Add alignment_software & alignment_software_version field in analysis_protocol

[arschat]

For which schema is a change/update being suggested? I would like to request an update to the analysis_file.json analysis_protocol.json schema.

What should the change/update be? I would like to add two new fields

1. alignment_software to allow data contributors to record the software used for the alignment of the FASTQ files' reads to a reference genome
2. alignment_software_version to allow data contributors to record the version of the software used for the alignment of the FASTQ files' reads to a reference genome This update constitutes a major change to the schema(s) it affects.

What new field(s) need to be changed/added?

* Field name: alignment_software
* Field description: Name of alignment software used to map the FASTQ files to the reference genome
* Field type: string
* Required: yes 
* Examples: cell ranger; kallisto bustools; GSNAP; STAR; Not Applicable
* CV or enum: no

* Field name: alignment_software_version
* Field description: Version of alignment software used to map the FASTQ files to the reference genome
* Field type: string
* Required: yes
* Examples: v1.0.1; 2.4.2a; Not Applicable
* CV or enum: no

Why is the change requested?

This field is needed to record the specific software used in order to align fastq files to a reference genome. Is one of the upcoming Tier 1 metadata proposed from HCA Integration Teams & Bionetwork

Affects which cells are filtered per dataset, and which reads (introns and exons or only exons) are counted as part of the reported transcriptome. This can convey batch effects.

[arschat]

PR HumanCellAtlas/metadata-schema#1534

[arschat]

alignment_software & alignment_software_version moved to analysis_protocol schema instead of analysis_file.