Input file does not exists (Nextflow/Docker)

[MartonHorvath98]

I have a similar issue to #326! I am trying to inplement a process using agat_convert_sp_gxf2gxf.pl, and agat_convert_sp_gff2bed.pl to convert my GTF reference to BED. When using my locally installed version of the tool in a conda environment it works perfectly!
But when I try to load it in the pipeline from the nextflow.config file, as:

process {
  withName: AGAT_CONVERT {
                  container = 'quay.io/biocontainers/agat:1.4.2--pl5321hdfd78af_0'
              }
}

the execution fails, and iget the same error message as #326 :

ERROR ~ Error executing process > 'AGAT_CONVERT (Convert GTF annotation to GFF3 and BED)'

Caused by:
  Process `AGAT_CONVERT (Convert GTF annotation to GFF3 and BED)` terminated with an error exit status (1)


Command executed:

  #STEP 1: convert gtf annotation to gff3 format
  agat_convert_sp_gxf2gxf.pl -g  /mnt/...path.../ref_annot.gtf -o ref_annot.gff
  
  #STEP 2: convert gff3 annotation to bed format
  agat_convert_sp_gff2bed.pl -g ref_annot.gff -o ref_annot.bed

Command exit status:
  1

Command output:
 ...
   --------------------------------- parsing file ---------------------------------
  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
  !/mnt/...path.../ref_annot.gtf does not exist. Please  !
  !verify the input file name/path                                !
  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

How could I solve the mounting issue?

[Juke34]

Did you set your nextflow config appropriately to use containers?

I.e.: docker.enabled = true
docker.runOptions='-u "$( id -u ):$( id -g )"'

[MartonHorvath98]

Hi @Juke34! Thank you for answering! I had the docker.enabled set true. I had not specified the container ownership as you did, but will might give it a go!

I have, in the meantime, circumnavigated my issue by using ucsc tools that ran without an issue.

[Juke34]

Here /mnt/...path.../ is weird

agat_convert_sp_gxf2gxf.pl -g  /mnt/...path.../ref_annot.gtf -o ref_annot.gff

I guess the command in the nextflow process was simply wrong

[MartonHorvath98]

Could be the reason. I instantiated the process in the workflow without an input as:

include { PROCESS } from 'modules/local/process/main.nf'

workflow {
PROCESS()
}

and used a parameter from the config file, params.gtf_file, in the script block instead to supply the input.

process PROCESS {
 publishDir ...

 output:
 path "*.gff", emit: agat_gff

 script:
 """
 agat_convert_sp_gxf2gxf.pl -g  $params.gtf_file -o ref_annot.gff
 """

Although this worked well in other local scripts with only bash or awk commands, but I guess could have confused the agat convert command.

I check, and yes as you noted, when using path from channels, only the basename shows, unlike here, when the absolute path showed up.