- envs: Update installation instructions (
9afec83
)
- 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
)
- 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
)
- Though the reversion does not impact apparent function significantly, the outputs and underlying analysis are changed enough to warrant this BREAKING. (
4398450
)
- counts.rst: Add missing report file (
10a45c2
) - rulegraph.svg: Update rulegraph for new pipeline (
1cca3e1
)
- move_coordinates.bash: Set
-x
for improved logging (85d88d0
)
- move_coordinates.bash: Use tmpfiles correctly (
44df2d0
) - convert_to_bed.py: Add newline (
8a8dc83
) - lift.yaml: Set lesser coordinate as start (
62da900
)
- 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
)
- 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
)
- I mean, it deletes all the analysis scripts... (
52f239c
) - The STAR dependency fundamentally changes the way the pipeline runs. (
a5d437a
)
- 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
)
- repo: Initialise project (
46146d8
)
- 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
)
- repo: Initiate repository (
28ea197
)