config.yaml

31 lines · skills/pacsomatic/config.yaml at 5f2bc03

1# Operator reference only. run_pacsomatic.py does not load this file.

2# CLI defaults are authoritative; use --help for all supported options.

3pipeline:

4 name: nf-core/pacsomatic

5 repo_url: https://github.com/nf-core/pacsomatic.git

6 default_version: "24c84cb371b0339c1d65a4de9451671945e19772"

7 status: development-commit-no-release-tag

8runtime:

9 conda_env: pacsomatic-nextflow

10 use_current_path: false

11 create_conda_env: false

12 conda_env_file: "" # Must be supplied explicitly to create an environment.

13execution:

14 profile: singularity

15 executor: local # Outer launcher only; pbs means PBS Pro/OpenPBS.

16 cpus: 16

17 memory_gb: 64

18 walltime: "48:00" # Helper always interprets this as hours:minutes.

19 queue: ""

20 project: ""

21 job_name: pacsomatic

22outputs:

23 samplesheet_name: samplesheet.csv

24 generated_params_name: pacsomatic.params.generated.yaml

25 default_workdir_name: work

26validation:

27 require_exactly_one_reference_mode: true

28 require_distinct_nonempty_bam_files: true

29 min_nextflow: "24.04.2"

30 min_java_major: 17

31 max_java_major: 26