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Update CHANGELOG.md
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CHANGELOG.md

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@@ -27,7 +27,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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- Saltshaker for downstream processing of mitochondrial SV calls from MitoSAlt [#775](https://github.com/nf-core/raredisease/pull/775)
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- Env variable NXF_SINGULARITY_NEW_PID_NAMESPACE = false to accommodate hisat2 running with latest Nextflow and Singularity [#775](https://github.com/nf-core/raredisease/pull/775)
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- Parameter `exclude_alt` to filter alignments to alt/unplaced contigs after alignment using samtools view, retaining only primary chromosomes (GRCh37: 1-22,X,Y,MT / GRCh38: chr1-chr22,chrX,chrY,chrM). Note that enabling this will restrict variant calling to these chromosomes [#803](https://github.com/nf-core/raredisease/pull/803)]
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- Run UPD_SITES, UPD_REGIONS, and CHROMOGRAPH for UPD only when analysis type is WGS [#805](https://github.com/nf-core/raredisease/pull/805)
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### `Changed`
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@@ -58,6 +57,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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- Include mitochonrdial SV calls in combined SV vcf, change call_sv output directory structure to remove mitochondria/ and genome/ [#775](https://github.com/nf-core/raredisease/pull/775)
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- Remove Qualimap and Haplogrep3 as they were made redundant by Picard and VerifyBamID2 [#801](https://github.com/nf-core/raredisease/pull/801)
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- Remove env variable NXF_SINGULARITY_NEW_PID_NAMESPACE from the config since this has to be set outside the subworkflow [#804](https://github.com/nf-core/raredisease/pull/804)
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- Run UPD_SITES, UPD_REGIONS, and CHROMOGRAPH for UPD only when analysis type is WGS [#806](https://github.com/nf-core/raredisease/pull/806)
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### `Fixed`
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