From e56c943822a47061471635e2193b173f8a19ef95 Mon Sep 17 00:00:00 2001 From: Kelly Sovacool Date: Tue, 9 Jan 2024 17:26:55 -0500 Subject: [PATCH 1/9] docs: create CITATION.cff --- CITATION.cff | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 CITATION.cff diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000..f48630d --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,20 @@ +cff-version: 1.2.0 +message: "Please cite XAVIER as below." +authors: + - family-names: Nousome + given-names: Darryl + - family-names: Mathur + given-names: Samarth + - family-names: Sovacool + given-names: Kelly + orcid: https://orcid.org/0000-0003-3283-829X + - family-names: Koparde + given-names: Vishal + orcid: https://orcid.org/0000-0001-8978-8495 +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 From d7848afc5d0b0929667be5a522a51ebb49701c8e Mon Sep 17 00:00:00 2001 From: Kelly Sovacool Date: Tue, 9 Jan 2024 17:32:20 -0500 Subject: [PATCH 2/9] chore: update CHANGELOG.md - add line for #68 - run prettier for the first time on this file, so other minor stylistic changes were made --- CHANGELOG.md | 22 ++++++++++++---------- 1 file changed, 12 insertions(+), 10 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index ec36d83..1e74cb9 100644 --- a/CHANGELOG.md +++ b/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. From 7e494d31c182c6c44ec5a9eb7277c10134b48057 Mon Sep 17 00:00:00 2001 From: samarth8392 Date: Tue, 9 Jan 2024 17:57:16 -0500 Subject: [PATCH 3/9] docs: added samarth's ORCID --- CITATION.cff | 1 + 1 file changed, 1 insertion(+) diff --git a/CITATION.cff b/CITATION.cff index f48630d..f6afb2f 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -5,6 +5,7 @@ authors: given-names: Darryl - family-names: Mathur given-names: Samarth + orcid: https://orcid.org/0000-0002-6446-5718 - family-names: Sovacool given-names: Kelly orcid: https://orcid.org/0000-0003-3283-829X From 2add23c79cd15f368b64f05eae1b04225d55e074 Mon Sep 17 00:00:00 2001 From: Kelly Sovacool Date: Wed, 10 Jan 2024 15:39:20 -0500 Subject: [PATCH 4/9] chore: add Sam + other contributors to citation file --- CITATION.cff | 30 +++++++++++++++++++----------- 1 file changed, 19 insertions(+), 11 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index f6afb2f..5f504d7 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1,17 +1,25 @@ cff-version: 1.2.0 message: "Please cite XAVIER as below." authors: - - family-names: Nousome - given-names: Darryl - - family-names: Mathur - given-names: Samarth - orcid: https://orcid.org/0000-0002-6446-5718 - - family-names: Sovacool - given-names: Kelly - orcid: https://orcid.org/0000-0003-3283-829X - - family-names: Koparde - given-names: Vishal - orcid: https://orcid.org/0000-0001-8978-8495 + - family-names: Nousome + given-names: Darryl + - family-names: Mathur + given-names: Samarth + orcid: https://orcid.org/0000-0002-6446-5718 + - family-names: Sovacool + given-names: Kelly + orcid: https://orcid.org/0000-0003-3283-829X + - family-names: Sevilla + given-names: Samantha + affiliation: Frederick National Laboratory for Cancer Research + - family-names: Kuhn + given-names: Skyler + orcid: https://orcid.org/0000-0003-0606-2125 + - family-names: Tandon + given-names: Mayank + - family-names: Koparde + given-names: Vishal + orcid: https://orcid.org/0000-0001-8978-8495 title: "XAVIER: eXome Analysis and Variant explorER" url: https://ccbr.github.io/XAVIER/ repository-code: https://github.com/CCBR/XAVIER From 5c91e90401d74bfed5c625206dd427a085cc952f Mon Sep 17 00:00:00 2001 From: Kelly Sovacool Date: Wed, 10 Jan 2024 15:40:08 -0500 Subject: [PATCH 5/9] chore: set tabwidth for *.cff files --- .prettierrc | 2 +- CITATION.cff | 38 +++++++++++++++++++------------------- 2 files changed, 20 insertions(+), 20 deletions(-) diff --git a/.prettierrc b/.prettierrc index 6385d00..81ee40a 100644 --- a/.prettierrc +++ b/.prettierrc @@ -1,7 +1,7 @@ overrides: - files: - "*.md" - - "citation.cff" + - "*.cff" - ".prettierrc" options: tabWidth: 2 diff --git a/CITATION.cff b/CITATION.cff index 5f504d7..8f13b37 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1,25 +1,25 @@ cff-version: 1.2.0 message: "Please cite XAVIER as below." authors: - - family-names: Nousome - given-names: Darryl - - family-names: Mathur - given-names: Samarth - orcid: https://orcid.org/0000-0002-6446-5718 - - family-names: Sovacool - given-names: Kelly - orcid: https://orcid.org/0000-0003-3283-829X - - family-names: Sevilla - given-names: Samantha - affiliation: Frederick National Laboratory for Cancer Research - - family-names: Kuhn - given-names: Skyler - orcid: https://orcid.org/0000-0003-0606-2125 - - family-names: Tandon - given-names: Mayank - - family-names: Koparde - given-names: Vishal - orcid: https://orcid.org/0000-0001-8978-8495 + - family-names: Nousome + given-names: Darryl + - family-names: Mathur + given-names: Samarth + orcid: https://orcid.org/0000-0002-6446-5718 + - family-names: Sovacool + given-names: Kelly + orcid: https://orcid.org/0000-0003-3283-829X + - family-names: Sevilla + given-names: Samantha + affiliation: Frederick National Laboratory for Cancer Research + - family-names: Kuhn + given-names: Skyler + orcid: https://orcid.org/0000-0003-0606-2125 + - family-names: Tandon + given-names: Mayank + - family-names: Koparde + given-names: Vishal + orcid: https://orcid.org/0000-0001-8978-8495 title: "XAVIER: eXome Analysis and Variant explorER" url: https://ccbr.github.io/XAVIER/ repository-code: https://github.com/CCBR/XAVIER From c1c2c87274c67a34fc7317d6ee1a00e72f1d5eba Mon Sep 17 00:00:00 2001 From: Darryl Nousome Date: Wed, 10 Jan 2024 16:59:09 -0500 Subject: [PATCH 6/9] docs: added orcid --- CITATION.cff | 1 + 1 file changed, 1 insertion(+) diff --git a/CITATION.cff b/CITATION.cff index 8f13b37..f4c872c 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -3,6 +3,7 @@ message: "Please cite XAVIER as below." authors: - family-names: Nousome given-names: Darryl + orcid: https://orcid.org/0000-0002-5259-8599 - family-names: Mathur given-names: Samarth orcid: https://orcid.org/0000-0002-6446-5718 From 986dcb5c28cd27865eda4b8f96e0791112b9c492 Mon Sep 17 00:00:00 2001 From: Kelly Sovacool Date: Thu, 11 Jan 2024 09:38:03 -0500 Subject: [PATCH 7/9] chore: add affiliations & Sam's ORCID --- CITATION.cff | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/CITATION.cff b/CITATION.cff index 8f13b37..f9301e5 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -6,11 +6,14 @@ authors: - family-names: Mathur given-names: Samarth orcid: https://orcid.org/0000-0002-6446-5718 + affiliation: Frederick National Laboratory for Cancer Research - family-names: Sovacool given-names: Kelly orcid: https://orcid.org/0000-0003-3283-829X + affiliation: Frederick National Laboratory for Cancer Research - family-names: Sevilla given-names: Samantha + orcid: https://orcid.org/0000-0002-8734-9875 affiliation: Frederick National Laboratory for Cancer Research - family-names: Kuhn given-names: Skyler @@ -20,6 +23,7 @@ authors: - family-names: Koparde given-names: Vishal orcid: https://orcid.org/0000-0001-8978-8495 + affiliation: Frederick National Laboratory for Cancer Research title: "XAVIER: eXome Analysis and Variant explorER" url: https://ccbr.github.io/XAVIER/ repository-code: https://github.com/CCBR/XAVIER From d641d3f2007feec2459b5bf78fe1e35b707758b6 Mon Sep 17 00:00:00 2001 From: Kelly Sovacool Date: Thu, 11 Jan 2024 13:40:41 -0500 Subject: [PATCH 8/9] chore: update .pre-commit-config.yaml --- .pre-commit-config.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 11ed0a7..12dc373 100644 --- a/.pre-commit-config.yaml +++ b/.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 From 3d38c5ec94d4857c8783000dc3b877670a118f64 Mon Sep 17 00:00:00 2001 From: Kelly Sovacool Date: Thu, 11 Jan 2024 13:41:52 -0500 Subject: [PATCH 9/9] chore: update affiliations + MT's ORCID --- CITATION.cff | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index 251aec0..1f9c9c8 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -4,28 +4,29 @@ authors: - family-names: Nousome given-names: Darryl orcid: https://orcid.org/0000-0002-5259-8599 - affiliation: Frederick National Laboratory for Cancer Research + 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: Frederick National Laboratory for Cancer Research + 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: Frederick National Laboratory for Cancer Research + 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: Frederick National Laboratory for Cancer Research + 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: Frederick National Laboratory for Cancer Research + 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