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Merge branch 'bam-telomere-estimation' of github.com:nf-core/modules into bam-telomere-estimation
2 parents b15db6b + 3bb5e48 commit 2d9103b

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‎modules/nf-core/bcftools/annotate/environment.yml‎

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@@ -5,6 +5,6 @@ channels:
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- bioconda
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dependencies:
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# renovate: datasource=conda depName=bioconda/htslib
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- bioconda::htslib=1.22.1
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- bioconda::htslib=1.23.1
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# renovate: datasource=conda depName=bioconda/bcftools
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- bioconda::bcftools=1.22
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- bioconda::bcftools=1.23.1

‎modules/nf-core/bcftools/annotate/main.nf‎

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Original file line numberDiff line numberDiff line change
@@ -4,8 +4,8 @@ process BCFTOOLS_ANNOTATE {
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conda "${moduleDir}/environment.yml"
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container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
7-
? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/47/474a5ea8dc03366b04df884d89aeacc4f8e6d1ad92266888e7a8e7958d07cde8/data'
8-
: 'community.wave.seqera.io/library/bcftools_htslib:0a3fa2654b52006f'}"
7+
? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/0b/0b4d52ca9a56d07be3f78a12af654e5116f5112908dba277e6796fd9dfb83fe5/data'
8+
: 'community.wave.seqera.io/library/bcftools_htslib:1.23.1--9f08ec665533d64a'}"
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input:
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tuple val(meta), path(input), path(index), path(annotations), path(annotations_index), path(columns), path(header_lines), path(rename_chrs)

‎modules/nf-core/bcftools/annotate/tests/main.nf.test.snap‎

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@@ -27,16 +27,16 @@
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[
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"BCFTOOLS_ANNOTATE",
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"bcftools",
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"1.22"
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"1.23.1"
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]
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]
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}
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],
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"timestamp": "2026-03-20T17:54:34.686330171",
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.10.3"
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},
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"timestamp": "2026-02-27T15:29:19.618749659"
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"nf-test": "0.9.4",
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"nextflow": "25.10.2"
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}
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},
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"sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index_tbi": {
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"content": [
@@ -66,16 +66,16 @@
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[
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"BCFTOOLS_ANNOTATE",
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"bcftools",
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"1.22"
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"1.23.1"
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]
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]
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}
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],
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"timestamp": "2026-03-20T17:53:48.564151048",
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.10.3"
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},
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"timestamp": "2026-02-27T15:28:43.350060834"
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"nf-test": "0.9.4",
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"nextflow": "25.10.2"
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}
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},
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"sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index_csi": {
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"content": [
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[
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"BCFTOOLS_ANNOTATE",
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"bcftools",
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"1.22"
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"1.23.1"
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]
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]
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}
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],
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"timestamp": "2026-03-20T17:53:38.715013376",
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.10.3"
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},
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"timestamp": "2026-02-27T15:28:36.101003418"
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"nf-test": "0.9.4",
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"nextflow": "25.10.2"
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}
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},
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"sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index_tbi - stub": {
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"content": [
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[
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"BCFTOOLS_ANNOTATE",
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"bcftools",
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"1.22"
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"1.23.1"
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]
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]
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}
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],
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"timestamp": "2026-03-20T17:54:52.117082881",
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.10.3"
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},
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"timestamp": "2026-02-27T15:29:34.19449127"
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"nf-test": "0.9.4",
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"nextflow": "25.10.2"
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}
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},
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"sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index_csi - stub": {
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"content": [
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[
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"BCFTOOLS_ANNOTATE",
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"bcftools",
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"1.22"
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"1.23.1"
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]
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]
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}
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],
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"timestamp": "2026-03-20T17:54:43.025430475",
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.10.3"
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},
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"timestamp": "2026-02-27T15:29:26.927815399"
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"nf-test": "0.9.4",
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"nextflow": "25.10.2"
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}
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},
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"sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index": {
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"content": [
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[
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"BCFTOOLS_ANNOTATE",
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"bcftools",
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"1.22"
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"1.23.1"
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]
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]
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}
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],
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"timestamp": "2026-03-20T17:53:29.538130871",
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.10.3"
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},
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"timestamp": "2026-02-27T15:28:28.891823681"
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"nf-test": "0.9.4",
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"nextflow": "25.10.2"
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}
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},
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"sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - stub": {
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"content": [
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[
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"BCFTOOLS_ANNOTATE",
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"bcftools",
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"1.22"
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"1.23.1"
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]
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]
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}
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],
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"timestamp": "2026-03-20T17:54:25.811513664",
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.10.3"
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},
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"timestamp": "2026-02-27T15:29:12.400301681"
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"nf-test": "0.9.4",
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"nextflow": "25.10.2"
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}
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},
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"sarscov2 - [vcf, [], annotation, annotation_tbi], [], header, [] - bcf_output": {
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"content": [
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[
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"BCFTOOLS_ANNOTATE",
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"bcftools",
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"1.22"
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"1.23.1"
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]
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]
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}
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],
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"timestamp": "2026-03-20T17:53:58.362749653",
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.10.3"
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},
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"timestamp": "2026-02-27T15:28:50.375384421"
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"nf-test": "0.9.4",
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"nextflow": "25.10.2"
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}
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},
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"sarscov2 - [vcf, [], annotation, annotation_tbi], [], [], [] - vcf_output": {
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"content": [
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[
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"BCFTOOLS_ANNOTATE",
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"bcftools",
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"1.22"
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"1.23.1"
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]
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]
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}
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],
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"timestamp": "2026-03-20T17:53:20.809593889",
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.10.3"
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},
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"timestamp": "2026-02-27T15:28:21.320211288"
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"nf-test": "0.9.4",
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"nextflow": "25.10.2"
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}
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},
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"sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_output": {
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"content": [
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[
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"BCFTOOLS_ANNOTATE",
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"bcftools",
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"1.22"
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"1.23.1"
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]
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]
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}
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],
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"timestamp": "2026-03-20T17:53:13.16941797",
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.10.3"
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},
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"timestamp": "2026-02-27T15:28:13.274072987"
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"nf-test": "0.9.4",
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"nextflow": "25.10.2"
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}
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},
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"sarscov2 - [vcf, [], annotation, annotation_tbi], [], header, rename_chrs - vcf_gz_index": {
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"content": [
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[
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"BCFTOOLS_ANNOTATE",
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"bcftools",
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"1.22"
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"1.23.1"
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]
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]
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}
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],
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"timestamp": "2026-03-20T17:54:16.229056032",
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.10.3"
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},
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"timestamp": "2026-02-27T15:29:05.094685409"
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"nf-test": "0.9.4",
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"nextflow": "25.10.2"
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}
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},
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"sarscov2 - [vcf, [], annotation, annotation_tbi], columns, [], [] - bcf_output": {
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"content": [
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[
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"BCFTOOLS_ANNOTATE",
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"bcftools",
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"1.22"
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"1.23.1"
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]
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]
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}
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],
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"timestamp": "2026-03-20T17:54:07.560097761",
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.10.3"
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},
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"timestamp": "2026-02-27T15:28:57.906382655"
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"nf-test": "0.9.4",
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"nextflow": "25.10.2"
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}
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}
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}

‎modules/nf-core/bcftools/call/environment.yml‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -5,6 +5,6 @@ channels:
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- bioconda
66
dependencies:
77
# renovate: datasource=conda depName=bioconda/htslib
8-
- bioconda::htslib=1.22.1
8+
- bioconda::htslib=1.23.1
99
# renovate: datasource=conda depName=bioconda/bcftools
10-
- bioconda::bcftools=1.22
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- bioconda::bcftools=1.23.1

‎modules/nf-core/bcftools/call/main.nf‎

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Original file line numberDiff line numberDiff line change
@@ -4,8 +4,8 @@ process BCFTOOLS_CALL {
44

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conda "${moduleDir}/environment.yml"
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container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
7-
? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/47/474a5ea8dc03366b04df884d89aeacc4f8e6d1ad92266888e7a8e7958d07cde8/data'
8-
: 'community.wave.seqera.io/library/bcftools_htslib:0a3fa2654b52006f'}"
7+
? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/0b/0b4d52ca9a56d07be3f78a12af654e5116f5112908dba277e6796fd9dfb83fe5/data'
8+
: 'community.wave.seqera.io/library/bcftools_htslib:1.23.1--9f08ec665533d64a'}"
99

1010
input:
1111
tuple val(meta), path(vcf), path(index)

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