Contribute back to nf-core

[LouisLeNezet]

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 GLIMPSE sbwf modules#9524
• minimac sbwf Add minimac4 imputation subworkfllow modules#9451
• beagle5 sbwf Add BEAGLE5 imputation 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