Conditional Workflow based on Amplicon or Whole Genome Data.

[ChabbyTMD]

The main workflow has been modified to execute either amplicon or whole genome analysis with the appropriate reference and variant calling SNP targets. Included in this pull request is a test dataset with amplicon sequence data.

A new rule has been written to cater for compression, tabix indexing and merging of vcf files for samples less than 1020. A conditional flow has been written that will activate the original BgzipTabixMerge rule when more than 1020 samples are supplied.

Calls to reference files are done without use of {ref} wildcard.

A GitHub CI action has been added, adapted from rna-seq-pop pipeline. Though advice on suitability for this particular pipeline is required.

[sanjaynagi]

Thanks Trevor, this is awesome!

I've looked, and it looks like the test dataset and reference logic is working well. Fantastic.

My only advice is that it's quite nice to have separate pull requests for different features, just so that it's easier to keep a record of what happened in each PR, and also, it decreases the likelihood that we will break something with a PR. I want to get the CI set up for pull requests in this repository, so that each time we make a PR, it runs the CI, to check everything is working properly. For that reason, I'm going to try and split this PR into two separate ones, one for CI, and one for the reference logic. Then we can hopefully use the CI in this PR to check its all working appropriately before we merge to the main branch.

Should also tag that this will solve issue #1 .

[sanjaynagi]

Im trying to remove commits from this PR, but it doesn't seem I have access to push back to this PR. Either that or I'm doing something wrong. Could I ask you to follow these steps... to remove some commits from this PR?

https://gist.github.com/loilo/930f141d9acf89e9e734ffa042acd750 specifically the comment by comfreek from point 2:

git rebase -i HEAD~10 because we want to modify the last 10 commits

An editor will pop up asking you configure how you want the last commits to survive:

pick 1234567 A
pick 789abcd B
pick 7654321 C
pick dcba987 D
pick 5674321 E

Replace pick by drop in the lines for every commit to do with CI (i think this is commit 1,3,4,10 in this case). This is to remove the CI commits, which are now on another branch and another PR #6 . 

push back to the repository as you did before

I'm hoping this will work. Let me know how you get on or if you run into trouble :) if not, ill be able to make a new branch and make a new PR with the commits, but it'll mean we lose your PR and it would be nice for you to do it!

[sanjaynagi]

Closing this PR now, please see #7 and #6.