v0.3.0 Fantastic Frituur

Added

1. Added the samplesheet to the pipeline output as OUTDIR/samplesheet.csv
2. Added the --bedpe parameter. This makes the pipeline output BEDPE files alongside the VCF files.
3. Added parallelization on SV type to the delly flow
4. Added a --gtf parameter for annotation of gene and transcript overlap using gatk SVAnnotate.
5. Added StrVCTVRE as a new annotation tool

Changes

1. Updated the pipeline to be compatible with future nextflow updates
2. Removed the max_cpus, max_memory and max_time parameter in favor of the new built-in resourceLimits
3. Replaced nf-validation with nf-schema
4. Updated to nf-core template v3.2.0
5. Fixed language server errors
6. Removed the old output publishing code and used the new workflow output definitions instead
7. Bumped the minimal nextflow version to 25.10.0
8. Changed the --annotations_filter parameter to a --filter parameter. This parameter takes an argument of bcftools filter to filter the resulting VCFs.
9. Removed the --delly_sv_types parameter.
10. Moved all wisecondorx and qdnaseq outputs to a separate directory in each sample output.
11. Bumped all annotation modules to the latest versions
12. Reworked the annotation structure to a per tool structure. Specify the annotations tools you want to run with --annotate_tools. This parameter takes a comma-separated list of tool names (options: vep, vcfanno, svannotate, strvctvre or all (=> all tools))
13. Updated to nf-core template v3.5.1
14. Removed AnnotSV from the pipeline
15. Removed the small_variants field from the samplesheet. Small variant VCFs are no longer used in the pipeline

Fixed

1. Fail the pipeline when the sex determination failed. This will now prompt the user to add the sex to the samplesheet so the pipeline doesn't do any wrong assumptions
2. Fixed the Jasmine module output VCFs being empty when no variants have been merged. This file now contains the header of one of the input VCFs
3. Fixed a map issue when the sex field is empty in the samplesheet

v0.2.0 Mighty Manneken Pis

Added

1. Added keyword shortcuts to the --callers parameter (these can also be used as comma-separated entries to the parameter):
   • all: Use all callers available in the pipeline
   • sv: Use all SV callers available in the pipeline
   • cnv: Use all CNV callers available in the pipeline
   • rre: Use all repeat region expansion callers available in the pipeline
2. Added the possibilty to annotate on HPO terms. Add the right HPO terms to the samplesheet in the hpo field

Changes

1. Updated all WisecondorX modules to version 1.2.6 and added the --seed argument to WisecondorX predict
2. Removed support for the phenotypes VEP plugin. Common VEP plugin support will be added later
3. Made the main workflow pluggable, making it possible to use this pipeline in a meta pipeline
4. Updated all modules to their latest version

Fixed

1. The smoove outputs are now correct when using --output_callers

v0.1.0 - Amazing Atomium

Initial release of nf-cmgg/structural, created with the nf-core template.

This is a beta release of the pipeline so this pipeline is not perfect yet. Please open up an issue if you encounter any bugs or have any suggestions on how to improve the pipeline!