I can't even start the pipeline
brunohhomem opened this issue · 2 comments
brunohhomem commented
Hello!
I'm trying to run the pipeline and this error appears all the time...
I alredy tried a lot of things, even running a older version of the code, but this error appears ever...
Can anyone help me please?
blur@epi_lab:~$ sudo nextflow run nf-core/lncpipe -profile docker
N E X T F L O W ~ version 19.01.0
Launching `nf-core/lncpipe` [chaotic_curran] - revision: 464f015763 [master]
ERROR ~ Process `Run_fastQC` is already define @ line 849, column 17.
process Run_fastQC {
^
_nf_script_3896f0c8: 875: Process `Run_afterQC` is already define @ line 875, column 17.
process Run_afterQC {
^
_nf_script_3896f0c8: 909: Process `Run_FastP` is already define @ line 909, column 17.
process Run_FastP {
^
_nf_script_3896f0c8: 1443: Process `Build_kallisto_index_of_GTF_for_quantification` is already define @ line 1443, column 17.
process Build_kallisto_index_of_GTF_for_quantification {
^
_nf_script_3896f0c8: 1460: Process `Run_kallisto_for_quantification` is already define @ line 1460, column 17.
process Run_kallisto_for_quantification {
^
_nf_script_3896f0c8: 1582: Process `Run_LncPipeReporter` is already define @ line 1582, column 17.
process Run_LncPipeReporter {
^
_nf_script_3896f0c8: 1628: Process `Run_LncPipeReporter_without_Design` is already define @ line 1628, column 17.
process Run_LncPipeReporter_without_Design {
^
7 errors
-- Check '.nextflow.log' file for details
pditommaso commented
This pipeline is defining multiple times the same process name which is not allowed any more is latest NF version. If you downgrade to a prior version, it should be fine eg.
NXF_VER=18.10.1 nextflow run .. etc
likelet commented
i have renamed the process names in the dev
version