fix: checkpoints inside modules are overwritten

[fgvieira]

Description

When including two modules with checkpoints (or the same module twice with different prefixes), only the checkpoint of the last loaded module is used.

In the example here, the checkpoint somestep is run twice the module test_b (under prefix b) while it should be run one for each prefix (as exemplified under expected-results).

Assuming unrestricted shared filesystem usage.
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Job stats:
job                 count
----------------  -------
all                     1
test_a_aggregate        1
test_b_aggregate        1
test_b_somestep         2
total                   5

Select jobs to execute...
Execute 1 jobs...

[Wed Apr 24 13:36:30 2024]
localcheckpoint test_b_somestep:
    output: b/somestep/a.txt
    jobid: 2
    reason: Missing output files: <TBD>
    wildcards: sample=a
    resources: tmpdir=/tmp
DAG of jobs will be updated after completion.

[Wed Apr 24 13:36:31 2024]
Finished job 2.
1 of 5 steps (20%) done
Select jobs to execute...
Execute 1 jobs...

[Wed Apr 24 13:36:31 2024]
localrule test_a_alt_intermediate:
    output: a/alt/a.txt
    jobid: 8
    reason: Missing output files: a/alt/a.txt
    wildcards: sample=a
    resources: tmpdir=/tmp

[Wed Apr 24 13:36:31 2024]
Finished job 8.
2 of 6 steps (33%) done
Select jobs to execute...
Execute 1 jobs...

[Wed Apr 24 13:36:31 2024]
localcheckpoint test_b_somestep:
    output: b/somestep/b.txt
    jobid: 4
    reason: Missing output files: <TBD>
    wildcards: sample=b
    resources: tmpdir=/tmp
DAG of jobs will be updated after completion.
[...]

QC

• The PR contains a test case for the changes or the changes are already covered by an existing test case.
• The documentation (docs/) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake).

[sonarcloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
No data about Coverage
No data about Duplication

See analysis details on SonarCloud