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Singularity ignored, if "lsf" profile is used #58

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vinjana opened this issue Mar 6, 2024 · 0 comments
Open

Singularity ignored, if "lsf" profile is used #58

vinjana opened this issue Mar 6, 2024 · 0 comments
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@vinjana
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vinjana commented Mar 6, 2024

With

nextflow run $repoDir/main.nf  \
    -profile singularity,lsf \
   --input=$repoDir/test/reference/test1_paired.bam,$repoDir/test/reference/test1_unpaired.bam  \
    --outputDir=test_out  \
    --sortFastqs=true

the process.container values turned out to be unset

$ nextflow config $repoDir/main.nf -profile lsf,singularity
manifest {
   homePage = 'https://github.com/DKFZ-ODCF/nf-bam2fastq'
   description = 'BAM-to-FASTQ conversion and FASTQ-sorting workflow'
   mainScript = 'main.nf'
   version = '1.2.0'
   author = 'Philip Reiner Kensche'
   nextflowVersion = '>= 22.07.1'
}

ext {
   containerVersion = '1.0.0'
}

executor {
   perTaskReserve = false
   perJobMemLimit = true
   jobName = { "nf-bam2fastq - $task.name - $task.hash" }
}

process {
   executor = 'lsf'
   clusterOptions = '-env none'
   // NO `container` option here.
}

singularity {
   enabled = true
   cacheDir = '$repoDir/cache/singularity'
   autoMounts = true
   runOptions = '--no-home'
}

It seems, that the process section is not merged, but overwritten.

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