Command error:
mv: cannot stat '/hpcnfs/scratch/EO/afranceschini/eo/work/e6/e5449d17aa55cfbb5514e5d49cf3cf/19W33_S3_L001_R1_001.bam': No such file or directory
I paste my code below:
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process moveFiles{
publishDir "${params.publishDir}"
input:
file bamF from bamCh
file baiF from baiCh
val goMoveFiles from bwaMemCompleteCh.collect()
output:
stdout moveFilesCompleteCh
"""
mkdir -p ${params.outputDir}/bam_files
mv \$(readlink -f ${params.publishDir}/${bamF}) ${params.outputDir}/bam_files/
mv \$(readlink -f ${params.publishDir}/${bamF}) ${params.outputDir}/bam_files/
"""
}
process linkFiles {
input:
val go from moveFilesCompleteCh.collect()
"""
ln -sf ${params.outputDir}/bam_files/* ${params.publishDir}/
"""
}
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Thankyou for the help