Merge pull request #359 from fellen31/patch

Patch release 0.3.1
genomic-medicine-sweden · Sep 11, 2024 · f0abc01 · f0abc01
2 parents 1453238 + af199d7
commit f0abc01
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,12 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v0.3.1 - [2024-09-11]
+
+### `Fixed`
+
+- [#359](https://github.com/genomic-medicine-sweden/nallo/pull/359) - Fixed single sample SNV VCFs containing variants from all samples, resuling in a large number of empty GT calls
+
 ## v0.3.0 - [2024-08-29]
 
 ### `Added`

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,6 +1,6 @@
 report_comment: >
 
-  This report has been generated by the <a href="https://github.com/genomic-medicine-sweden/nallo/releases/tag/0.3.0" target="_blank">genomic-medicine-sweden/nallo</a>
+  This report has been generated by the <a href="https://github.com/genomic-medicine-sweden/nallo/releases/tag/0.3.1" target="_blank">genomic-medicine-sweden/nallo</a>
   analysis pipeline.
 
 report_section_order:

diff --git a/conf/modules/general.config b/conf/modules/general.config
@@ -49,6 +49,7 @@ process {
 
     withName: '.*:NALLO:BCFTOOLS_PLUGINSPLIT' {
         ext.args = [
+            '-i \'GT="alt"\'',
             '--output-type z',
             '--write-index=tbi'
         ].join(' ')

diff --git a/docs/output.md b/docs/output.md
@@ -306,8 +306,11 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ
 
 - `{outputdir}/databases/echtvar/encode/{project}/`
   - `*.zip`: Database with AF and AC for all samples run
-- `{outputdir}/snvs/{single_sample,multi_sample/{project}/`
-  - `*_snvs_annotated*.vcf.gz`: VCF with annotated variants
+- `{outputdir}/snvs/{single_sample/{sample}/`
+  - `*_snvs_annotated*.vcf.gz`: VCF with annotated variants with alternative genotypes from a certain sample
+  - `*_snvs_annotated*.vcf.gz.tbi`: Index of the corresponding VCF file
+- `{outputdir}/snvs/multi_sample/{project}/`
+  - `*_snvs_annotated*.vcf.gz`: VCF with annotated variants from all samples
   - `*_snvs_annotated*.vcf.gz.tbi`: Index of the corresponding VCF file
 - `{outputdir}/snvs/stats/single_sample/`
   - `*.stats.txt`: Variant statistics
@@ -327,10 +330,10 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ
 <summary>Output files</summary>
 
 - `{outputdir}/snvs/single_sample/{sample}/`
-  - `{sample}_snv_annotated_ranked.vcf.gz`: VCF with annotated and ranked variants
+  - `{sample}_snv_annotated_ranked.vcf.gz`: VCF with annotated and ranked variants with alternative genotypes from a certain sample
   - `{sample}_snv_annotated_ranked.vcf.gz.tbi`: Index of the corresponding VCF file
 - `{outputdir}/snvs/multi_sample/{project}/`
-  - `{project}_snv_annotated_ranked.vcf.gz`: VCF with annotated and ranked variants
+  - `{project}_snv_annotated_ranked.vcf.gz`: VCF with annotated and ranked variants from all samples
   - `{project}_snv_annotated_ranked.vcf.gz.tbi`: Index of the corresponding VCF file
   </details>
 

diff --git a/nextflow.config b/nextflow.config
@@ -288,7 +288,7 @@ manifest {
     description     = """Long-read variant calling pipeline"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '0.3.0'
+    version         = '0.3.1'
     doi             = ''
 }