Working to the next release

.github/workflows/main.yml

@@ -1,54 +1,19 @@
-name: Tests
+name: CI
 
 on:
   push:
-    branches: [ main ]
+    branches: [main]
   pull_request:
-    branches: [ main ]
-
+    branches: [main]
 
 jobs:
-  Formatting:
+  # pixi test
+  Test:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - name: Formatting
-        uses: github/super-linter@v4
-        env:
-          VALIDATE_ALL_CODEBASE: false
-          DEFAULT_BRANCH: main
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          VALIDATE_SNAKEMAKE_SNAKEFMT: true
-
-  Linting:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v2
-    - name: Lint workflow
-      uses: snakemake/snakemake-github-action@v1.24.0
-      with:
-        directory: .
-        snakefile: workflow/Snakefile
-        args: "--lint"
-
-  Testing:
-    runs-on: ubuntu-latest
-    needs: 
-      - Linting
-      - Formatting
-    steps:
-    - uses: actions/checkout@v2
-
-    - name: Test workflow
-      uses: snakemake/snakemake-github-action@v1.24.0
-      with:
-        directory: .test
-        snakefile: workflow/Snakefile
-        args: "--use-conda --show-failed-logs --cores 3 --conda-cleanup-pkgs cache --all-temp --configfile config.yml"
-
-#    - name: Test report
-#      uses: snakemake/snakemake-github-action@v1.24.0
-#      with:
-#        directory: .test
-#        snakefile: workflow/Snakefile
-#        args: "--report report.zip"
+      - uses: actions/checkout@v4
+      - uses: prefix-dev/setup-pixi@v0.8.1
+        with:
+          pixi-version: v0.37.0
+          cache: true
+      - run: pixi run test

.gitignore

@@ -142,7 +142,7 @@ figures/
 old/
 phasing/
 run_scripts/
-trackHub/
+trackHub-{v}/
 trackHub_altius/
 XCI/
 altius/
@@ -158,7 +158,6 @@ config/**
 .vscode/*
 .DS_Store
 
-
 # stats
 Rdata/
 Rplots.pdf
@@ -177,4 +176,6 @@ misc/
 new-agg-test/
 scATAC/
 test/
-
+test-data/
+bigtools-test/
+fire-test-data/

CHANGELOG.md

@@ -0,0 +1,3 @@
+# v0.1.0
+
+First major release of the FIRE pipeline. This release includes a refactor to reduce the computation by increased use of ft, changes to the output file names to include the fire version among other things, and finally a new launching method for the pipeline that uses pixi. Results are very similar to v0.0.7 of the pipeline; however, there are minor differences in the peak calls and the output names.

INSTALL.md

@@ -1,18 +1,17 @@
 # Install
 
-You will need **snakemake** which you can install using conda/mamba, e.g.:
-```
-mamba create -c conda-forge -c bioconda -n snakemake 'snakemake>=8.4'
-```
+If you wish to distribute jobs across a cluster you will need to install the appropriate [snakemake executor plugin](https://snakemake.github.io/snakemake-plugin-catalog/). For example, to use SLURM you can install the `snakemake-executor-slurm` plugin using pip:
 
-Finally, if you wish to distribute jobs across a cluster you will need to install the appropriate [snakemake executor plugin](https://snakemake.github.io/snakemake-plugin-catalog/). For example, to use SLURM you can install the `snakemake-executor-slurm` plugin using pip:
-```  
+```
+pixi shell
 pip install snakemake-executor-plugin-slurm
 ```
 
 We recommend adding a snakemake conda prefix to your `bashrc`, e.g. in the Stergachis lab add:
+
 ```bash
 export SNAKEMAKE_CONDA_PREFIX=/mmfs1/gscratch/stergachislab/snakemake-conda-envs
 export APPTAINER_CACHEDIR=/mmfs1/gscratch/stergachislab/snakemake-conda-envs/apptainer-cache
 ```
+
 Then snakemake installs all the additional requirements as conda envs in that directory.

README.md

@@ -1,47 +1,10 @@
 # 🔥 **FIRE**: <ins>F</ins>iber-seq <ins>I</ins>nferred <ins>R</ins>egulatory <ins>E</ins>lements
 
 [![DOI](https://zenodo.org/badge/561430995.svg)](https://zenodo.org/doi/10.5281/zenodo.10023811)
+[![Actions Status](https://github.com/fiberseq/FIRE/workflows/CI/badge.svg)](https://github.com/mrvollger/FIRE/actions)
 
-A Snakemake workflow for calling Fiber-seq Inferred Regulatory Elements (FIREs) on single molecules. For a more detailed description and methods see the [docs](/docs/README.md), or [watch](https://youtu.be/RiZrMltAiWM?si=sSo64goaNQxgyfcc) my lab meeting on FIRE.
+A Snakemake workflow for calling Fiber-seq Inferred Regulatory Elements (FIREs) on single molecules.
 
-## Install
+## Installation and Usage
 
-Please install `snakemake` and all the UCSC Kent utilities. For detailed instructions see the [installation README](/INSTALL.md).
-
-## Configuring
-
-See the [configuration README](/config/README.md), the example [configuration file](/config/config.yaml), and the example [manifest file](/config/config.tbl) for configuration options.
-
-
-## Run
-
-We have a run script that executes the FIRE snakemake called `fire`, and any extra parameters are passed directly to snakemake. For example:
-
-```bash
-./fire --configfile config/config.yaml
-```
-
-If you want to do a dry run:
-
-```bash
-./fire --configfile config/config.yaml -n
-```
-
-If you want to execute across a cluster (modify `profiles/slurm-executor` as needed for distributed execution):
-
-```bash
-./fire --configfile config/config.yaml --profile profiles/slurm-executor
-```
-
-You can also run snakemake directly, e.g.:
-
-```bash
-snakemake \
-  --configfile config/config.yaml \
-  --profile profiles/slurm-executor \
-  --local-cores 8 -k
-```
-
-## Test data
-
-You can find input data to test against at [this url](https://s3-us-west-2.amazonaws.com/stergachis-public1/index.html?prefix=FIRE/test-data/).
+See the [docs](https://fiberseq.github.io/fire/run.html) for detailed installation and usage instructions.

config/README.md

@@ -17,6 +17,11 @@ manifest: config/config.tbl
 
 
 ## Optional input options
+Specify that the input BAM file is an ONT Fiber-seq file. Default is `False`.
+```
+ont: True
+```
+
 Max number of threads to use in very distributed steps:
 ```
 max_t: 4