Merge branch 'dev' into 387-ped-phasing2

Author: tetedange13

CHANGELOG.md

@@ -34,16 +34,19 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#954](https://github.com/genomic-medicine-sweden/nallo/pull/954) - Changed to topic versions in `HIPHASE`
 - [#957](https://github.com/genomic-medicine-sweden/nallo/pull/957) - Moved requirement of `--somalier_sites` to `--skip_sex_check` instead of `--skip_alignment` since it is not needed for the alignment
 - [#959](https://github.com/genomic-medicine-sweden/nallo/pull/959) - Updated PR template
+- [#964](https://github.com/genomic-medicine-sweden/nallo/pull/957) - Limit `--snv_calling_processes` to `1` for sentieon due to issues with duplicated variants (see #926)
 
 ### Removed
 
 - [#950](https://github.com/genomic-medicine-sweden/nallo/pull/950) - Stray TODO statement
 - [#951](https://github.com/genomic-medicine-sweden/nallo/pull/951) - Removed unused `SOMALIER_PED` import
+- [#961](https://github.com/genomic-medicine-sweden/nallo/pull/961) - Removed `docs/CITATIONS.md` since the information is available in the MultiQC report
 
 ### Fixed
 
 - [#939](https://github.com/genomic-medicine-sweden/nallo/pull/939) - Fixed nf-test not triggering on changes to `conf/`, which can affect pipeline outputs
 - [#960](https://github.com/genomic-medicine-sweden/nallo/pull/960) - Fixed crash when preparing for chromograph while skipping annotating variants
+- [#964](https://github.com/genomic-medicine-sweden/nallo/pull/957) - Fix sentieon spanning deletion calls crashing most_severe_consequence script due to missing CSQ
 
 ### Parameters
 

README.md

@@ -112,4 +112,4 @@ This pipeline uses code and infrastructure developed and maintained by the [nf-c
 >
 > _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).
 
-An extensive list of references for the tools used by the pipeline can be found in the [`docs/CITATIONS.md`](docs/CITATIONS.md) file.
+An extensive list of references for the tools used by the pipeline can be found in the Software Versions section of the MultiQC report generated with the pipeline.

conf/modules/annotate_snvs.config

@@ -29,7 +29,11 @@ process {
         ext.args = { [
             '--output-type z',
             '--write-index=tbi',
-            "${params.pre_vep_snv_filter_expression}"
+            "${params.pre_vep_snv_filter_expression}",
+            // Drop spanning deletion ("*") alleles from Sentieon.
+            // They are redundant (covered by upstream DELs) and break VEP annotation,
+            // causing downstream MSC/PLI scripts to crash.
+            params.variant_caller == 'sentieon' ? '-e \'ALT="*"\'' : ''
         ].join(" ") }
     }
 

docs/CITATIONS.md

@@ -151,7 +151,7 @@ Workflow options specific to genomic-medicine-sweden/nallo
 | `methbat_female_label` | Label used for female samples in methbat profile. | `string` | FEMALE |  |  |
 | `modkit_modified_bases` | Modkit modified bases, separated by space. E.g. '5mC 5hmC' | `string` | 5mC |  |  |
 | `alignment_processes` | If alignment_processes is bigger than 1, input files will be split and aligned in parallel to reduce processing time. | `integer` | 8 |  |  |
-| `snv_calling_processes` | If snv_calling_processes is bigger than 1, short variant calling will be done in parallel to reduce processing time. | `integer` | 13 |  |  |
+| `snv_calling_processes` | If snv_calling_processes is bigger than 1, short variant calling will be done in parallel to reduce processing time. Must be `1` when `--snv_caller sentieon` is used. | `integer` | 13 |  |  |
 | `vep_cache_version` | VEP cache version | `integer` | 110 |  |  |
 | `vep_plugin_files` | Path to a CSV/TSV/JSON/YAML file with vep_files as header, and then paths to vep plugin files. Paths to pLI_values.txt and LoFtool_scores.txt are required. | `string` |  |  |  |
 | `force_sawfish_joint_call_single_samples` | Force sawfish to run joint-call on single samples instead of all samples from the same family. This effectively causes SVDB to merge the samples into family VCFs instead. | `boolean` |  |  |  |

docs/parameters.md

@@ -188,6 +188,8 @@ This subworkflow depends on the alignment subworkflow, and requires PARs.
 
 By default the pipeline uses [DeepVariant](https://github.com/google/deepvariant) for long-read SNV calling. To enable [Sentieon DNAscope Long Read](https://github.com/Sentieon/sentieon-cli/blob/main/docs/dnascope-longread.md), set `--snv_caller sentieon`. Make the Sentieon license available by adding a base64-encoded license string to the Nextflow secrets store (`nextflow secrets set SENTIEON_LICENSE_BASE64 ...`) or by exporting the same variable before running the pipeline.
 
+When using Sentieon, `--snv_calling_processes` must be set to `1`.
+
 | Parameter     | Description                                                                                                                                              |
 | ------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | `par_regions` | A BED file with PAR regions (e.g. [GRCh38_PAR.bed](https://storage.googleapis.com/deepvariant/case-study-testdata/GRCh38_PAR.bed)). Used by DeepVariant. |

docs/usage.md

@@ -9,7 +9,6 @@ nav:
   - Usage: usage.md
   - Output: output.md
   - Parameters: parameters.md
-  - Citations: CITATIONS.md
 
 theme:
   name: material