This PR will merge current version of joss_manuscript to the master branch to bring it up to date, and then we will cut a new release. Note that joss_manuscript branch will not be deleted and it will continue to serve as the branch to be used for JOSS reviews.
This PR includes several PRs as follows:
67
70
72
73
75
80
Changelog corresponding to this PR is listed below:
2023-06-22 Manavalan Gajapathy
Refactors CLI script to accounting for user's environment specific slurm args requirements when submitting job to
slurm (#76)
Removes CLI option --rerun_failed and instead configures it via snakemake-slurm profile
(src/slurm/slurm_profile/config.yaml)
Removes --subtasks_slurm option and --snakemake_slurm as they were redundant
Checks if tool dependencies are available in user environment.
Adds time resource to configs/snakemake_cluster_config.json
Removes PR trigger from system testing github actions.
Tests if singularity is working as expected in user machine
2023-05-31 Manavalan Gajapathy
Adds system testing as github actions workflow
2023-05-18 Manavalan Gajapathy
Constructs snakemake's sbatch command using args and values from cluster config file supplied via
--cluster_config.
Updates doc to include cluster config as a requirement
2023-05-09 Manavalan Gajapathy
Adds a verification step in the CLI wrapper script to check if the file/dirpaths to be mounted to singularity already
exist as expected (#71)
Resolves dirpaths of datasets in the workflow config file to obtain their full path
2023-04-10 Manavalan Gajapathy
Refactors snakemake pipeline to fully run jobs in direct singularity containers. No more creation of conda environment
using singularity containers! (#69)
2023-04-04 Manavalan Gajapathy
Retires use of cheaha-specific env variable $USER_SCRATCH
Auto-creates user-provided dir structures for --outdir, --tmp_dir, and --log_dir
Please fill in the checklist below and comment as needed.
[x] Was code modified? Briefly describe. Yes, but changes were already reviewed as part of earlier PRs
[x] Was documentation modified? Briefly describe. Yes, but changes were already reviewed as part of earlier PRs
[x] Is this a bug-fix? Briefly describe. Yes, but changes were already reviewed as part of earlier PRs
[x] Is this a feature addition? Briefly describe. Yes, but changes were already reviewed as part of earlier PRs
[x] Did you modify QuaC-Watch config file? If so, did you modify multiqc template
configs/multiqc_config_template.jinja2 and script src/quac_watch/create_mutliqc_configs.py as necessary? No
[x] Did you perform system-level testing manually as described in master readme doc? Did it pass completely? If not why? Yes
[x] Updated Changelog.md file with change logs in recommended format?
Pull request
This PR will merge current version of
joss_manuscriptto themasterbranch to bring it up to date, and then we will cut a new release. Note thatjoss_manuscriptbranch will not be deleted and it will continue to serve as the branch to be used for JOSS reviews.This PR includes several PRs as follows:
67
70
72
73
75
80
Changelog corresponding to this PR is listed below:
2023-06-22 Manavalan Gajapathy
--rerun_failedand instead configures it via snakemake-slurm profile (src/slurm/slurm_profile/config.yaml)--subtasks_slurm optionand--snakemake_slurmas they were redundanttimeresource toconfigs/snakemake_cluster_config.json2023-05-31 Manavalan Gajapathy
2023-05-18 Manavalan Gajapathy
sbatchcommand using args and values from cluster config file supplied via--cluster_config.2023-05-09 Manavalan Gajapathy
2023-04-10 Manavalan Gajapathy
2023-04-04 Manavalan Gajapathy
--outdir,--tmp_dir, and--log_dirPlease fill in the checklist below and comment as needed.
configs/multiqc_config_template.jinja2and scriptsrc/quac_watch/create_mutliqc_configs.pyas necessary? NoChangelog.mdfile with change logs in recommended format?Anything else reviewer should know?