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snakemake / snakemake-executor-plugin-tes

A Snakemake executor plugin for submitting jobs via GA4GH TES.
MIT License
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All files including Snakefile, conda env files, rule script files, output files must be in the same working directory: workflow vs /local_folder_in_cnt/.snakemake/tmp.9r3j7va6/snakejob.make_regenie_pheno.6.sh #15

Closed lvarin closed 2 days ago

lvarin commented 2 weeks ago

Hello,

I am trying to execute the workflow located at: https://github.com/Ax-Sch/asso_smk_smpl/blob/main/workflow/Snakefile using a TES server but I am getting an error:

host: 95edcc33a4a4
Building DAG of jobs...
Unable to retrieve additional files from git. This is not a git repository.
Uploading source archive to storage provider...
Using shell: /usr/bin/bash
Provided remote nodes: 1
Conda environments: ignored
Singularity containers: ignored
Job stats:
job                      count
---------------------  -------
PCA_for_cov                  1
all                          1
convert_imputed_vcf          1
generate_qq_plots            1
make_regenie_cov             1
make_regenie_pheno           1
merge_regenie_results        1
prune_common                 1
regenie_association          1
total                        9

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

[Wed Sep 18 13:05:01 2024]
rule make_regenie_pheno:
    input: s3://test-snakemake/input_files/samples_phenotypes.tsv (retrieve from storage)
    output: s3://test-snakemake/results/pheno_cov/pheno.pheno (send to storage)
    jobid: 6
    reason: Missing output files: s3://test-snakemake/results/pheno_cov/pheno.pheno (send to storage)
    resources: tmpdir=<TBD>, cpus=1, mem_mb=5000, mem_mib=4769, time_job=720, partition=medium

WorkflowError:
WorkflowError:
    All files including Snakefile, conda env files, rule script files, output files must be in the same working directory: workflow vs /local_folder_in_cnt/.snakemake/tmp.9r3j7va6/snakejob.make_regenie_pheno.6.sh

I am a bit lost. Could you help?

lvarin commented 2 days ago

The issue was that the Snakefile was in the workflow folder. Apparently this plugin does not like that, but I do not know enough of Snakemake to know who is right here 😄 . Without this plugin, the location workflow was a supported one by Snakemake.