Dears,
i have written a pipeline in nextflow and on the subset of the data it works well, but when i used the whole dataset strange error in publishsing the output data at the final step pops up. detail of that mentioned here:
my last process in nextflow:
process Genepy_score {
publishDir "${params.output}/Genepy_score/Genepy2_score", mode: "copy", overwrite: true
input:
path("Meta_files")
output:
path("*")
script:
"""
source activate drop
mkdir -p Genepy2_score
python "${params.genepy_py}" "Meta_files" "Genepy2_score"
"""
}
######### Error:
Jun-18 19:50:25.911 [PublishDir-41] DEBUG nextflow.processor.PublishDir - Failed to publish file: /Nextflow/next_test/ttt2/ibdplexus.recalibrated/work/98/5e5cca770739477501ef3130b45307/Genepy2_score; to: /Nextflow/next_test/ttt2/ibdplexus.recalibrated/Results/Genepy_score/Genepy2_score/Genepy2_score [copy] -- attempt: 1; reason: /Nextflow/next_test/ttt2/ibdplexus.recalibrated/Results/Genepy_score/Genepy2_score/Genepy2_score/ENSG00000114124.3_GRK7_._.meta.txt
ERROR nextflow.processor.PublishDir - Failed to publish file: /Nextflow/next_test/ttt2/ibdplexus.recalibrated/work/20/aea26e000f573e86e7b8482ac85139/Genepy2_score; to: /Nextflow/next_test/ttt2/ibdplexus.recalibrated/Results/Genepy_score/Genepy2_score/Genepy2_score [copy] -- See log file for details
dev.failsafe.FailsafeException: java.nio.file.DirectoryNotEmptyException: /Nextflow/next_test/ttt2/ibdplexus.recalibrated/Results/Genepy_score/Genepy2_score/Genepy2_score
#################################
basically the gene which mentioned there doesnt exist in the mentioned work directory!!!
any helps?
thank you