Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

--keep-going ignored by MissingInputException #3306

Open
jorgenriseth opened this issue Feb 20, 2025 · 0 comments
Open

--keep-going ignored by MissingInputException #3306

jorgenriseth opened this issue Feb 20, 2025 · 0 comments
Labels
bug Something isn't working

Comments

@jorgenriseth
Copy link

jorgenriseth commented Feb 20, 2025

Snakemake version
v8.28.0

Describe the bug
--keep-going does not keep going if there is a MissingInputException.

Given a list of desired outputs created from independent dags(as shown in image), I would expect snakemake to keep running the workflows that are not affected by the missing files. This does not seems to be the case.

Image

Minimal example
Snakefile

rule testrule:
  input:
    "{name}.txt"
  output:
    "{name}.out"
  shell:
    "touch {output}"

Execution:

touch {a,b}.txt
snakemake {a,b,c}.out --keep-going

Logs

Building DAG of jobs...
MissingInputException in rule testrule in file /home/jorgen/snakeminimalex/Snakefile, line 1:
Missing input files for rule testrule:
    output: c.out
    wildcards: name=c
    affected files:
        c.txt

DAG when run only for existing files shows independent "DAGs" (single rule for this example).

touch {a,b}.txt
snakemake {a,b}.out --dag | dot -Tpdf > dag.pdf

Image

@jorgenriseth jorgenriseth added the bug Something isn't working label Feb 20, 2025
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
bug Something isn't working
Projects
None yet
Development

No branches or pull requests

1 participant