diff --git a/CHANGELOG.md b/CHANGELOG.md index 446159c5..de7940b3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -25,9 +25,11 @@ description: A full list of Bactopia releases and a description of the changes. ### `Fixed` -- missing schema for clean-yer-reads +- missing schema for clean-yer-reads and teton - use `--infile-list` with `csvtk concat` to support 10k+ inputs - `pangenome` when Bakta GFF (`*.gff3`) files are provided +- missing file export in `gubbins` + ### `Enhancements to OSS` diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md index 02e46a3b..ec395e26 100644 --- a/CODE_OF_CONDUCT.md +++ b/CODE_OF_CONDUCT.md @@ -55,11 +55,11 @@ further defined and clarified by project maintainers. ## Enforcement Instances of abusive, harassing, or otherwise unacceptable behavior may be -reported by contacting the project team at robert.petit@emory.edu (Robert Petit) -or tdread@emory.edu (Tim Read). All complaints will be reviewed and investigated -and will result in a response that is deemed necessary and appropriate to the -circumstances. The project team is obligated to maintain confidentiality with -regard to the reporter of an incident. Further details of specific enforcement +reported by contacting the project team at robbie.petit@gmail.com (Robert Petit) +or tdread@emory.edu (Tim Read). All complaints will be reviewed and investigated +and will result in a response that is deemed necessary and appropriate to the +circumstances. The project team is obligated to maintain confidentiality with +regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately. Project maintainers who do not follow or enforce the Code of Conduct in good diff --git a/modules/nf-core/srahumanscrubber/scrub/params-teton.json b/modules/nf-core/srahumanscrubber/scrub/params-teton.json new file mode 100644 index 00000000..d83f9854 --- /dev/null +++ b/modules/nf-core/srahumanscrubber/scrub/params-teton.json @@ -0,0 +1,29 @@ +{ + "$schema": "http://json-schema.org/draft-07/schema", + "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/nf-core/srahumanscrubber/scrub/params.json", + "title": "sra-human-scrubber Module", + "description": "A module detecting and removing human reads from FASTQs", + "type": "object", + "definitions": { + "srahumanscrubber_scrub_parameters": { + "title": "Scrubber (sra-human-scrubber) Parameters", + "type": "object", + "description": "", + "default": "", + "fa_icon": "fas fa-exclamation-circle", + "properties": { + "use_srascrubber": { + "type": "boolean", + "default": false, + "description": "Use SRAHumanScrubber for scrubbing human reads", + "fa_icon": "fas fa-file-alt" + } + } + } + }, + "allOf": [ + { + "$ref": "#/definitions/srahumanscrubber_scrub_parameters" + } + ] +}