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CHANGELOG.md

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Changelog

v2.0.1 (2022-01-17)

Fix

  • envs: Update installation instructions (9afec83)

Documentation

  • README.md: Update project information (fc3c6b8)
  • .snakemake-workflow-catalog.yml: Correct usage instructions (419ea80)
  • LICENSE.md: Update copyright year (19eb5cf)
  • CONTRIBUTING.md: Correct repo link (15fb83b)
  • documentation.md: Update technical documentation (0fdb462)
  • config/README.md: Include update parameters (4e39a2d)
  • README.md: Note switch to cellranger (a276364)

v2.0.0 (2021-12-22)

Feature

  • lift.smk: Mask gtf_converted as tempfile (082ef70)
  • rules: Support CellRanger (4398450)

Fix

  • input_resources.smk: Add conda environment (0383d86)
  • cellranger.smk: Correct mkref and count (df1ee8a)
  • common.smk: Remove print statement (890902b)
  • cellranger_resources.smk: Correct allowed biotypes (0426d07)
  • qc_reads.smk: Increase threads for fastqc (d2ce90d)
  • lift.smk: Correct to benchmarks (d10adf7)
  • cellranger_resources.smk: Correct directory location (10cfd2a)
  • Snakefile: Specify correct outputs (7e383b2)
  • qc_reads.smk: Remove star aggregation (89a727b)
  • common.smk: Change aggregation functions (482740a)
  • schema: Expand CellRanger parameters (efcd9d8)
  • qc_reads.smk: Corret FastQ collection (a4938a6)
  • input_resources.smk: Disable container (c8612fb)
  • star.smk: Correct input (89592ff)

Breaking

  • Though the reversion does not impact apparent function significantly, the outputs and underlying analysis are changed enough to warrant this BREAKING. (4398450)

Documentation

  • counts.rst: Add missing report file (10a45c2)
  • rulegraph.svg: Update rulegraph for new pipeline (1cca3e1)

v1.1.0 (2021-12-06)

Feature

  • move_coordinates.bash: Set -x for improved logging (85d88d0)

v1.0.1 (2021-12-06)

Fix

  • move_coordinates.bash: Use tmpfiles correctly (44df2d0)
  • convert_to_bed.py: Add newline (8a8dc83)
  • lift.yaml: Set lesser coordinate as start (62da900)

v1.0.0 (2021-12-06)

Feature

  • rules: Add move_coordinate rule (f1ec1c4)
  • rules: Add liftover rules (4193eaf)
  • convert_to_bed: Add convert_to_bed rule (fba0dd0)
  • config: Add over.chain urls (9828920)
  • envs: Add env for lift (80518b4)
  • schemas: Provide validation for lift.yaml (b0b5b9c)
  • envs_scripts: Include only necessary environments (52f239c)
  • rules: Convert to star (a5d437a)

Fix

  • rule:move_coordinates: Improve error handling (29d4f59)
  • config.yaml: Correct urls (1e1a4b6)
  • resources.smk: Correct formatting (ae12c68)
  • qc_reads.smk: Correct multiqc wrapper (f9a75ef)
  • common.smk: Forrect f-string usage (a901850)

Breaking

  • I mean, it deletes all the analysis scripts... (52f239c)
  • The STAR dependency fundamentally changes the way the pipeline runs. (a5d437a)

Documentation

  • technical: Updates technica ldocumenation in necessary locations to provide a correct and accurate view of the steps now performed by the pipeline (1b21a8f)
  • reports: Correct report files (78b0d60)
  • documentation.md: Correct technical notes (d13e47b)
  • README: Desribe new project aims (53611e0)

v0.2.0 (2021-11-22)

Feature

  • repo: Initialise project (46146d8)

v0.1.1 (2021-11-02)

Fix

  • config: Correct sample name (d22da64)
  • schema: Disallow non-word characters (5648893)

Documentation

  • README: Correct erroneous link (4956f50)
  • README/CONTRIBUTING: Correct erroneous links (09c755a)
  • README: Include install instructions (a0679c5)
  • README: Correct ci/cd badge (db9e476)
  • README: Apply formatting (4d6fdbe)

v0.1.0 (2021-10-27)

Feature

  • repo: Initiate repository (28ea197)

Documentation