zarp-cli - v1.0.0-rc.1

What's Changed

• feat: add configuration models by @uniqueg in https://github.com/zavolanlab/zarp-cli/pull/17
• ci: migrate to GH Actions by @AngryMaciek in https://github.com/zavolanlab/zarp-cli/pull/27
• feat: config & sample management by @uniqueg in https://github.com/zavolanlab/zarp-cli/pull/29
• feat: add arg for rule config by @uniqueg in https://github.com/zavolanlab/zarp-cli/pull/32
• feat: write Snakemake run config file by @uniqueg in https://github.com/zavolanlab/zarp-cli/pull/33
• feat: add generic Snakemake executor by @dominikburri in https://github.com/zavolanlab/zarp-cli/pull/23
• docs: build & publish on GH Pages by @uniqueg in https://github.com/zavolanlab/zarp-cli/pull/40
• docs: fix broken/outdated badges by @uniqueg in https://github.com/zavolanlab/zarp-cli/pull/45
• docs: fix page title by @uniqueg in https://github.com/zavolanlab/zarp-cli/pull/47
• docs: build API reference for all modules by @uniqueg in https://github.com/zavolanlab/zarp-cli/pull/49
• feat: support for fetching libraries from SRA by @uniqueg in https://github.com/zavolanlab/zarp-cli/pull/50
• refactor: major code cleanup by @uniqueg in https://github.com/zavolanlab/zarp-cli/pull/51
• feat: implement sample processing flow by @uniqueg in https://github.com/zavolanlab/zarp-cli/pull/52
• feat: set sample config defaults by @uniqueg in https://github.com/zavolanlab/zarp-cli/pull/54
• feat: set dummy data by @uniqueg in https://github.com/zavolanlab/zarp-cli/pull/57
• fix: use defaults from user config by @uniqueg in https://github.com/zavolanlab/zarp-cli/pull/58
• feat: fetch genome resources and set paths by @uniqueg in https://github.com/zavolanlab/zarp-cli/pull/61
• feat: infer missing metadata by @balajtimate in https://github.com/zavolanlab/zarp-cli/pull/60
• feat: execute ZARP by @uniqueg in https://github.com/zavolanlab/zarp-cli/pull/63
• fix: bind input file locations to Singularity by @uniqueg in https://github.com/zavolanlab/zarp-cli/pull/65
• build: use Conda for dev environment setup by @uniqueg in https://github.com/zavolanlab/zarp-cli/pull/67
• docs: provide extensive documentation by @uniqueg in https://github.com/zavolanlab/zarp-cli/pull/71
• build: fix installation by @uniqueg in https://github.com/zavolanlab/zarp-cli/pull/75
• feat: restructure HTSinfer output dir tree by @uniqueg in https://github.com/zavolanlab/zarp-cli/pull/76
• feat: pass Snakemake profile to ZARP workflow by @uniqueg in https://github.com/zavolanlab/zarp-cli/pull/77
• fix: mount TMP directories for Singularity by @ninsch3000 in https://github.com/zavolanlab/zarp-cli/pull/79
• fix: propagate HTSinfer inferences by @uniqueg in https://github.com/zavolanlab/zarp-cli/pull/80
• fix: various pre-release fixes by @uniqueg in https://github.com/zavolanlab/zarp-cli/pull/82
• fix: various prerelease fixes by @uniqueg in https://github.com/zavolanlab/zarp-cli/pull/83
• fix(htsinfer): set Singularity bind args for Conda by @uniqueg in https://github.com/zavolanlab/zarp-cli/pull/86
• feat: Conda support for HTSinfer workflow by @uniqueg in https://github.com/zavolanlab/zarp-cli/pull/87
• docs: minor fixes by @uniqueg in https://github.com/zavolanlab/zarp-cli/pull/88
• build: v1.0.0-rc.1 by @uniqueg in https://github.com/zavolanlab/zarp-cli/pull/89

New Contributors

• @AngryMaciek made their first contribution in https://github.com/zavolanlab/zarp-cli/pull/27
• @dominikburri made their first contribution in https://github.com/zavolanlab/zarp-cli/pull/23
• @ninsch3000 made their first contribution in https://github.com/zavolanlab/zarp-cli/pull/79

Full Changelog: https://github.com/zavolanlab/zarp-cli/commits/v1.0.0-rc.1

- Python
Published by uniqueg about 2 years ago