diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml index 19d6c5f..bb5d480 100644 --- a/.github/workflows/ci-tests.yml +++ b/.github/workflows/ci-tests.yml @@ -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: | diff --git a/modules/local/compression/compression_encryption_vcf.nf b/modules/local/compression/compression_encryption_vcf.nf index eb4a106..fb8dd2c 100644 --- a/modules/local/compression/compression_encryption_vcf.nf +++ b/modules/local/compression/compression_encryption_vcf.nf @@ -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 ]]