Standardized channel output for different files

[LouisLeNezet]

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)

[nvnieuwk]

I like this as it will make implementation a lot simpler :partying_face: