karlkashofer
karlkashofer
WDL is a powerful language to script bioinformatics pipelines. Specs are here: https://github.com/openwdl/wdl/blob/main/versions/1.0/SPEC.md Would it be possible to add .wdl as supported filetype for markup et al ? What needs...
We run custom WDL genomics pipelines and also parts of the BioWDL somaticcalling pipeline (https://biowdl.github.io/) using the broadinstitute/cromwell:64 cromwell container with a gridengine backend. Occasionally we see errors like the...
Using the standard 16gb library and some bacterial reads we seem to get empty taxonomic level fields in the kraken2 report file. For example, the root and bacteria lines have...
Hi ! I implemented decrypt_keyctl on my debian server with encrypted root and several other encrypted disks. I am asked for the passphrase in the initramfs, but as its not...
I use your code in a exome pipeline which includes manta. Manta is super picky about the input bam files and it chokes on one of our current bams with...
Hi ! I am looking for ways to parallelize umicollapse. What does -t: parallelize the deduplication of each separate alignment position. Using this is discouraged as it is lacking many...
Running umicollapse on 200mio paired end reads (400 reads total) runs out of Java heap space even with -Xmx96G. Is that normal ?
Is it somehow possible to keep the unmapped reads in the output file, or at least write out the unmapped reads to a separate file instead of discarding them ?
I am trying to move a old legacy java app into docker and need to set up a specific user account inside the container as this account is hardcoded in...
Dear Iustin ! Also came here via planet debian and really like your project. It would be a great way to make my large, but somewhat unorganized collection of images...