From ad40ad38d80d55b57e006831c5e2c770631ab865 Mon Sep 17 00:00:00 2001 From: hassanfa Date: Mon, 14 Jun 2021 12:21:04 +0200 Subject: [PATCH 1/3] add vcf2cytosure as pip dependency --- BALSAMIC/containers/annotate/annotate.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/BALSAMIC/containers/annotate/annotate.yaml b/BALSAMIC/containers/annotate/annotate.yaml index 9421b9d8b..f39d020b4 100644 --- a/BALSAMIC/containers/annotate/annotate.yaml +++ b/BALSAMIC/containers/annotate/annotate.yaml @@ -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 From 009f04b4d44afbc772e65a5bfe78729c3d8c29e7 Mon Sep 17 00:00:00 2001 From: hassanfa Date: Mon, 14 Jun 2021 12:55:30 +0200 Subject: [PATCH 2/3] ignore pip installs in conda env --- BALSAMIC/utils/cli.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/BALSAMIC/utils/cli.py b/BALSAMIC/utils/cli.py index 576d2c499..768b37e23 100644 --- a/BALSAMIC/utils/cli.py +++ b/BALSAMIC/utils/cli.py @@ -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: @@ -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") \ No newline at end of file + LOG.info(f"File {pon_sym_file} exists, skipping") From d32a04fbe182de97ade2f5526e1eafaa0c5d184c Mon Sep 17 00:00:00 2001 From: hassanfa Date: Mon, 14 Jun 2021 12:57:06 +0200 Subject: [PATCH 3/3] changelog --- CHANGELOG.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index d5f2b35e6..757b1a27c 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -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: