Contribute back to nf-core #112
Description
Description of feature
Some of the subworkflows developped and modules modification done in phaseimpute might be interesting to add to nf-core and others might already be present and might need update
Add to nf-core modules:
- vcf_split_bcftools
- vcf_concat_bcftools
- bam_downsample_samtools New sbwf bam_subsampledepth_samtools modules#6019
- bam_chr_rename_samtools
- vcf_chr_rename_bcftools
- bcftools modules
- samtools modules
- stitch sbwf Add stitch imputation subworkflow modules#9438
- quilt sbwf Add quilt imputation subworkflow modules#9443
- glimpse2 sbwf Update glimpse2 imputation subworkflow modules#9434
- glimpse sbwf Update
GLIMPSEsbwf modules#9524 - minimac sbwf Add minimac4 imputation subworkfllow modules#9451
- beagle5 sbwf Add
BEAGLE5imputation subworkflow modules#9550 - shapeit5 sbwf Update shapeit test and input tuple modules#9463
Add to pipeline:
- vcf_split_bcftools
- vcf_concat_bcftools
- bam_downsample_samtools
- bam_chr_rename_samtools
- vcf_chr_rename_bcftools
- vcf_phase_shapeit5
- bcftools modules
- samtools modules
- stitch sbwf Move to nf-core sbwf for
STITCH#239 - quilt sbwf
- glimpse2 sbwf Move to nf-core sbwf for
GLIMPSE2#240 - glimpse sbwf
- minimac sbwf
- beagle5 sbwf