Test run fails out of the box with docker (touch: cannot touch '.command.trace': Permission denied)

[gldlv]

Description of the bug

I installed the latest version of docker on Ubuntu LTS 22.04 and it fails to run the test pipeline.

Note 1 / Nextflow was installed within a mamba-created environment here. But the same happens when I install nextflow as a root user

Note 2 / The test pipeline runs correctly with conda

Command used and terminal output

(nf) delevoye@delevoye-HP-ZBook-Fury-16-G10-Mobile-Workstation-PC:~$ docker run hello-world

Hello from Docker!
This message shows that your installation appears to be working correctly.

To generate this message, Docker took the following steps:
 1. The Docker client contacted the Docker daemon.
 2. The Docker daemon pulled the "hello-world" image from the Docker Hub.
    (amd64)
 3. The Docker daemon created a new container from that image which runs the
    executable that produces the output you are currently reading.
 4. The Docker daemon streamed that output to the Docker client, which sent it
    to your terminal.

To try something more ambitious, you can run an Ubuntu container with:
 $ docker run -it ubuntu bash

Share images, automate workflows, and more with a free Docker ID:
 https://hub.docker.com/

For more examples and ideas, visit:
 https://docs.docker.com/get-started/
(nf) delevoye@delevoye-HP-ZBook-Fury-16-G10-Mobile-Workstation-PC:~$ nextflow run pgscatalog/pgsc_calc -profile test,docker

 N E X T F L O W   ~  version 24.04.2

Launching `https://github.com/pgscatalog/pgsc_calc` [friendly_woese] DSL2 - revision: cc3a26ecde [main]



------------------------------------------------------
  pgscatalog/pgsc_calc v2.0.0-beta-gcc3a26e
------------------------------------------------------
Core Nextflow options
  revision                  : main
  runName                   : friendly_woese
  containerEngine           : docker
  launchDir                 : /home/delevoye
  workDir                   : /home/delevoye/work
  projectDir                : /home/delevoye/.nextflow/assets/pgscatalog/pgsc_calc
  userName                  : delevoye
  profile                   : test,docker
  configFiles               : 

Input/output options
  input                     : /home/delevoye/.nextflow/assets/pgscatalog/pgsc_calc/assets/examples/samplesheet.csv
  scorefile                 : /home/delevoye/.nextflow/assets/pgscatalog/pgsc_calc/assets/examples/scorefiles/PGS001229_22.txt
  outdir                    : /home/delevoye/.nextflow/assets/pgscatalog/pgsc_calc/results

Reference options
  ref_samplesheet           : /home/delevoye/.nextflow/assets/pgscatalog/pgsc_calc/assets/ancestry/reference.csv
  ld_grch37                 : /home/delevoye/.nextflow/assets/pgscatalog/pgsc_calc/assets/ancestry/high-LD-regions-hg19-GRCh37.txt
  ld_grch38                 : /home/delevoye/.nextflow/assets/pgscatalog/pgsc_calc/assets/ancestry/high-LD-regions-hg38-GRCh38.txt
  ancestry_checksums        : /home/delevoye/.nextflow/assets/pgscatalog/pgsc_calc/assets/ancestry/checksums.txt

Compatibility options
  target_build              : GRCh37

Max job request options
  max_cpus                  : 2
  max_memory                : 6.GB
  max_time                  : 6.h

Other parameters
  config_profile_name       : Test profile
  config_profile_description: Minimal test dataset to check pipeline function

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use pgscatalog/pgsc_calc for your analysis please cite:

* The Polygenic Score Catalog
  https://doi.org/10.1101/2024.05.29.24307783
  https://doi.org/10.1038/s41588-021-00783-5

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/pgscatalog/pgsc_calc/blob/main/CITATIONS.md

executor >  local (2)
[34/d0ce04] process > PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES (1)                        [100%] 1 of 1, failed: 1 ✘
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELBIM                         -
[9d/3234b8] process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_RELABELPVAR (cineca chromosome 22) [  0%] 0 of 1
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF                                -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_VARIANTS                                      -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:MATCH:MATCH_COMBINE                                       -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:PLINK2_SCORE                                  -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:SCORE_AGGREGATE                               -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:REPORT:SCORE_REPORT                                       -
[-        ] process > PGSCATALOG_PGSCCALC:PGSCCALC:DUMPSOFTWAREVERSIONS                                      -
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Error executing process > 'PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES (1)'

Caused by:
  Process `PGSCATALOG_PGSCCALC:PGSCCALC:INPUT_CHECK:COMBINE_SCOREFILES (1)` terminated with an error exit status (1)


Command executed:

  pgscatalog-combine -s PGS001229_22.txt             -t GRCh37             -o scorefiles.txt.gz             -l log_scorefiles.json             -v             -v
  
  cat <<-END_VERSIONS > versions.yml
  COMBINE_SCOREFILES:
      pgscatalog.core: $(echo $(python -c 'import pgscatalog.core; print(pgscatalog.core.__version__)'))
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  touch: cannot touch '.command.trace': Permission denied

Work dir:
  /home/delevoye/work/34/d0ce0453c92a65d4b8f4848a6aa1dd

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

 -- Check '.nextflow.log' file for details
ERROR ~ ERROR: Matching subworkflow failed

 -- Check '.nextflow.log' file for details

(nf) delevoye@delevoye-HP-ZBook-Fury-16-G10-Mobile-Workstation-PC:~$ docker --version
Docker version 27.0.3, build 7d4bcd8
(nf) delevoye@delevoye-HP-ZBook-Fury-16-G10-Mobile-Workstation-PC:~$ nextflow -v
nextflow version 24.04.2.5914
(nf) delevoye@delevoye-HP-ZBook-Fury-16-G10-Mobile-Workstation-PC:~$ which docker
/usr/local/bin/docker
(nf) delevoye@delevoye-HP-ZBook-Fury-16-G10-Mobile-Workstation-PC:~$ which nextflow
/home/delevoye/miniforge3/envs/nf/bin/nextflow

Relevant files

No response

System information

Nextflow version : 24.04.02 Executor: local OS: Ubuntu LTS 22.04 Hardware: Desktop Container : Docker Version of pgs_calcv 2.0.0-beta-gcc3a26e

[nebfield]

It might help to install Nextflow using your normal user outside of a conda environment.

$ curl -s https://get.nextflow.io | bash 

and then run the Nextflow executable that gets created:

$ ./nextflow run pgscatalog/pgsc_calc -profile test,docker

If this works for you, then you could move the executable to your home bin directory.

[nebfield]

Closing this now. Please feel free to create a new issue if you still experience problems.