Hi, so I am publishing these different outputs in my main wf:
output {
merged_reads {
path { meta, _reads -> "merged_reads/${meta.donor}" }
}
qc_html {
path { meta, _html -> "fastqc/html/${meta.donor}" }
mode 'copy'
}
multiqc_report {
path "multiqc/report"
mode 'copy'
}
trimmed_reads {
path { meta, _reads -> "trimmed_reads/${meta.donor}" }
}
qc_html_trimmed {
path { meta, _html -> "fastqc/html_trimmed/${meta.donor}" }
mode 'copy'
}
}
This copy for light files (reports) doesn’t work and it relinks all the outputs because in my main config I have this:
includeConfig 'conf/params.config'
includeConfig 'conf/singularity.config'
includeConfig 'conf/process.config'
outputDir = "${baseDir}/NorwagianWoods"
workflow.output.mode = 'rellink'
How can I solve this without defining mode for each output? Thanks