Sprint completions - VertebrateResequencing/vr-pipe GitHub Wiki

This page shows things that used to be on the Product Backlog that were implemented during a sprint. It does not represent a complete VRPipe feature list, since most of the base functionality was implemented before the Product Backlog was created and we started scrum development.

cj

    5e. SNP calling pipeline
        5e.1. Bam chr chunking method/step
        5e.2. samtools mpileup step
        5e.3. gatk snp calling step
        5e.4. Investigate need for other snp caller steps
        5e.5. VCF merge step
    13a. Resolve issues with indexing
    13b. Resolve issues with column types

jm

sb

7. Complete vrpipe-setup interface:
    7a. Allow PipelineSetups to be created
    7b. Allow PipelineSetups to be turned off and on
    7c. User who created a PipelineSetup should be recorded, so they can by default see only their own PipelineSetups when they use the various front-end interfaces

        5j.1. VRPipe::File must know about files moving, so it knows StepOutputFiles haven't been deleted 

delete unimproved mapped g1k bams
new bas column, make code installable externally

15. Step-stats table, to track details on how long each step takes to run and how much memory is used, overall and per PipelineSetup
    15a. Current average+2sd to be used to override default Requirements

3. Design a generic (DataSource-like?) DataSink API (decided not to do this; we VRTrack output steps instead)

    5k. Investigate need for import (bam/fasta from file/iRods) pipelines?
4. Investigate need for iRods DataSource (decided not to do this; we have an iRods import step instead)

    5j. Design a generic system equivalent of the StoreLane/Path pipeline (implemented as the archive_files pipeline)

        5f.2. QC stats & graphs step that generically works on genome & exome bams

sm

1. New DataSource that can use other VRPipe PipelineSetups as the input

    5a. Merge-up pipeline
        5a.1. Tag-strip step
        5a.2. Bam merge step
        5a.3. Mark duplicates step
        5a.4. Extract intervals step

    5c. Bam splitting pipeline
        5c.1. Bam split step

cram-related steps

nw

2. Extended and completed VRTrack DataSource:
    2a. Fast way of checking if results have changed
    2b. Method to get lane fastqs with metadata
    2c. Investigate if other methods are needed
        2c.1. Implement other methods