Merge pull request #68 from CCBR/citation

docs: create CITATION.cff

.pre-commit-config.yaml

@@ -3,7 +3,8 @@ default_stages: [pre-commit]
 exclude: |
   (?x)(
       ^assets/|
-      ^docs/.*.html
+      ^docs/.*.html|
+      ^_extensions/
    )
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
@@ -12,6 +13,7 @@ repos:
       - id: check-added-large-files
       - id: end-of-file-fixer
       - id: trailing-whitespace
+      - id: check-json
   # spell check
   - repo: https://github.com/codespell-project/codespell
     rev: v2.2.4

.prettierrc

@@ -1,7 +1,7 @@
 overrides:
   - files:
       - "*.md"
-      - "citation.cff"
+      - "*.cff"
       - ".prettierrc"
     options:
       tabWidth: 2

CHANGELOG.md

@@ -1,22 +1,24 @@
-# Version changes
-
 ## development version
 
+- Create `CITATION.cff` to describe how to cite XAVIER. (#68, @kelly-sovacool)
+
 ## v3.0.2
- - Documentation updates for GUI and other genome references 
- - Additional IUPAC changes to play nice with GATK tools (non ACGTN codes convert to N)
-
+
+- Documentation updates for GUI and other genome references
+- Additional IUPAC changes to play nice with GATK tools (non ACGTN codes convert to N)
+
 ## v3.0.1
 
 Hotfixes for all!
- - Increased memory for somatic merge rule
- - Fixed spooker/runner calls for run info
- - Fixed vcf2maf which missed the Intersection of calls
+
+- Increased memory for somatic merge rule
+- Fixed spooker/runner calls for run info
+- Fixed vcf2maf which missed the Intersection of calls
 
 ## v3.0.0
 
 - added [FRCE](https://ncifrederick.cancer.gov/staff/frce/welcome) support.
 - adding `$triggeroptions` to _snakemake_ cli.
 - using `SLURM_SUBMIT_HOST` as a secondary environmental variable to extract cluster name information on compute nodes.
-- `func set_tmp()` added to repeat `tmpdir` assignments accross multiple rules.
-- `vcf2maf` fix applied. 
+- `func set_tmp()` added to repeat `tmpdir` assignments across multiple rules.
+- `vcf2maf` fix applied.

CITATION.cff

@@ -0,0 +1,36 @@
+cff-version: 1.2.0
+message: "Please cite XAVIER as below."
+authors:
+  - family-names: Nousome
+    given-names: Darryl
+    orcid: https://orcid.org/0000-0002-5259-8599
+    affiliation: Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
+  - family-names: Mathur
+    given-names: Samarth
+    orcid: https://orcid.org/0000-0002-6446-5718
+    affiliation: Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
+  - family-names: Sovacool
+    given-names: Kelly
+    orcid: https://orcid.org/0000-0003-3283-829X
+    affiliation: Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
+  - family-names: Sevilla
+    given-names: Samantha
+    orcid: https://orcid.org/0000-0002-8734-9875
+    affiliation: Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
+  - family-names: Kuhn
+    given-names: Skyler
+    orcid: https://orcid.org/0000-0003-0606-2125
+  - family-names: Tandon
+    given-names: Mayank
+    orcid: https://orcid.org/0000-0002-1675-5040
+  - family-names: Koparde
+    given-names: Vishal
+    orcid: https://orcid.org/0000-0001-8978-8495
+    affiliation: Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
+title: "XAVIER: eXome Analysis and Variant explorER"
+url: https://ccbr.github.io/XAVIER/
+repository-code: https://github.com/CCBR/XAVIER
+license: MIT
+type: software
+version: 3.0.2
+date-released: 2023-12-19