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Hi
I will like to output the unmapped reads after mapping to human genome (hg19)
Hence, after executing the following code, how can I use `write()` to output R1 and R2 fastq.gz?
```
human_mapped…
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In https://github.com/ngless-toolkit/ng-meta-profiler/blob/4b7b49aebb1f766274d2fbbf084852b34187193a/marine-profiler.ngl#L4 we refer `om-rgc 0.9` but we only have `om-rgc 0.0`.
Should we `a)` create t…
unode updated
5 years ago
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Hi,
I'm testing ngless version 1.0 (and 0.6.x) for a metagenomics project. Unfortunately, I do not manage to download the reference for Mus musculus; neither mm10.p5 nor mm10.p2 or working. I've te…
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I put the files on eagle under the emma folder. Here is what you have:
orf.fna - entire metagnome assembly
proteins.prodigal.faa - translation of metagenome assembly
orfMG...fna - assemblies of ind…
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In [ngless-contrib fastx](https://github.com/ngless-toolkit/ngless-contrib/blob/9d83b60cc9a4769d6461800faaa0489889b97002/fastx.ngm/0.1.0/module.yaml#L10) the module explicitly sets `can_gzip: false` b…
unode updated
5 years ago
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I've contacted the developer of NGLess with this question, but it has been about a week and he hasn't responded so I'm hoping someone here can help!
I have managed to successfully assemble metagenome…
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Hi,
I've packaged ngless 0.9.1 for GNU Guix. I tried to upgrade the package to 0.10.0 today, but the build fails with this error:
~~~
...
[40 of 84] Compiling StandardModules.Mappers.Minimap2…
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Currently, tar expansion is done in such a way that files are expanded in memory as they are extracted. The relevant function is: https://github.com/ngless-toolkit/ngless/blob/89309c6309fdde53e5392258…
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I ran across one article discussing using bionix instead of cwl. I am curious to hear tradeoffs on that bionix approach with ngless
ghost updated
5 years ago
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According to the FAQ ngless is supposed to check all input files prior to execution.
In the case below it doesn't check if the `fafile` or the folder containing it exists before executing.
Instead…
unode updated
5 years ago