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Add vcf2cytosure as dependency #650

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merged 3 commits into from
Jun 14, 2021
Merged

Add vcf2cytosure as dependency #650

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ad40ad3
add vcf2cytosure as pip dependency
hassanfa Jun 14, 2021
009f04b
ignore pip installs in conda env
hassanfa Jun 14, 2021
d32a04f
changelog
hassanfa Jun 14, 2021
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2 changes: 2 additions & 0 deletions BALSAMIC/containers/annotate/annotate.yaml
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Expand Up @@ -9,3 +9,5 @@ dependencies:
- bcftools>=1.10
- vcfanno=0.3.2
- gxx_linux-64
- pip:
- git+https://github.com/NBISweden/vcf2cytosure@0.5.1
4 changes: 3 additions & 1 deletion BALSAMIC/utils/cli.py
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Expand Up @@ -447,6 +447,8 @@ def get_bioinfo_tools_version(bioinfo_tools: dict,
with open(yaml_file, "r") as f:
packages = yaml.safe_load(f).get("dependencies")
for p in packages:
if isinstance(p, dict):
continue
name = p.split("=")[0]
version = "=".join(p.split("=")[1:])
if name not in bioinfo_tools:
Expand Down Expand Up @@ -621,4 +623,4 @@ def create_pon_fastq_symlink(pon_fastqs, symlink_dir):
LOG.info(f"Creating symlink {fastq_name} -> {pon_sym_file}")
os.symlink(pon_fastq, pon_sym_file)
except FileExistsError:
LOG.info(f"File {pon_sym_file} exists, skipping")
LOG.info(f"File {pon_sym_file} exists, skipping")
1 change: 1 addition & 0 deletions CHANGELOG.rst
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Expand Up @@ -7,6 +7,7 @@ Added:
* samtools flagstats and stats to workflow and MultiQC
* PASSed SV calls from Manta to clinical delivery
* An extra filter to VarDict tumor-normal to remove variants with STATUS=Germline, all other will still be around
* Added ``vcf2cytosure``` to annotate container


Changed:
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