Skip to content

fix: Small tweaks #31

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
fgvieira wants to merge 2 commits into
base: main
Choose a base branch
from
Open

fix: Small tweaks #31

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
8c5a696
Small tweaks
fgvieira Aug 27, 2026
4fca393
Update DAGs
fgvieira Aug 27, 2026
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
0 ...d/stats/reports/multiqc_taxon.upload.flag → ...ted/temp/reports/multiqc_taxon.upload.log
View file
Open in desktop
File renamed without changes.
2 changes: 1 addition & 1 deletion examples/euk_prok_virus/.tests/unit/test_multiqc_taxon_upload.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@ def test_multiqc_taxon_upload(conda_prefix):
"python",
"-m",
"snakemake",
"stats/reports/multiqc_taxon.upload.flag",
"temp/reports/multiqc_taxon.upload.log",
"--snakefile",
"../../workflow/Snakefile",
"-f",
Expand Down
2,310 changes: 1,155 additions & 1,155 deletions examples/euk_prok_virus/dag.svg
View file
Open in desktop
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
70 changes: 35 additions & 35 deletions examples/euk_prok_virus/filegraph.svg
View file
Open in desktop
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
72 changes: 36 additions & 36 deletions examples/euk_prok_virus/rulegraph.svg
View file
Open in desktop
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
580 changes: 325 additions & 255 deletions pixi.lock
View file
Open in desktop

Large diffs are not rendered by default.

20 changes: 9 additions & 11 deletions workflow/Snakefile
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -87,18 +87,16 @@ from snakemake.logging import logger

base_dir = Path(workflow.basedir).resolve(strict=True)
repo = git.Repo(base_dir.parent)
tag_recent = [
[tag.name, commit.hexsha]
for commit in repo.iter_commits()
for tag in repo.tags
if commit.hexsha == tag.commit.hexsha
][0]
# Latest reachable tag
tag_recent = repo.git.describe("--tags", "--abbrev=0")
logger.info(
"Git commit: {commit_hash} [{tag_flag}{commit_tag}] ({commit_time})".format(
commit_hash=repo.head.commit.hexsha,
commit_time=repo.head.commit.committed_datetime.strftime("%Y-%m-%d %H:%M:%S"),
tag_flag="" if tag_recent[1] == repo.head.commit.hexsha else ">",
commit_tag=tag_recent[0],
tag_flag=(
"" if repo.commit(tag_recent).hexsha == repo.head.commit.hexsha else ">"
),
commit_tag=tag_recent,
)
)
config_json = json.dumps(config, sort_keys=True).encode("utf-8")
Expand Down Expand Up @@ -150,7 +148,7 @@ rule multiqc_trim_upload:
rules.target_trim.input,
zip=rules.multiqc_trim.output.data,
output:
"stats/reports/multiqc_trim.upload.flag",
temp("temp/reports/multiqc_trim.upload.log"),
log:
"logs/reports/multiqc_trim.upload.log",
localrule: True
Expand Down Expand Up @@ -199,7 +197,7 @@ use rule multiqc_trim_upload as multiqc_derep_upload with:
rules.target_derep.input,
zip=rules.multiqc_derep.output.data,
output:
touch("stats/reports/multiqc_derep.upload.flag"),
temp("temp/reports/multiqc_derep.upload.log"),
log:
"logs/reports/multiqc_derep.upload.log",

Expand Down Expand Up @@ -244,6 +242,6 @@ use rule multiqc_trim_upload as multiqc_taxon_upload with:
rules.target_taxon.input,
zip=rules.multiqc_taxon.output.data,
output:
touch("stats/reports/multiqc_taxon.upload.flag"),
temp("temp/reports/multiqc_taxon.upload.log"),
log:
"logs/reports/multiqc_taxon.upload.log",
Loading