Skip to content

feat: add wrapper for rbt vcf_fix_iupac_alleles #1209

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
wants to merge 6 commits into
base: master
Choose a base branch
from
Open

feat: add wrapper for rbt vcf_fix_iupac_alleles #1209

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
e2ccf1e
Added wrapper
fgvieira Apr 5, 2023
d5357ed
Added input and output descr
fgvieira Apr 5, 2023
951f0f7
Fix test
fgvieira Apr 5, 2023
ef2f74a
removed index and added BCF test
fgvieira Apr 28, 2023
33b0a10
Bump bcftools version
fgvieira Apr 28, 2023
612926d
Merge branch 'master' into vcf_fix_iupac_alleles
fgvieira Jan 1, 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
8 changes: 8 additions & 0 deletions bio/rbt/vcf_fix_iupac_alleles/environment.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,8 @@
channels:
- conda-forge
- bioconda
- nodefaults
dependencies:
- rust-bio-tools =0.42.0
- bcftools =1.17
- snakemake-wrapper-utils =0.5.3
Comment on lines +6 to +8
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

💡 Verification agent

❓ Verification inconclusive

Unpin secondary dependencies; keep only the main tool fixed

Wrapper guidelines recommend pinning only the primary software (rust-bio-tools) and letting Bioconda resolve compatible versions for helper tools. Exact pins for bcftools and snakemake-wrapper-utils increase the risk of conflicts with other wrappers and make future updates harder.

   - rust-bio-tools =0.42.0
-  - bcftools =1.17
-  - snakemake-wrapper-utils =0.5.3
+  - bcftools
+  - snakemake-wrapper-utils

(Spacing around the = is already correct – nice job).

Unpin secondary dependencies in environment.yaml

Only the primary tool (rust-bio-tools) should be version‐pinned; helper packages (bcftools, snakemake-wrapper-utils) can be left unpinned so Bioconda can resolve compatible versions.

Please update in bio/rbt/vcf_fix_iupac_alleles/environment.yaml (lines 6–8):

   - rust-bio-tools =0.42.0
-  - bcftools =1.17
-  - snakemake-wrapper-utils =0.5.3
+  - bcftools
+  - snakemake-wrapper-utils
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
- rust-bio-tools =0.42.0
- bcftools =1.17
- snakemake-wrapper-utils =0.5.3
- rust-bio-tools =0.42.0
- bcftools
- snakemake-wrapper-utils
🤖 Prompt for AI Agents 
In bio/rbt/vcf_fix_iupac_alleles/environment.yaml lines 6 to 8, unpin the
versions of the secondary dependencies bcftools and snakemake-wrapper-utils by
removing the version numbers (=1.17 and =0.5.3) so that only rust-bio-tools
remains version-pinned. This allows Bioconda to resolve compatible versions for
the helper packages.

10 changes: 10 additions & 0 deletions bio/rbt/vcf_fix_iupac_alleles/meta.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,10 @@
name: rbt vcf-fix-iupac-alleles
description: |
Convert any IUPAC codes in alleles into Ns (in order to comply with VCF 4 specs).
url: https://github.com/rust-bio/rust-bio-tools
authors:
- Filipe G. Vieira
input:
- VCF
output:
- VCF/BCF
22 changes: 22 additions & 0 deletions bio/rbt/vcf_fix_iupac_alleles/test/Snakefile
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,22 @@

rule vcf_fix_iupac_alleles_vcf:
input:
"{file}.vcf.gz",
output:
vcf="results/{file}.vcf.gz",
log:
"logs/{file}.vcf.log",
params:
extra="",
threads: 1
resources:
mem_mb=1024,
wrapper:
"master/bio/rbt/vcf_fix_iupac_alleles"


use rule vcf_fix_iupac_alleles_vcf as vcf_fix_iupac_alleles_bcf with:
output:
bcf="results/{file}.bcf",
log:
"logs/{file}.bcf.log",
Binary file added bio/rbt/vcf_fix_iupac_alleles/test/homo_sapiens-chrMT.vcf.gz
View file
Open in desktop
Binary file not shown.
18 changes: 18 additions & 0 deletions bio/rbt/vcf_fix_iupac_alleles/wrapper.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,18 @@
__author__ = "Filipe G. Vieira"
__copyright__ = "Copyright 2023, Filipe G. Vieira"
__license__ = "MIT"

import tempfile
from snakemake.shell import shell
from snakemake_wrapper_utils.bcftools import get_bcftools_opts


bcftools_opts = get_bcftools_opts(snakemake, parse_ref=False)
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
extra = snakemake.params.get("extra", "")


with tempfile.TemporaryDirectory() as tmpdir:
shell(
"(rbt vcf-fix-iupac-alleles {extra} < {snakemake.input[0]} | bcftools sort --temp-dir {tmpdir} {bcftools_opts}) {log}"
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Why the sort? rbt vcf-fix-iupac-alleles does not change the order of the records.

Copy link
Collaborator Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

The main idea was to allow for automatic output on any format (bcf, vcf, vcf.gz).
Since I was using it to standardize resources (known variation from ensembl), I thought that sort would be a nice-to-have (just to be sure the output was sorted) and the extra runtime would be ok since it would only be run once.

But I can also remove it (or switch to view), if you prefer to keep the wrapper more general.

Copy link
Collaborator Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Ping @johanneskoester

)
15 changes: 14 additions & 1 deletion test.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6121,13 +6121,26 @@ def test_verifybamid2():


@skip_if_not_modified
def test_collapse_reads_to_fragments_bam():
def test_rbt_collapse_reads_to_fragments_bam():
run(
"bio/rbt/collapse_reads_to_fragments-bam",
["snakemake", "--cores", "1", "--use-conda", "-F"],
)


@skip_if_not_modified
def test_rbt_vcf_fix_iupac_alleles():
run(
"bio/rbt/vcf_fix_iupac_alleles",
["snakemake", "--cores", "1", "--use-conda", "-F", "results/homo_sapiens-chrMT.vcf.gz"],
)

run(
"bio/rbt/vcf_fix_iupac_alleles",
["snakemake", "--cores", "1", "--use-conda", "-F", "results/homo_sapiens-chrMT.bcf"],
)


@skip_if_not_modified
def test_gatk_mutect2_calling_meta():
run(
Expand Down