Contribute back to nf-core

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 https://github.com/nf-core/modules/pull/6019
• bam_chr_rename_samtools
• vcf_chr_rename_bcftools
• bcftools modules
• samtools modules
• stitch sbwf https://github.com/nf-core/modules/pull/9438
• quilt sbwf https://github.com/nf-core/modules/pull/9443
• glimpse2 sbwf https://github.com/nf-core/modules/pull/9434
• glimpse sbwf https://github.com/nf-core/modules/pull/9524
• minimac sbwf https://github.com/nf-core/modules/pull/9451
• beagle5 sbwf https://github.com/nf-core/modules/pull/9550
• shapeit5 sbwf https://github.com/nf-core/modules/pull/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 https://github.com/nf-core/phaseimpute/pull/239
• quilt sbwf
• glimpse2 sbwf https://github.com/nf-core/phaseimpute/pull/240
• glimpse sbwf
• minimac sbwf
• beagle5 sbwf

Review the unchecked module and subworkflow entries under “Add to nf-core modules” and “Add to pipeline,” then compare them with the merged pull requests 139, 239, and 240. Start by inspecting the existing phaseimpute workflow and those completed contributions. Done means the applicable remaining entries are contributed to nf-core and integrated into the pipeline, with the checklist updated.