v2.0.1

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

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

Feature

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

v1.0.1

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

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

Feature

• repo: Initialise project (46146d8)