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mashehumashehu
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add sarek release
1 parent af34379 commit 0b9b7cf

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Lines changed: 158 additions & 4 deletions

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‎bin/pipelines.json.js‎

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@@ -334,7 +334,6 @@ export const writePipelinesJson = async () => {
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// remove empty values from releases (usually from draft releases)
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releases = releases.filter((release) => release.tag_name !== "" && release.draft === false);
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console.log(`Releases for ${name}:`, releases.map((release) => release.tag_name));
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// remove releases that are already in the pipelines.json file
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const pipelineIndex = pipelines.remote_workflows.findIndex((workflow) => workflow.name === name);
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let new_releases = releases;

‎public/pipelines.json‎

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@@ -52103,10 +52103,10 @@
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"avatar_url": "https://avatars.githubusercontent.com/u/21218078?v=4"
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}
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],
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"released_after_tools": false,
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"released_after_tools": true,
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"head_sha": "b97952e5bac68d5deb93d4a3349a45f146be9830",
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"last_release_is_head": false,
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"last_release_vs_default_compare_url": "https://github.com/nf-core/sarek/compare/b97952e5bac68d5deb93d4a3349a45f146be9830...4bd2948f98c5bf7b785c91cf6708fffccab25467",
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"last_release_is_head": true,
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"last_release_vs_default_compare_url": "https://github.com/nf-core/sarek/compare/b97952e5bac68d5deb93d4a3349a45f146be9830...b97952e5bac68d5deb93d4a3349a45f146be9830",
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"commits_to_dev": 30,
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"is_DSL2": true,
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"has_nf_test": true,
@@ -52132,6 +52132,161 @@
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},
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"dev_uses_params_block": false,
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"releases": [
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{
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"tag_name": "3.9.0",
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"published_at": "2026-06-30T11:34:06Z",
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"tag_sha": "b97952e5bac68d5deb93d4a3349a45f146be9830",
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"has_schema": true,
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"doc_files": [
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"docs/output.md",
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"docs/usage.md",
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"docs/usage/variantcalling/interpretation.md",
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"docs/usage/variantcalling/introduction.md",
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"docs/usage/variantcalling/sarek.md",
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"docs/usage/variantcalling/theory.md"
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],
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"components": {
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"modules": [
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"ascat",
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"bbmap_bbsplit",
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"bcftools_annotate",
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"bcftools_concat",
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"bcftools_isec",
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"bcftools_merge",
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"bcftools_mpileup",
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"bcftools_norm",
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"bcftools_sort",
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"bcftools_stats",
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"bcftools_view",
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"bwa_index",
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"bwa_mem",
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"bwamem2_index",
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"bwamem2_mem",
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"cat_cat",
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"cat_fastq",
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"cnvkit_antitarget",
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"cnvkit_batch",
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"cnvkit_call",
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"cnvkit_export",
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"cnvkit_genemetrics",
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"cnvkit_reference",
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"controlfreec_assesssignificance",
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"controlfreec_freec",
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"controlfreec_freec2bed",
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"controlfreec_freec2circos",
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"controlfreec_makegraph2",
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"deepvariant_rundeepvariant",
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"dragmap_align",
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"dragmap_hashtable",
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"ensemblvep_download",
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"ensemblvep_vep",
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"fastp",
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"fastqc",
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"fgbio_callmolecularconsensusreads",
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"fgbio_copyumifromreadname",
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"fgbio_fastqtobam",
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"fgbio_groupreadsbyumi",
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"freebayes",
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"gatk4_applybqsr",
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"gatk4_applyvqsr",
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"gatk4_baserecalibrator",
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"gatk4_calculatecontamination",
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"gatk4_cnnscorevariants",
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"gatk4_createsequencedictionary",
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"gatk4_estimatelibrarycomplexity",
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"gatk4_filtermutectcalls",
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"gatk4_filtervarianttranches",
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"gatk4_gatherbqsrreports",
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"gatk4_gatherpileupsummaries",
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"gatk4_genomicsdbimport",
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"gatk4_genotypegvcfs",
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"gatk4_getpileupsummaries",
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"gatk4_haplotypecaller",
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"gatk4_intervallisttobed",
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"gatk4_learnreadorientationmodel",
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"gatk4_markduplicates",
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"gatk4_mergemutectstats",
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"gatk4_mergevcfs",
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"gatk4_mutect2",
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"gatk4_variantrecalibrator",
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"gatk4spark_applybqsr",
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"gatk4spark_baserecalibrator",
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"gatk4spark_markduplicates",
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"gawk",
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"goleft_indexcov",
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"gunzip",
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"lofreq_callparallel",
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"manta_germline",
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"manta_somatic",
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"manta_tumoronly",
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"mosdepth",
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"msisensor2_msi",
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"msisensorpro_msisomatic",
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"msisensorpro_scan",
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"multiqc",
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"muse_call",
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"muse_sump",
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"ngscheckmate_ncm",
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"parabricks_fq2bam",
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"rbt_vcfsplit",
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"samtools_bam2fq",
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"samtools_collatefastq",
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"samtools_convert",
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"samtools_faidx",
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"samtools_index",
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"samtools_merge",
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"samtools_mpileup",
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"samtools_stats",
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"samtools_view",
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"sentieon_applyvarcal",
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"sentieon_bwamem",
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"sentieon_dedup",
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"sentieon_dnamodelapply",
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"sentieon_dnascope",
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"sentieon_gvcftyper",
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"sentieon_haplotyper",
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"sentieon_tnscope",
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"sentieon_varcal",
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"snpeff_download",
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"snpeff_snpeff",
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"snpsift_annmem",
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"snpsift_annmemcreate",
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"spring_decompress",
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"strelka_germline",
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"strelka_somatic",
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"svdb_merge",
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"tabix_bgziptabix",
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"tabix_tabix",
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"tiddit_sv",
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"untar",
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"unzip",
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"varlociraptor_callvariants",
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"varlociraptor_estimatealignmentproperties",
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"varlociraptor_preprocess",
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"vcflib_vcffilter",
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"vcftools",
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"yte"
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],
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"subworkflows": [
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"bam_ngscheckmate",
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"cache_download_ensemblvep_snpeff",
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"utils_annotation_cache",
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"utils_nextflow_pipeline",
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"utils_nfcore_pipeline",
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"utils_nfschema_plugin",
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"vcf_annotate_snpeff"
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]
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},
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"nextflow_version": "!>=25.10.2",
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"nf_core_version": "3.5.1",
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"plugins": [
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"nf-core-utils@0.4.0",
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"nf-fgbio@1.0.0",
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"nf-prov@1.7.0",
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"nf-schema@2.7.2"
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],
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"co2footprint_files": null
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},
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{
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"tag_name": "3.8.1",
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"published_at": "2026-02-12T08:50:37Z",

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