Cache fail when specific conditions are met

Bug report

The scenario: A pipeline step succeeds (but on a retry attempt), then the pipeline continues and fails on a later step, but then on pipeline resume, the on-retry-succeeded step is not picked up, and that step runs again. This isn’t always the case; it only happens when that step had attempted to re-run in a previous execution, at least once (i.e., having a relevant work folder for that module/step created). Relevant blog post here

Expected behavior and actual behavior

Expected behaviour: The on-retry-succeeded step is properly cached, and pipeline executes resumes from where it left
Actual behaviour: Even though it completed successfully on a retry, it won't be cached, and re-runs.

Steps to reproduce the problem

1. clone proteinfamilies
2. alter conf/test.config here to make it fail on the 1st attempt, but pass on the 2nd:

withName: 'NFCORE_PROTEINFAMILIES:PROTEINFAMILIES:FAA_SEQFU_SEQKIT:SEQKIT_SEQ' {
       memory = { task.attempt == 1 ? 1.MB : 2.GB } // memory = { 1.4.GB * task.attempt }
       time   = { 2.m    * task.attempt }
   }

3. Your executor has to be able to stop a process when it requires excess memory than what was defined (or use docker), so I used slurm with this slurm.config:

profiles {
   slurm {
       executor {
           name              = "slurm"
           queueSize         = 100
           queueGlobalStatus = true

       }
       workDir = "/path/to/work_proteinfamilies_cache_test/"
       process {
           queue  = 'standard'
           cache  = 'lenient'
       }
       params {
           // Boilerplate options
           outdir = "${launchDir}/results"
       }
   }
}

4. Run with command:
   NXF_VER=25.10.4 nextflow run proteinfamilies -c conf/slurm.config -profile singularity,test,slurm -resume
5. As soon as the work folder for SEQKIT_SEQ is created, kill the pipeline (ctrl +C) (this step is improtant, otherwise if it passes on the 2nd attempt, without pre-failing at least once, the cache will work properly)
6. Resume the pipeline with the same command, and wait for SEQKIT_SEQ to complete successfully on its 2nd attempt.
7. Kill the pipeline again.
8. Resume the pipeline with the same command. Verdict: SEQKIT_SEQ will begin to run again, while SEQFU_STATS_BEFORE, which has run in parallel and completed on its first attempt, will have been cached properly.

Program output

Irrelevant

Environment

• Nextflow version: NXF_VER=25.10.4
• Java version:

openjdk 21.0.3 2024-04-16 LTS
OpenJDK Runtime Environment Temurin-21.0.3+9 (build 21.0.3+9-LTS)
OpenJDK 64-Bit Server VM Temurin-21.0.3+9 (build 21.0.3+9-LTS, mixed mode, sharing)

• Operating system: Linux, slurm
• Bash version: GNU bash, version 5.1.8(1)-release (x86_64-redhat-linux-gnu)

Additional context

Dummy bot PR with attempt to pinpoint the bug in the codebase here

Reproduce with the proteinfamilies pipeline using conf/test.config and conf/slurm.config and the Nextflow command given in the report. Read PR #6882 for the attempted diagnosis, then trace the retry and resume behavior; done means SEQKIT_SEQ is cached after succeeding on its second attempt and is not rerun on the next resume.