fix: use env(CCBR_PIPELINER_DIR) in place of absolute paths

.github/workflows/build.yml

@@ -67,6 +67,24 @@ jobs:
         with:
           name: nextflow-log
           path: .nextflow.log
+
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.11
+          cache: "pip"
+      - name: Install pre-commit and dependencies
+        run: |
+          python -m pip install --upgrade pip setuptools
+          pip install pre-commit
+      - name: Run pre-commit hooks
+        run: |
+          pre-commit run --all-files --show-diff-on-failure
+
   build-status: # https://github.com/orgs/community/discussions/4324#discussioncomment-3477871
     runs-on: ubuntu-latest
     needs: [build]

.pre-commit-config.yaml

@@ -6,18 +6,24 @@ exclude: |
       ^docs/.*.html|
       ^_extensions/|
       ^nextflow_schema.json|
-      ^.*.svg |
-      ^.github/CONTRIBUTING.md
+      ^.*.svg|
+      ^.github/CONTRIBUTING.md|
+      ^tests/data/
    )
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v1.2.3
+    rev: v6.0.0
     hooks:
       - id: check-added-large-files
         args: ["--maxkb=10240"]
       - id: end-of-file-fixer
       - id: trailing-whitespace
       - id: check-json
+  - repo: https://github.com/CCBR/Tools
+    rev: precommit-hooks
+    hooks:
+      - id: detect-absolute-paths
+        exclude: ^.gitignore, .*.gitignore, .*.diff$
   # spell check
   - repo: https://github.com/codespell-project/codespell
     rev: v2.4.1
@@ -26,24 +32,24 @@ repos:
         args: ["--ignore-words-list=bais"]
   # Python formatting
   - repo: https://github.com/psf/black
-    rev: 23.7.0
+    rev: 26.1.0
     hooks:
       - id: black
   # R formatting
   - repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.1.2
+    rev: v0.4.3.9020
     hooks:
       - id: style-files
   # general linting
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: "v3.1.0"
+    rev: "v4.0.0-alpha.8"
     hooks:
       - id: prettier
         additional_dependencies:
           - prettier@3.4.0
   # 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]

README.md

@@ -45,14 +45,14 @@ Initialize and run champagne with test data:
 ```sh
 # copy the champagne config files to your project directory.
 # --output is optional and defaults to your current working directory.
-champagne init --output /data/$USER/champagne_project
+champagne init --output path/to/champagne_project/
 
 # preview the champagne jobs that will run with the test dataset
-champagne run --output /data/$USER/champagne_project \
+champagne run --output path/to/champagne_project/ \
   --mode local -profile test -preview
 
 # launch a champagne run on slurm with the test dataset
-champagne run --output /data/$USER/champagne_project \
+champagne run --output path/to/champagne_project/ \
   --mode slurm -profile test
 ```
 
@@ -66,7 +66,7 @@ Once you've created a samplesheet with paths to your fastq files,
 run champagne with the `--input` option to specify the path to your sample sheet:
 
 ```sh
-champagne run --output /data/$USER/champagne_project \
+champagne run --output path/to/champagne_project/ \
     --mode slurm \
     --input samplesheet.csv \
     --genome hg38
@@ -91,7 +91,7 @@ run_qc: true
 You can then use these parameters with the `-params-file` option:
 
 ```sh
-champagne run --output /data/$USER/champagne_project \
+champagne run --output path/to/champagne_project/ \
     --mode slurm \
     -params-file assets/params.yml
 ```
@@ -112,7 +112,7 @@ If your experiment uses a spike-in control, you can specify the spike-in genome
 with the `--spike_genome` parameter:
 
 ```sh
-champagne run --output /data/$USER/champagne_project \
+champagne run --output path/to/champagne_project/ \
     --mode slurm \
     --input samplesheet.csv \
     --genome hg38 \

conf/biowulf.config

@@ -7,28 +7,28 @@ params {
     max_cpus = 32
     max_time = '72 h'
 
-    igenomes_base = '/fdb/igenomes/'
+    igenomes_base = '/fdb/igenomes/' // abs-path:ignore
 
     // CCBR shared resource paths
-    index_dir = '/data/CCBR_Pipeliner/db/PipeDB/Indices'
+    index_dir = "${env('CCBR_PIPELINER_DIR')}/db/PipeDB/Indices"
 
     fastq_screen_conf = "${projectDir}/assets/fastq_screen_biowulf.conf"
-    fastq_screen_db_dir = '/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen_db/'
+    fastq_screen_db_dir = "${env('CCBR_PIPELINER_DIR')}/db/PipeDB/lib/fastq_screen_db/"
 
     publish_dir_mode = 'link'
 }
 
 singularity {
     enabled = true
     autoMounts = true
-    cacheDir = "/data/CCBR_Pipeliner/SIFs"
+    cacheDir = "${env('CCBR_PIPELINER_DIR')}/SIFs"
     envWhitelist='https_proxy,http_proxy,ftp_proxy,DISPLAY,SLURM_JOBID,SINGULARITY_BINDPATH'
 }
 
-env.SINGULARITY_CACHEDIR = "/data/CCBR_Pipeliner/SIFs"
+env.SINGULARITY_CACHEDIR = "${env('CCBR_PIPELINER_DIR')}/SIFs"
 
 process.clusterOptions = ' --gres=lscratch:200 '
-process.scratch = '/lscratch/$SLURM_JOB_ID'
+process.scratch = '/lscratch/$SLURM_JOB_ID' // abs-path:ignore
 process.stageInMode = 'symlink'
 process.stageOutMode = 'rsync'
 // https://www.nextflow.io/docs/latest/reference/process.html#cache

docs/_genomes_tail.md

@@ -4,10 +4,10 @@ If you'd like to override the default blacklist used by one of the built-in geno
 you can provide a custom blacklist bed file or fasta file:
 
 ```sh
-champagne run --output /data/$USER/champagne_project \
+champagne run --output path/to/champagne_project/ \
     --mode slurm \
     --genome hg38 \
-    --blacklist /path/to/blacklist.bed
+    --blacklist path/to/blacklist.bed
 ```
 
 If you're providing a custom blacklist bed file, make sure its regions refer to
@@ -26,7 +26,7 @@ If you'd like to use a custom genome, you'll need the following files:
 Prepare your custom reference genome with:
 
 ```sh
-champagne run --output /data/$USER/champagne_project \
+champagne run --output path/to/champagne_project/ \
     --mode slurm \
     -entry MAKE_REFERENCE \
     --genome custom_genome \
@@ -40,7 +40,7 @@ The reference files and a config file for the genome will be written in `results
 Then you can run champagne using your custom genome:
 
 ```sh
-champagne run --output /data/$USER/champagne_project \
+champagne run --output path/to/champagne_project/ \
     --mode slurm -profile biowulf \
     --input samplesheet.csv \
     --genome custom_genome \

docs/_params_head.md

@@ -4,7 +4,7 @@ Any parameter can be set via the CLI using two hyphens (`--`) followed by the
 parameter name and value. For example:
 
 ```sh
-champagne run --output /data/$USER/champagne_project \
+champagne run --output path/to/champagne_project/ \
     --input assets/samplesheet_full_mm10.csv \
     --contrasts assets/contrasts_full_mm10.csv \
     --genome mm10 \
@@ -31,7 +31,7 @@ run_qc: true
 You can then use these parameters with the `-params-file` option:
 
 ```sh
-champagne run --output /data/$USER/champagne_project \
+champagne run --output path/to/champagne_project/ \
     -params-file assets/params.yml
 ```
 

docs/devs/contributors.md

@@ -1,7 +1,7 @@
 # Contributors
 
-|                                                                                                                                                                                                                                                                                          |                                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                                                                   |
-| ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| | | |
+|---|---|---|
 | <a href='https://github.com/kelly-sovacool' title='Kelly Sovacool, PhD' style='display: inline-block; text-align: center;'><img src='https://avatars.githubusercontent.com/u/17768269?v=4' alt='Kelly Sovacool, PhD' style='border-radius: 50%; width: 30%;'><br>Kelly Sovacool, PhD</a> | <a href='https://github.com/slsevilla' title='Samantha' style='display: inline-block; text-align: center;'><img src='https://avatars.githubusercontent.com/u/20726305?v=4' alt='Samantha' style='border-radius: 50%; width: 30%;'><br>Samantha</a> | <a href='https://github.com/kopardev' title='Vishal Koparde, PhD' style='display: inline-block; text-align: center;'><img src='https://avatars.githubusercontent.com/u/1882209?v=4' alt='Vishal Koparde, PhD' style='border-radius: 50%; width: 30%;'><br>Vishal Koparde, PhD</a> |
 
-View the [contributors graph on GitHub](https://github.com/CCBR/CHAMPAGNE/graphs/contributors) for more details.
+View the [contributors graph on GitHub](https://github.com/CCBR/CHAMPAGNE/graphs/contributors) for more details.

docs/guide/genomes.md

@@ -80,17 +80,16 @@ These genomes can be passed to the `--spike_genome` parameter.
 - blacklist_bed: `NO_FILE`
 - effective_genome_size: `4641652`
 - chrom_sizes: `${params.index_dir}/ecoli_k12/Chromosomes/chrom.sizes`
-
 ### Custom blacklist
 
 If you'd like to override the default blacklist used by one of the built-in genomes,
 you can provide a custom blacklist bed file or fasta file:
 
 ```sh
-champagne run --output /data/$USER/champagne_project \
+champagne run --output path/to/champagne_project/ \
     --mode slurm \
     --genome hg38 \
-    --blacklist /path/to/blacklist.bed
+    --blacklist path/to/blacklist.bed
 ```
 
 If you're providing a custom blacklist bed file, make sure its regions refer to
@@ -109,7 +108,7 @@ If you'd like to use a custom genome, you'll need the following files:
 Prepare your custom reference genome with:
 
 ```sh
-champagne run --output /data/$USER/champagne_project \
+champagne run --output path/to/champagne_project/ \
     --mode slurm \
     -entry MAKE_REFERENCE \
     --genome custom_genome \
@@ -123,7 +122,7 @@ The reference files and a config file for the genome will be written in `results
 Then you can run champagne using your custom genome:
 
 ```sh
-champagne run --output /data/$USER/champagne_project \
+champagne run --output path/to/champagne_project/ \
     --mode slurm -profile biowulf \
     --input samplesheet.csv \
     --genome custom_genome \

docs/guide/output.md

@@ -6,7 +6,7 @@ After running the pipeline, the output directory will also contain `results/`,
 `log/`, `work/`, and `submit_slurm.sh` (if using `--mode slurm`).
 
 ```
-/data/$USER/champagne_project
+path/to/champagne_project/
 ├── assets/
 ├── conf/
 ├── log/
@@ -30,7 +30,7 @@ After running the pipeline, the output directory will also contain `results/`,
 
 Workflow output files will be written to the `results/` directory by default in your pipeline run output directory.
 
-For example, if you ran champagne with `champagne run --output /data/$USER/champagne_project`, the results files will be in `/data/$USER/champagne_project/results/`.
+For example, if you ran champagne with `champagne run --output path/to/champagne_project/`, the results files will be in `path/to/champagne_project//results/`.
 
 All paths listed below are relative to the `results/` directory.