Standardized channel output for different files

Is your feature request related to a problem? Please describe

If we take as example the bamtools, samtools and bcftools the output channel are inconsistent.

• BAMTOOLS_CONVERT:

output:
    tuple val(meta), path("*.{bed,fasta,fastq,json,pileup,sam,yaml}"), emit: data

• BCFTOOLS_VIEW:

output:
    tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf
    tuple val(meta), path("*.tbi")                    , emit: tbi, optional: true
    tuple val(meta), path("*.csi")                    , emit: csi, optional: true

• SAMTOOLS_VIEW:

output:
    tuple val(meta), path("${prefix}.bam"),                                    emit: bam,              optional: true
    tuple val(meta), path("${prefix}.cram"),                                   emit: cram,             optional: true
    tuple val(meta), path("${prefix}.sam"),                                    emit: sam,              optional: true
    tuple val(meta), path("${prefix}.${file_type}.bai"),                       emit: bai,              optional: true
    tuple val(meta), path("${prefix}.${file_type}.csi"),                       emit: csi,              optional: true
    tuple val(meta), path("${prefix}.${file_type}.crai"),                      emit: crai,             optional: true
    tuple val(meta), path("${prefix}.unselected.${file_type}"),                emit: unselected,       optional: true
    tuple val(meta), path("${prefix}.unselected.${file_type}.{bai,csi,crsi}"), emit: unselected_index, optional: true

Describe the solution you'd like

We should stick to one guidelines across all modules.
There is two solutions each one with it's inconvenient:

• group every similar file in one channel: tuple val(meta), path("*.{tbi,csi}") , emit: index, optional: true
• spread them with one file type per channel and put them all optional (same as samtools)

Additional context

This decision has huge consequence on the management of the output channel and their aggregation afterwards.

• group everything:

BCFTOOLS_VIEW.out.vcf.join(BCFTOOLS_VIEW.out.index)

• spread by file type:

ch_vcf = BCFTOOLS_VIEW.out.vcf.mix(BCFTOOLS_VIEW.out.bcf, BCFTOOLS_VIEW.ou.vcfgz)
ch_index = BCFTOOLS_VIEW.out.csi.mix(BCFTOOLS_VIEW.out.tbi)
ch_vcf_index = ch_vcf.join(ch_index)

Compare the output declarations shown for BAMTOOLS_CONVERT, BCFTOOLS_VIEW, and SAMTOOLS_VIEW, then review how their channels are joined or mixed in downstream aggregation. The issue is done only after one output-channel guideline is decided and consistently applied across the affected modules.