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Fix for input VCFs which have # character in non-header lines #31

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Merged
lcoombe merged 2 commits into from
Oct 11, 2024
Merged

Fix for input VCFs which have # character in non-header lines #31

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5758e8d
Ensure grep takes lines that start with # only
lcoombe Oct 11, 2024
1501e3d
Pin python
lcoombe Oct 11, 2024
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4 changes: 2 additions & 2 deletions azure-pipelines.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down
4 changes: 2 additions & 2 deletions ntroot_run_pipeline.smk
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Expand Up @@ -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
Expand All @@ -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 !~ /^</' | grep -v '#' |sort -k1,1 -k2,2n) > {output}" """
"""{params.benchmark} sh -c "(echo '##fileformat=VCFv4.2' ; {params.cat_cmd} {input.vcf} | awk '\$5 !~ /^</' | grep -v '^#' |sort -k1,1 -k2,2n) > {output}" """

rule bedtools_intersect:
input:
Expand Down