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JAFFAL pipeline crashes when singularity is used #239

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marcDabad opened this issue May 4, 2023 · 1 comment
Open

JAFFAL pipeline crashes when singularity is used #239

marcDabad opened this issue May 4, 2023 · 1 comment
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@marcDabad
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Description of the bug

JAFFAL pipeline crashes when singularity is used because singularity container has not minimap2 (at least)

Command used and terminal output

nextflow run nf-core/nanoseq--input samplesheet.csv --outdir first --protocol cDNA --skip_demultiplexing --skip_vc --skip_sv -profile slurm,singularity --jaffal_ref_dir ${PWD}/for_jaffal

Relevant files

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System information

  • Nextflow 22.10.1
  • HPC
  • slurm
  • Singularity
  • Centos
  • nanoseq 3.1.0
@marcDabad marcDabad added the bug Something isn't working label May 4, 2023
@zya067025
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Hi, I have the same issue when I am running nanoseq 3.1.0

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@marcDabad @zya067025