Nextflow stdout:

N E X T F L O W  ~  version 24.12.0-edge
Launching `/home/runner/work/rnaseq/rnaseq/.nf-test-448cc38f562b3a594f13242d3d0c44c2.nf` [infallible_shaw] DSL2 - revision: 9609345052
Downloading plugin [email protected]
Downloading plugin [email protected]
[7d/4d683d] Submitted process > GTF_FILTER (genome.fasta)
ERROR ~ Error executing process > 'GTF_FILTER (genome.fasta)'

Caused by:
  Process `GTF_FILTER (genome.fasta)` terminated with an error exit status (126)


Command executed:

  filter_gtf.py \
      --gtf genome.gtf \
      --fasta genome.fasta \
      --prefix genome
  
  cat <<-END_VERSIONS > versions.yml
  "GTF_FILTER":
      python: $(python --version | sed 's/Python //g')
  END_VERSIONS

Command exit status:
  126

Command output:
  (empty)

Command error:
  Unable to find image 'quay.io/biocontainers/python:3.9--1' locally
  3.9--1: Pulling from biocontainers/python
  c1a16a04cedd: Pulling fs layer
  4ca545ee6d5d: Pulling fs layer
  5f7a6762e5ca: Pulling fs layer
  4ca545ee6d5d: Verifying Checksum
  4ca545ee6d5d: Download complete
  c1a16a04cedd: Verifying Checksum
  c1a16a04cedd: Download complete
  c1a16a04cedd: Pull complete
  4ca545ee6d5d: Pull complete
  5f7a6762e5ca: Verifying Checksum
  5f7a6762e5ca: Download complete
  5f7a6762e5ca: Pull complete
  Digest: sha256:d97d2b329b4e44d2e07a9737ba348b185d6a47f34fba0ef301d44d11669cac60
  Status: Downloaded newer image for quay.io/biocontainers/python:3.9--1
  /bin/bash: line 9: .command.run: Permission denied

Work dir:
  /home/runner/work/rnaseq/rnaseq/~/tests/448cc38f562b3a594f13242d3d0c44c2/work/7d/4d683d77a616e740296a285633eb72

Container:
  quay.io/biocontainers/python:3.9--1

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

 -- Check '/home/runner/work/rnaseq/rnaseq/~/tests/448cc38f562b3a594f13242d3d0c44c2/meta/nextflow.log' file for details
Execution cancelled -- Finishing pending tasks before exit
Nextflow stderr:

Nextflow stdout:

N E X T F L O W  ~  version 24.12.0-edge
Launching `/home/runner/work/rnaseq/rnaseq/.nf-test-9c4ced86a381759a0b9f50e2adfbb44c.nf` [drunk_pesquet] DSL2 - revision: 9609345052
[cf/edb799] Submitted process > GTF_FILTER (genome.fasta)
ERROR ~ Error executing process > 'GTF_FILTER (genome.fasta)'

Caused by:
  Process `GTF_FILTER (genome.fasta)` terminated with an error exit status (126)


Command executed:

  touch genome.filtered.gtf
  
  cat <<-END_VERSIONS > versions.yml
  "GTF_FILTER":
      python: $(python --version | sed 's/Python //g')
  END_VERSIONS

Command exit status:
  126

Command output:
  (empty)

Command error:
  /bin/bash: line 9: .command.run: Permission denied

Work dir:
  /home/runner/work/rnaseq/rnaseq/~/tests/9c4ced86a381759a0b9f50e2adfbb44c/work/cf/edb799d013fe502651aee5fb488280

Container:
  quay.io/biocontainers/python:3.9--1

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

 -- Check '/home/runner/work/rnaseq/rnaseq/~/tests/9c4ced86a381759a0b9f50e2adfbb44c/meta/nextflow.log' file for details
Execution cancelled -- Finishing pending tasks before exit
Nextflow stderr: