Add ARM support for kraken2

Open pinin4fjords opened this issue 1 year ago • 2 comments

Kraken2 is currently lacking ARM support in Bioconda/ conda-forge, so will not work here: https://anaconda.org/bioconda/kraken2

The fix will be driving for a new kraken2 build in those channels with ARM support.

Oct 23 '24 10:10 pinin4fjords

This one done:

kraken2-2.14 | pl5321h1e84f2d_0 3.2 MB bioconda

Apr 14 '25 08:04 dslarm

Let's leave this open until we've updated the nf-core module for ARM support and then installed the update here.

Apr 14 '25 08:04 pinin4fjords

ARM support for Kraken2 has been added to the pipeline. The conf/arm.config file now includes an ARM-compatible container for Kraken2:

The process uses the ARM-compatible container: community.wave.seqera.io/library/kraken2_coreutils_pigz:2a28cee7c0427b32

Users can now run the pipeline with Kraken2 on ARM architecture using:

nextflow run nf-core/rnaseq -profile <docker/singularity>,arm <OTHER_PARAMETERS>

Closing this issue as resolved.

Nov 14 '25 12:11 pinin4fjords