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bwa-mem2 Container Issue Affects RareDisease Pipeline #676

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pnolabs opened this issue Feb 6, 2025 · 0 comments
Open

bwa-mem2 Container Issue Affects RareDisease Pipeline #676

pnolabs opened this issue Feb 6, 2025 · 0 comments
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@pnolabs
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pnolabs commented Feb 6, 2025

Description of the bug

I have already posted this to Biocontainers here:
BioContainers/containers#591

I came across this error when trying to run the nf-core/raredisease pipeline with nextflow.

Docker version 27.5.1, build 9f9e405
nextflow version 24.10.3.5933
conda 24.7.1
nf-core 3.1.1 pypi_0 pypi
python --version Python 3.9.20
nf-core/raredisease v2.2.0-gfa61a65

Status: Downloaded newer image for quay.io/biocontainers/bwa-mem2:2.2.1--he513fc3_0
ERROR: fail to find the right executable

Thank you very much for looking into this!

Command used and terminal output

nextflow run nf-core/raredisease -profile test,docker --outdir /path/to

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@pnolabs pnolabs added the bug Something isn't working label Feb 6, 2025
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