No such file or directory for .fasta (when using Singularity)

[bgbrink]

I am trying to run Companion using Singularity instead of docker, but it seems that the paths are not mounted correctly.

This is my config:

env {
    GT_RETAINIDS = "yes"
    AUGUSTUS_CONFIG_PATH = "/opt/data/augustus"
    FILTER_SHORT_PARTIALS_RULE = "/opt/data/filters/filter_short_partials.lua"
    PFAM = "/opt/pfam/Pfam-A.hmm"
    PFAM2GO = "/opt/data/pfam2go/pfam2go.txt"
    RATT_CONFIG = "/opt/RATT/RATT.config_euk_NoPseudo_SpliceSite"
}

params.GO_OBO = "/opt/go.obo"
params.NCRNA_MODELS = "/opt/data/cm/rnas.cm"
params.CIRCOS_CONFIG_FILE = "/opt/data/circos/circos.debian.conf"
params.CIRCOS_BIN_CONFIG_FILE = "/opt/data/circos/circos.bin.debian.conf"
params.SPECFILE = "/opt/data/speck/output_check.lua"
params.AUGUSTUS_EXTRINSIC_CFG = "/opt/data/augustus/extrinsic.cfg"

process {
    container = 'sangerpathogens/companion:latest'
}

singularity {
    enabled = true
}

executor {
    name = 'local'
    queueSize = 2
    pollInterval = '3sec'
}

I can start the pipeline, but I receive the following error:

Error executing process > 'truncate_input_headers'

Caused by:
  Process `truncate_input_headers` terminated with an error exit status (1)

Command executed:

  truncate_header.lua < phased.1_scaffolds_FINAL.fasta > truncated.fasta

Command exit status:
  1

Command output:
  (empty)

Command error:
  .command.sh: line 2: phased.1_scaffolds_FINAL.fasta: No such file or directory

Work dir:
  /work/project/ladsie_002/work/77/1854982bdacdd60fbe447554ab153b

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

However, when I look into the path, the file does indeed exist:

$ ll /work/project/ladsie_002/work/77/1854982bdacdd60fbe447554ab153b
total 1
lrwxrwxrwx 1 bbrink users 76 30. Aug 13:44 phased.1_scaffolds_FINAL.fasta -> /work/project/ladsie_002/companion/input/pleo/phased.1_scaffolds_FINAL.fasta

I tried to find a solution for this, but I was unable to do so. Do you have any insights for me?