz
     0 reads  .nf-test/tests/c4fc34643a2860da654ec49f35bec2d9/work/1f/f805be6a762bd19fa3b0187db5a186/test-both.1.fq.gz
     0 reads  .nf-test/tests/c4fc34643a2860da654ec49f35bec2d9/work/1f/f805be6a762bd19fa3b0187db5a186/test-both.2.fq.gz
   100 reads  .nf-test/tests/c4fc34643a2860da654ec49f35bec2d9/work/1f/f805be6a762bd19fa3b0187db5a186/test-graft.1.fq.gz
   100 reads  .nf-test/tests/c4fc34643a2860da654ec49f35bec2d9/work/1f/f805be6a762bd19fa3b0187db5a186/test-graft.2.fq.gz
     0 reads  .nf-test/tests/c4fc34643a2860da654ec49f35bec2d9/work/1f/f805be6a762bd19fa3b0187db5a186/test-host.1.fq.gz
     0 reads  .nf-test/tests/c4fc34643a2860da654ec49f35bec2d9/work/1f/f805be6a762bd19fa3b0187db5a186/test-host.2.fq.gz
     0 reads  .nf-test/tests/c4fc34643a2860da654ec49f35bec2d9/work/1f/f805be6a762bd19fa3b0187db5a186/test-neither.1.fq.gz
     0 reads  .nf-test/tests/c4fc34643a2860da654ec49f35bec2d9/work/1f/f805be6a762bd19fa3b0187db5a186/test-neither.2.fq.gz
     0 reads  .nf-test/tests/c4fc34643a2860da654ec49f35bec2d9/work/1f/f805be6a762bd19fa3b0187db5a186/test-sites.1.fq.gz
     0 reads  .nf-test/tests/c4fc34643a2860da654ec49f35bec2d9/work/1f/f805be6a762bd19fa3b0187db5a186/test-sites.2.fq.gz

Looks like they are all going in the graft output. I have therefore removed 'graft' from unstableKeys and now the tests and linting finally passes. Tests and linting is passing now