hydra-genetics v1.2.0

Features

• add mkdocs snakemake rule plugin (fc1b22f)
• add rule parameter table via plugin (8261eda)
• added icons (671c69d)
• apply plugin used to convert schemas to tables (9922831)
• update snakemake version, allow range up to version 8 (7789297)

Bug Fixes

• edit basepath in to work with pymdownx 10.0 (e89f6a7)
• new schemas and input names (8d0c655)
• remove tumor_content as requirment in samples.tsv (534090e)
• update version of mkdocs-snakemake-rule-plugin (89dc789)

Documentation

• add dag graph (3e54df8)
• added index and build files (53074e6)
• added rule info (49efa84)
• added value in fastp (637d194)
• fix rtd rule plugin bug (e46180c)
• moved rule graph to intro (3c76df6)
• remove dag part from intro (0bf2019)
• schemas with improved descriptions (920ca7f)
• some spelling and links (69282f0)
• update module part in README with latest version of module (c927944)
• update project name in mkdocs.yaml (7457a05)
• update readme with link to readthe docs (348bb6e)
• update readme with link to readthe docs (2b95d95)
• updated schemas (43bd5f8)

hydra-genetics v1.1.0

Features

• removed support for conda (fd1e638)
• removed marrip as codeowner (fd1e638)

hydra-genetics v1.0.0

⚠ BREAKING CHANGES

• fixed wildcard order in merged_input in common (aed119c)

Bug Fixes

• missing temp on fastp output (9cef1c7)
• update readme and introduce breaking change message (2f99562)

hydra-genetics v0.5.0

Features

• common: update flowcell constraint (6c9ecaf)

Bug Fixes

• Update requirements.txt (33b2084)

Documentation

• add image logo (f8f80c0)
• README: change header image (f8f80c0)
• Update README.md (a7a6b3b)

hydra-genetics v0.4.0

Features

• make config.yaml location more flexible (3f13746)
• make configfile/confgilefiles argument mandatory (c434fc6)
• set configfile argument for jenkins (b700259)
• update snakemake version (6459187)

Bug Fixes

• allow - in barcode string (53228d3)
• set strict mode fore conda (67252b4)

Documentation

• update README (080fd07)

hydra-genetics v0.3.1

Documentation

• Add info about SortMeRNA (87c5e89)

v0.3.0

What's Changed

• ci: update dependencies by @Smeds in #54
• feat: add sortmerna by @marrip in #55
• fix: flag output directories correctly by @marrip in #56
• ci: add jenkins file used to validate result of module by @Smeds in #57
• fix: copy config.yaml to correct location for jenkins by @Smeds in #58
• fix: Fix jenkins by @Smeds in #59
• fix: remote extra "," from json by @Smeds in #60
• chore: revert "chore: release 0.1.0" by @marrip in #62
• docs: update rule graph plots by @Smeds in #63
• fix: update hydra-genetics version by @Smeds in #65

Full Changelog: v0.2.0...v0.3.0

hydra-genetics v0.2.0

Features

• add more wildcard constraints (f076813)

Bug Fixes

• add missing temp for output merged (1cb28c0)

hydra-genetics v0.1.1

Bug Fixes

• added barcode to fastq names to handle merging (d9b998c)
• lock singularity version to 3.8.6 (862a430)
• requirement bump (54f6e04)
• unit index (53605c9)
• update to lasted tools image (9d0eee7)

hydra-genetics v0.1.0

Features

• Adapt rules and Snakefile to standard (ef7398c)
• Adapt rules and Snakefile to standard (7b9664e)
• add conventional-prs workflow (8ca4a86)
• add conventional-prs workflow (badc260)
• added release-please workflow (b3a4324)
• added release-please workflow (0dbef4d)
• setup resources for job (83735d2)
• setup resources for job (793727e)
• Upgrade to hydra-genetics package v0.7.0 (d8a8702)
• Upgrade to hydra-genetics package v0.7.0 (ce03b47)
• Use tumor_content instead of TC (5b94294)
• Use tumor_content instead of TC (15cee79)

Bug Fixes

• dry run for fastp + merge workflow. (06199d0)
• dry run for fastp + merge workflow. (ad682a9)
• fix failing lint test (ba86565)
• fix failing lint test (cf6da56)
• handle case when rule have settings but no resources set (5ff2616)
• handle case when rule have settings but no resources set (b5bdeae)
• handle case when rule have settings but no resources set (34590d0)
• handle case when rule have settings but no resources set (38d24a5)

Documentation

• Add better explanation for tsv files (1a9c94d)
• Add better explanation for tsv files (1564882)
• Badging (7f25fd6)
• Badging (ce034d7)
• Change hydra-genetics version in README (2a73c19)
• Change hydra-genetics version in README (c9db54c)
• Layouting ReadMe (646a7ff)
• Layouting ReadMe (2223285)
• pull-request template (cba7607)
• pull-request template (7e359f2)
• Put output in table (f460a68)
• Put output in table (34a8204)
• update example files (45b3f46)
• update example files (dc9f476)
• Update README (a4e5d14)
• Update README (fd1632a)