Dennis Schmitz
Dennis Schmitz
When there is time to properly validate it, change the aligner in the ILM-RA workflow to `minimap2`. Should be significantly faster than current aligner but I'm unsure if it breaks...
This is a result of a vcf file being empty (only contains headers and no SNPs), see https://github.com/igvteam/igv.js/issues/1148. For now, ignore the error.
**TLDR** *The `Jovian` output is only comparable between systems/installations with 12 or more computing threads.* After running a demo dataset, with known outputs/hashes, on a system with limited resources (
See RUN25 sample 01 for a test case. This sample had an unexpectedly large number of reads. This caused `samtools sort` from the `HuGo_removal_pt1` to crash due to lack of...
I will update this post if more information becomes available. See also related issue #102. On certain off-site servers we see the error shown below. Even with datasets that have...
We should stop assuming that the user's `$PATH` is correct when executing stuff from within a `conda` env. Likewise, we should stop hard-coding software location with shebangs. Usually this functions...
See Nextseq run 24, 2019, sample 18 for a test-case. Bug submitted by @jeroencremer. The fragment length analysis step crashes on low-quality/low-abundance samples in default mode. The reason; due to...
This issue was emailed to me by @RozemarijnVanDerPlaats. One specific sample kept crashing in the `SNP_calling` step, see DRMAA log below: ``` Error in rule SNP_calling: jobid: 0 output: data/scaffolds_filtered/4_S4_scaffolds_ge500nt.fasta.fai,...
### Problem: 1. Scaffolds 5' and 3' ends are often of poor quality. Sometimes we see the RNA/DNA seems to fold in on itself (hairpin) and generates a reverse-complement sequence...
Instead of having a brach per version, @florianzwagemaker suggested to use a continuous dev-branch. Likewise, we should setup Travis-CI to make sure that every commit and merge functions properly (see...