Skip to content
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

fix: bug in pon workflow #1412

Merged
merged 2 commits into from
Mar 7, 2024
+4 −3
Merged

fix: bug in pon workflow #1412

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
a88c85f
fix container name
mathiasbio Mar 6, 2024
ced9e66
changelog
mathiasbio Mar 6, 2024
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/snakemake_rules/pon/cnvkit_create_pon.rule
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ rule create_target:
target_bed = cnv_dir + "target.bed",
offtarget_bed = cnv_dir + "antitarget.bed"
singularity:
Path(singularity_image, "varcall_cnvkit.sif").as_posix()
Path(singularity_image, "cnvkit.sif").as_posix()
benchmark:
Path(benchmark_dir, "cnvkit.targets.tsv").as_posix()
shell:
Expand All @@ -27,7 +27,7 @@ rule create_coverage:
target_cnn = cnv_dir + "{sample}.targetcoverage.cnn",
antitarget_cnn = cnv_dir + "{sample}.antitargetcoverage.cnn"
singularity:
Path(singularity_image, "varcall_cnvkit.sif").as_posix()
Path(singularity_image, "cnvkit.sif").as_posix()
benchmark:
Path(benchmark_dir, "cnvkit_{sample}.coverage.tsv").as_posix()
shell:
Expand All @@ -43,7 +43,7 @@ rule create_reference:
output:
ref_cnn = pon_reference
singularity:
Path(singularity_image, "varcall_cnvkit.sif").as_posix()
Path(singularity_image, "cnvkit.sif").as_posix()
benchmark:
Path(benchmark_dir, "cnvkit.reference.tsv").as_posix()
shell:
Expand Down
1 change: 1 addition & 0 deletions CHANGELOG.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,7 @@ Fixed:
^^^^^^
* ASCAT-Ngs container https://github.com/Clinical-Genomics/BALSAMIC/pull/1395
* bcftools in manta_tumor_normal uses correct column for tumor read filtering https://github.com/Clinical-Genomics/BALSAMIC/pull/1400
* Corrected name of CNVkit container in the CNVkit PON creation workflow https://github.com/Clinical-Genomics/BALSAMIC/pull/1412


[13.0.1]
Expand Down
Loading