Threads via variable.

[rajwanir]

1. Renames the max_threads parameter to cores (925d5c6).
2. Uses workflow.cores to define threads in rules convert_bcf_to_plink_bed and merge_gtc_to_bcf_batches instead of hardcoded 44 (acc7df7).

The max_threads seems inaccessible at the rule level. The cores does the trick. They both seem synonymous anyway per the Snakemake documentation.

Please let me know if you encounter any issues. Thanks.

[jaamarks]

ACK - will test.

[jaamarks]

LGTM

Testing confirms the logging information is now correct, accurately displaying the allocated threads based on workflow.cores inherited from the generic_slurm and ccad2 cluster profiles. good job

[jaamarks]

The cgrq queue is not available to all users; access must be granted explicitly. If a user lacks access, it's unclear to me whether this would result in an error or simply bypassing the queue. For example, @carynwillis does not have access, so would the whole pipeline fail or continue without using this queue?

---

To be clear, I do quite like this feature.

Maybe there is a way we could implemented an option in the config with which you could specify if you have access to additional partitions (e.g., cgrq) over the defaults. Else just use the default partitions given in the cluster profiles. And might be useful to make generic enough so that you could do this with Biowulf too.
What do you think?

[jaamarks]

I like this idea. I am still seeing the same behavior as before. That is, there is a discrepancy in the number of threads shown allocated in the job-specific log vs the whole-pipeline log. Here is what I see.

• invocation: cgr submit --ccad2
• commit: git rev-parse HEAD # 070cd684b8
• sacct:

$ sacct -j 2154090 --format=JobID,JobName,Partition,AllocCPUs,State,ExitCode
JobID           JobName  Partition  AllocCPUS      State ExitCode
------------ ---------- ---------- ---------- ---------- --------
2154090      convert_b+       cgrq          8  COMPLETED      0:0
2154090.bat+      batch                     8  COMPLETED      0:0

• job-specific log:

Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 40
Rules claiming more threads will be scaled down.
Select jobs to execute...

rule convert_bcf_to_plink_bed:
    input: sample_level/samples.bcf
    output: sample_level/samples.bed, sample_level/samples.bim, sample_level/samples.fam
    log: sample_level/samples.log
    jobid: 0
    benchmark: benchmarks/convert_bcf_to_plink_bed.500.tsv
    threads: 40
    resources: mem_mb=1059, disk_mb=18132, tmpdir=/tmp, time_hr=1

• whole-pipeline log:

[Fri Feb 21 13:15:28 2025]
rule convert_bcf_to_plink_bed:                                                                                              
    input: sample_level/samples.bcf
    output: sample_level/samples.bed, sample_level/samples.bim, sample_level/samples.fam
    log: sample_level/samples.log                                                                                           
    jobid: 2
    benchmark: benchmarks/convert_bcf_to_plink_bed.500.tsv
    threads: 8
    resources: tmpdir=/tmp, mem_mb=1059, time_hr=1
 plink2 --allow-extra-chr 0 --keep-allele-order --double-id --bcf sample_level/samples.bcf --update-sex /tmp/tmpl2_fp7jj --output-chr 26 --split-par hg38 --make-pgen --out sample_level/bcf2plink  --memory 1059 --threads 8 ;plink2 --pfile sample_level/bcf2plink --make-pgen --sort-vars --out sample_level/bcf2plink-sorted --threads 8 --memory 1059  ;plink2 --pfile sample_level/bcf2plink-sorted --make-bed --out sample_level/samples --threads 8 --memory 1059 ;rm sample_level/bcf2plink.{pgen,psam,pvar,log} sample_level/bcf2plink-sorted.{pgen,psam,pvar,log} /tmp/tmpl2_fp7jj                            
Submitted job 2 with external jobid '2154090'.

[jaamarks]

I just submitted another test with invocation cgr submit --slurm to see what the logs look like when using the generic_slurm cluster profile. Should be cores/threads 8.

[jaamarks]

I can confirm that when I use the invocation cgr submit --slurm both the whole-pipeline log and the job-specific log show that the number of threads allocated is 8.