Sergey Venev
Sergey Venev
Hey @ewels ! this is a "Work in progress" for the [pairtools](https://github.com/mirnylab/pairtools) module: - `pairtools` is a set of command line framework for common operations on ["pairs"](https://github.com/4dn-dcic/pairix/blob/master/pairs_format_specification.md) generated by Hi-C...
when balancing genome-wide and invoking `ignore_diags` (which is 2 by default) cooler will ignore neighboring trans data as well ... in case there are tiny-tiny chromosomes, e.g. 1-pixel in size:...
Rather major stuff! as discovered by @Marlies1993 `bwa mem` yields empty alignments for sequences of 25bp ... apparently it isn't designed for 25bp, and something like `bwa aln` should be...
@Marlies1993 was running a distiller with some SRA-s as an input and the pipeline kept crashing at the sra step... After closer inspection it appears that some of the links...
@golobor do you know why travis is failing to download the sample fastq-s ? it is sad to see this failing tests all the time ... _Originally posted by @sergpolly...
we commented the extra mapping options in the `project.yml`: https://github.com/mirnylab/distiller-nf/blob/5b5da693f3835e2ed57635fbda13ef0d170c4f29/test/test_project.yml#L99 and the whole thing crashed - nextflow/groovy level crash that was: ```sh N E X T F L O W...
`storeDir` is a huge troublemaker in a cluster environment: whenever some process fails downstream, for whatever reason, some upstream processes can be copying intermediate results to `storeDir` location. After the...
https://github.com/nextflow-io/nextflow/issues/577 Something along these lines: ``` time = { task.exitStatus==140 ? '12h' : '12h' } time = { task.attempt
https://www.nextflow.io/docs/latest/config.html#scope-mail https://www.nextflow.io/docs/latest/config.html#scope-notification enable pipeline notifications by email - useful in case it fails, or to know when it completes
https://github.com/open2c/distiller-nf/blob/master/configs/cluster.config