From 5758e8de0c5c592b0ef812f4ede52fdc7305aed5 Mon Sep 17 00:00:00 2001 From: lcoombe Date: Fri, 11 Oct 2024 12:06:50 -0700 Subject: [PATCH 1/2] Ensure grep takes lines that start with # only --- ntroot_run_pipeline.smk | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/ntroot_run_pipeline.smk b/ntroot_run_pipeline.smk index 819edd7..04a3509 100644 --- a/ntroot_run_pipeline.smk +++ b/ntroot_run_pipeline.smk @@ -139,7 +139,7 @@ rule sort_vcf_input: benchmark = f"{time_command} sort_vcf_{input_vcf_basename}.time", cat_cmd = "gunzip -c" if f"{input_vcf}".endswith(".gz") else "cat" shell: - """{params.benchmark} sh -c '(echo "##fileformat=VCFv4.2" ; {params.cat_cmd} {input.vcf} |grep -v "#" |sort -k1,1 -k2,2n) > {output.vcf_sorted}'""" + """{params.benchmark} sh -c '(echo "##fileformat=VCFv4.2" ; {params.cat_cmd} {input.vcf} |grep -v "^#" |sort -k1,1 -k2,2n) > {output.vcf_sorted}'""" rule sort_vcf_l: input: vcf = l @@ -148,7 +148,7 @@ rule sort_vcf_l: benchmark = f"{time_command} sort_vcf_l.time", cat_cmd = "gunzip -c" if f"{l}".endswith(".gz") else "cat" shell: - """{params.benchmark} sh -c "(echo '##fileformat=VCFv4.2' ; {params.cat_cmd} {input.vcf} | awk '\$5 !~ /^ {output}" """ + """{params.benchmark} sh -c "(echo '##fileformat=VCFv4.2' ; {params.cat_cmd} {input.vcf} | awk '\$5 !~ /^ {output}" """ rule bedtools_intersect: input: From 1501e3d5ca18724ea5609ded494a2d7842a936bf Mon Sep 17 00:00:00 2001 From: lcoombe Date: Fri, 11 Oct 2024 12:13:08 -0700 Subject: [PATCH 2/2] Pin python --- azure-pipelines.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/azure-pipelines.yml b/azure-pipelines.yml index 3b020ca..de31389 100644 --- a/azure-pipelines.yml +++ b/azure-pipelines.yml @@ -18,7 +18,7 @@ jobs: displayName: Create Anaconda environment - script: | source activate ntroot_CI - conda install --yes --name ntroot_CI -c conda-forge -c bioconda python mamba + conda install --yes --name ntroot_CI -c conda-forge -c bioconda python=3.12 mamba mamba install --yes -c conda-forge -c bioconda meson ninja snakemake perl 'ntedit>=2.0.1' samtools bedtools mamba install --yes -c conda-forge -c bioconda libcxx llvm meson ninja btllib zlib boost cmake compilers displayName: Install Conda packages @@ -58,7 +58,7 @@ jobs: - script: | source activate ntroot_CI - mamba install --yes -c conda-forge -c bioconda python + mamba install --yes -c conda-forge -c bioconda python=3.12 mamba install --yes -c conda-forge -c bioconda snakemake perl 'ntedit>=2.0.1' samtools bedtools mamba install --yes -c conda-forge -c bioconda libcxx llvm meson ninja btllib zlib boost cmake compilers displayName: Install Conda packages