ERROR ~ A process input channel evaluates to null -- Invalid declaration ` val mito_name`
JiahuaQu opened this issue · 3 comments
Description of the bug
Hi, I had problems in downloading the complete and correct pipelines. I tried many versions but always failed with the similar errors:
ERROR Cannot parse container string in
'nf-core-atacseq-2.0/workflow/modules/nf-core/bowtie2/align/main.
nf':
${ workflow.containerEngine ==
⚠ Skipping this singularity image..
downloading with singularity images.txt
Then I determied to download without singularity images.
However, when running the program in my institute's HPC, the same error always showed:
ERROR ~ A process input channel evaluates to null -- Invalid declaration val mito_name
my.log
test.sh.o9702320.txt
Hope get your help. Thank you.
Command used and terminal output
No response
Relevant files
No response
System information
nextflow # version: 22.10.6
HPC
GSE
With or without singularity
CentOS
I tried various versions:
nf-core-atacseq-dev
nf-core-atacseq-2.0
nf-core-atacseq-master
nf-core-atacseq-1.2.2
nf-core-atacseq-modules-update
Yes, these are two known bugs of the current released version that are fixed in the dev
version of the pipeline see #270 and #286. Anyway, if you want to use the release version you can:
1- Just can use the nf-core download and do not care about the error. The reason is that the the bwa image will be downloaded anyways since bwa/mem uses the same image and there it is correctly tagged. More info about the download
command here.
2- Just provide an empty or a fake mito_name
adding this to your command --mito_name ''
or --mito_name dummy
Yes, these are two known bugs of the current released version that are fixed in the
dev
version of the pipeline see #270 and #286. Anyway, if you want to use the release version you can: 1- Just can use the nf-core download and do not care about the error. The reason is that the the bwa image will be downloaded anyways since bwa/mem uses the same image and there it is correctly tagged. More info about thedownload
command here. 2- Just provide an empty or a fakemito_name
adding this to your command--mito_name ''
or--mito_name dummy
Thank you for your answer.
Now I used the version 2.0 and added the command --mito_name ''
.
Although the program could be ran further than before, there was a new error with the BWA-MEM. Details in the attachment.
Hope get further help. Thank you again.
new_error.txt
Since this is being discussed already in nf-core/chipseq#356. I close this issue now in favor of the former.