Renato Alves
Renato Alves
Scenario: 1) 12 samples are being processed using the `parallel` machinery `lock1()` and `collect()`. 2) 10 samples complete and 2 fail. 3) The 2 failing samples are considered bad and...
When using external modules we currently provide an `init` phase in addition to the actual execution phase. `init` can be used to test if all requirements to execute the module...
Currently if a user keeps updating their ngless version they will accumulate binaries and resources in `~/.local/share/ngless` for different versions. This can be perceived as wasteful and requires that users...
We can currently `count()` reads overlapping with regions defined in a GFF file. However this is only accessible for counting. Another use-case is within `select()` in order to keep/drop reads...
Fixing this to handle position sorted bam/sam files will require a similar approach to #72 and keeping an index of read headers in-memory. An easier solution is to detect if...
This is related to #74 and to some degree with #73 . The current formats (`{fastq}`, `{mapping}`) are somewhat hard use. Both formats leak internal information (e.g. `1:file preproc.lno10.pairs.1`) and...
The machinery that performs computation of statistics (`mapstats`, `fqstats`) is tied to the creation of HTML reports. When processing lots of samples there's unnecessary overhead in producing and storing partially...
Using only information contained in a fqstats file it is currently impossible to distinguish between processing `pair.1`, `pair.2` and `singles` using pairing information `paired(..., singles=...)` versus treating each file independently...
When using external modules one can specify ``` arg1: atype: 'readset' can_gzip: true ``` which passes one (.1.fq), two (.1.fq, .2.fq), or three (.1.fq, .2.fq, .single.fq) files depending on what...
As part of the split-map strategy implemented in ngless 0.6 symlinks are created to avoid copying split files. As of this version symlinks use absolute paths. While this works on...