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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
process.container
$ 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.
The text was updated successfully, but these errors were encountered:
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With
the
process.container
values turned out to be unsetIt seems, that the process section is not merged, but overwritten.
The text was updated successfully, but these errors were encountered: