Skip to content

chore: lower headjob mem #1641

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
mathiasbio wants to merge 3 commits into
base: develop
Choose a base branch
from
Open

chore: lower headjob mem #1641

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
b2d8cb2
Merge branch 'develop' of github.com:Clinical-Genomics/BALSAMIC into …
mathiasbio Nov 25, 2025
9009cc2
500M headjob
mathiasbio Nov 25, 2025
dd2877d
changelog
mathiasbio Nov 26, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 3 additions & 3 deletions BALSAMIC/constants/workflow_profile/config.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -99,7 +99,7 @@ set-resources:
runtime: 360
bedtools_pad_bedfile:
mem_mb: min(230000, 1000 * attempt)
runtime: 20
runtime: 40
vardict_sort:
mem_mb: min(230000, 15000 * attempt)
runtime: 30
Expand Down Expand Up @@ -200,10 +200,10 @@ set-resources:
runtime: 350
mem_mb: min(230000, 40000 * attempt)
bedtools_sort_and_merge:
runtime: 20
runtime: 40
mem_mb: min(230000, 400 * attempt)
extend_short_bedregions:
runtime: 20
runtime: 40
mem_mb: min(230000, 400 * attempt)
create_coverage:
runtime: 360
Expand Down
2 changes: 1 addition & 1 deletion BALSAMIC/models/sbatchsubmitter.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -71,7 +71,7 @@ def _build_sbatch_header(self) -> str:
f"#SBATCH --output={self.log_path}/BALSAMIC_snakemake_submit.{self.case_id}.%j.out",
f"#SBATCH --error={self.log_path}/BALSAMIC_snakemake_submit.{self.case_id}.%j.err",
"#SBATCH --ntasks=1",
"#SBATCH --mem=5G",
"#SBATCH --mem=500M",
f"#SBATCH --time={self.max_run_hours}:00:00",
f"#SBATCH --qos={self.qos}",
"#SBATCH --cpus-per-task=1",
Expand Down
2 changes: 2 additions & 0 deletions CHANGELOG.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,8 @@ Added:

Changed:
^^^^^^^^
* increased runtime for a couple of small rules https://github.com/Clinical-Genomics/BALSAMIC/pull/1641
* decreased memory for headjobs to 500mb https://github.com/Clinical-Genomics/BALSAMIC/pull/1641

Removed:
^^^^^^^^
Expand Down
Loading