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seppinho wants to merge 4 commits into from
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Improve compression by writing no intermediate files #68

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99419fd
Improve compression by writing no intermediate files
seppinho Dec 8, 2025
c4bf0af
Set tests to static Nextflow version
seppinho Dec 8, 2025
3ca4cd7
Update 7zip to latest version
seppinho Dec 8, 2025
736585a
Revert change due to missing zip codecs
seppinho Dec 9, 2025
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2 changes: 1 addition & 1 deletion .github/workflows/ci-tests.yml
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Expand Up @@ -24,7 +24,7 @@ jobs:
- name: Setup Nextflow
uses: nf-core/setup-nextflow@v1
with:
version: "latest-edge"
version: "25.10.0"

- name: Install nf-test
run: |
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5 changes: 2 additions & 3 deletions modules/local/compression/compression_encryption_vcf.nf
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Expand Up @@ -29,12 +29,11 @@ process COMPRESSION_ENCRYPTION_VCF {
bcftools concat --threads ${task.cpus} -n ${info_joined} -o ${info_name} -Oz

# concat dosage files and update header
bcftools concat --threads ${task.cpus} -n ${imputed_joined} -o intermediate_${imputed_name} -Oz
echo "##mis_pipeline=${workflow.manifest.version}" > add_header.txt
echo "##mis_phasing=${params.phasing.engine}" >> add_header.txt
echo "##mis_panel=${panel_version}" >> add_header.txt
bcftools annotate --threads ${task.cpus} -h add_header.txt intermediate_${imputed_name} -o ${imputed_name} -Oz
rm intermediate_${imputed_name}
bcftools concat --threads ${task.cpus} -n ${imputed_joined} -Oz | \
bcftools annotate --threads ${task.cpus} -h add_header.txt -Oz -o ${imputed_name}

# write meta files
if [[ "${params.imputation.meta}" = true ]]
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