Added CICD and github standards

.Rbuildignore

@@ -0,0 +1,2 @@
+^\.github$
+^metadata\.yaml$

.github/workflows/CICD-base.yaml

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+---
+name: CICD-base
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  CICD-base:
+    runs-on: ubuntu-latest
+
+    timeout-minutes: 15
+
+    steps:
+      # Checkout codebase
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      # Run CICD-base
+      - name: CICD-base
+        uses: docker://blcdsdockerregistry/cicd-base:latest
+        env:
+          VALIDATE_R: false

.github/workflows/R-CMD-check.yaml

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+---
+name: R-CMD-check
+
+on:
+  - push
+  - pull_request
+
+jobs:
+  R-CMD-check:
+    runs-on: ubuntu-latest
+
+    timeout-minutes: 15
+
+    container:
+      image: blcdsdockerregistry/bl-r-devel:latest
+
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          path: SeqKat
+      - run: R CMD build SeqKat
+      - run: R CMD check --as-cran SeqKat_*.tar.gz

DESCRIPTION

@@ -2,7 +2,7 @@ Package: SeqKat
 Type: Package
 Title: Detection of Kataegis
 Version: 0.0.8
-Date: 2019-04-23
+Date: 2020-03-09
 Author: Fouad Yousif, Xihui Lin, Fan Fan, Christopher Lalansingh, John Macdonald
 Maintainer: Paul C. Boutros <[email protected]>
 Description: Kataegis is a localized hypermutation occurring when a region is enriched in somatic SNVs. Kataegis can result from multiple cytosine deaminations catalyzed by the AID/APOBEC family of proteins. This package contains functions to detect kataegis from SNVs in BED format. This package reports two scores per kataegic event, a hypermutation score and an APOBEC mediated kataegic score. Yousif, F. et al.; The Origins and Consequences of Localized and Global Somatic Hypermutation; Biorxiv 2018 <doi:10.1101/287839>.

metadata.yaml

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+---
+Category: tool
+Description: Kataegis is a localized hypermutation occurring when a region is enriched in somatic SNVs. Kataegis can result from multiple cytosine deaminations catalyzed by the AID/APOBEC family of proteins. This package contains functions to detect kataegis from SNVs in BED format. This package reports two scores per kataegic event, a hypermutation score and an APOBEC mediated kataegic score.
+Maintainers: Paul Boutros
+Contributors:
+  - Fouad Yousif
+  - Xihui Lin
+  - Fan Fan
+  - Christopher Lalansingh
+  - John Macdonald
+Languages:
+  - R
+  - C
+  - C++
+Dependencies:
+  - R (>= 2.15.1)
+  - foreach
+  - doParallel
+References: "https://doi.org/10.1101/287839"
+Version: 0.0.8