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nf-core / atacseq

ATAC-seq peak-calling and QC analysis pipeline

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ERROR ~ A process input channel evaluates to null -- Invalid declaration ` val mito_name`

JiahuaQu opened this issue · comments

commented

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

commented

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

commented

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

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

commented

Since this is being discussed already in nf-core/chipseq#356. I close this issue now in favor of the former.