[pre-commit.ci] pre-commit autoupdate

.github/CONTRIBUTING.md

@@ -49,26 +49,26 @@ cd ASPEN
 
 - Install the python dependencies with pip
 
-  ```sh
-  pip install .
-  ```
+    ```sh
+    pip install .
+    ```
 
-  If you're developing on biowulf, you can use our shared conda environment which already has these dependencies installed
+    If you're developing on biowulf, you can use our shared conda environment which already has these dependencies installed
 
-  ```sh
-  . "/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh"
-  conda activate py311
-  ```
+    ```sh
+    . "/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh"
+    conda activate py311
+    ```
 
 - Install [`pre-commit`](https://pre-commit.com/#install) if you don't already
   have it. Then from the repo's root directory, run
 
-  ```sh
-  pre-commit install
-  ```
+    ```sh
+    pre-commit install
+    ```
 
-  This will install the repo's pre-commit hooks.
-  You'll only need to do this step the first time you clone the repo.
+    This will install the repo's pre-commit hooks.
+    You'll only need to do this step the first time you clone the repo.
 
 ### Create a branch
 

.pre-commit-config.yaml

@@ -8,36 +8,36 @@ exclude: |
    )
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v1.2.3
+    rev: v6.0.0
     hooks:
       - id: check-added-large-files
       - id: end-of-file-fixer
       - id: trailing-whitespace
       - id: check-json
   # spell check
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.4
+    rev: v2.4.2
     hooks:
       - id: codespell
         # https://github.com/codespell-project/codespell/issues/1498
   # Python formatting
-  - repo: https://github.com/psf/black
-    rev: 23.7.0
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 26.3.0
     hooks:
       - id: black
   # R formatting
   - repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.1.2
+    rev: v0.4.3.9021
     hooks:
       - id: style-files
   # general linting
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v2.7.1
+    rev: v4.0.0-alpha.8
     hooks:
       - id: prettier
   # enforce commit format
   - repo: https://github.com/compilerla/conventional-pre-commit
-    rev: v2.3.0
+    rev: v4.4.0
     hooks:
       - id: conventional-pre-commit
         stages: [commit-msg]

docs/deployment.md

@@ -138,11 +138,11 @@ MACS2 parameters can be changed by editing this block in the `config.yaml`:
 
 ```yaml
 macs2:
-  extsize: 200
-  shiftsize: 100
-  p: 0.01
-  qfilter: 0.05
-  annotatePeaks: True
+    extsize: 200
+    shiftsize: 100
+    p: 0.01
+    qfilter: 0.05
+    annotatePeaks: True
 ```
 
 #### Genrich
@@ -151,14 +151,14 @@ Genrich paramaters can be changed by editing this block in the `config.yaml`:
 
 ```yaml
 genrich:
-  s: 5
-  m: 6
-  q: 1
-  l: 100
-  g: 100
-  d: 100
-  qfilter: 0.05
-  annotatePeaks: True
+    s: 5
+    m: 6
+    q: 1
+    l: 100
+    g: 100
+    d: 100
+    qfilter: 0.05
+    annotatePeaks: True
 ```
 
 #### Contrasts

resources/frip/README.md

@@ -43,23 +43,20 @@ optional arguments:
 Sources:
 
 - HACER
-
-  - hg19 : http://bioinfo.vanderbilt.edu/AE/HACER/download/T1.txt
+    - hg19 : http://bioinfo.vanderbilt.edu/AE/HACER/download/T1.txt
 
 - FANTOM
-
-  - hg38 : http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_latest/extra/enhancer/F5.hg38.enhancers.bed.gz
-  - hg19 : http://fantom.gsc.riken.jp/5/datafiles/latest/extra/Enhancers/human_permissive_enhancers_phase_1_and_2.bed.gz
-  - mm9 : http://fantom.gsc.riken.jp/5/datafiles/latest/extra/Enhancers/mouse_permissive_enhancers_phase_1_and_2.bed.gz
-  - mm10 : http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_latest/extra/enhancer/F5.mm10.enhancers.bed.gz
+    - hg38 : http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_latest/extra/enhancer/F5.hg38.enhancers.bed.gz
+    - hg19 : http://fantom.gsc.riken.jp/5/datafiles/latest/extra/Enhancers/human_permissive_enhancers_phase_1_and_2.bed.gz
+    - mm9 : http://fantom.gsc.riken.jp/5/datafiles/latest/extra/Enhancers/mouse_permissive_enhancers_phase_1_and_2.bed.gz
+    - mm10 : http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_latest/extra/enhancer/F5.mm10.enhancers.bed.gz
 
 - DBSuper
-
-  - mm9 : http://asntech.org/dbsuper/data/bed/mm9/all_mm9_bed.bed
-  - hg19 : http://asntech.org/dbsuper/data/bed/hg19/all_hg19_bed.bed
+    - mm9 : http://asntech.org/dbsuper/data/bed/mm9/all_mm9_bed.bed
+    - hg19 : http://asntech.org/dbsuper/data/bed/hg19/all_hg19_bed.bed
 
 - EnhancerAtlas:
-  - fasta files were downloaded using the following commands for hg19 and mm9 data:
+    - fasta files were downloaded using the following commands for hg19 and mm9 data:
 
 ```
 % for i in 3T3-L1	416B	AtT-20	BAT	Bone_marrow	Brain_E14.5	Brown_preadipocyte_E18.5	C3H10Thalf	CD19+	CD4+CD8+	CD4+Treg	CD4+	CD8+	Cerebellum	Cerebellum_neonate	CH12	CMP	Cortex	Dendritic_cell	EpiLC	EpiSC	Erythroid_fetal_liver	Erythroid_spleen	ESC_Bruce4	ESC_J1	ESC_KH2	ESC_NPC	Forebrain_E11.5	Forebrain_E12.5	Forelimb_bud_embryo	Forelimb_E11	Forelimb_E13	G1E-ER4	G1E	GMP	Heart_E11.5	Heart_E12.5	Heart_E14.5	Heart	Hepatocyte	HFSC	Hindbrain_E11.5	Intestine	IPSC	Kidney	Large_intestine_epithelial	Lens_P1	Limb_E11.5	Limb_E14.5	Liver_E14.5	Liver	Lung_E14.5	Lung	Lung_neonate	MC3T3-E1	Megakaryocyte	MEL	Microglia	Midbrain_E11	Neuron_cortical	NIH-3T3	NKC_spleen	NKT	NPC	Olfactory_bulb	Pancreas	Pancreatic_islet	PDC_BM	PDC	Peritoneal_macrophage	Placenta	Pre-B	Pre-pro-B	Pro-B_BM	Prostate	Rib_chondrocyte_P1	Spermatid	Spleen	Stomach_neonate	Striatum	Testis	Th1	Th2	Thymus	Treg_cell	Uterus	V6.5	WAT	ZHBTc4;do

resources/tssBed/README.md

@@ -8,8 +8,8 @@
 - is strand aware
 - extracts chrom, start, geneid, geneName from the "gene" line for gene_type == "protein_coding" only
 - creates 400 bins around the TSS
-  - start if on + strand
-  - end if on - strand
+    - start if on + strand
+    - end if on - strand
 - each bin is 10 bp width so total -2k through +2k rgeion is covered in the 400 bins
 
 ```bash