fix: improve CLI help & set mode=slurm as default (#97)

* docs: improve CLI help & set mode=slurm as default

* chore: update CHANGELOG.md

* ci: use mode=local

* ci: remove reference to deprecated code

* fix: ensure bins are executable

* ci: bump python to 3.11

Author: kelly-sovacool

.github/workflows/build.yml

@@ -17,7 +17,7 @@ jobs:
     timeout-minutes: 2
     strategy:
       matrix:
-        python-version: ["3.10"]
+        python-version: ["3.11"]
 
     steps:
       - uses: actions/checkout@v3
@@ -34,7 +34,6 @@ jobs:
         run: |
           python -m pip install --upgrade pip setuptools
           pip install .[dev,test]
-          python -c 'from logan.src.util import chmod_bins_exec; chmod_bins_exec()'
       - name: Check CLI basics
         run: |
           which logan
@@ -43,12 +42,14 @@ jobs:
       - name: Test stub run for Fastqs
         run: |
           logan init
-          logan run -profile ci_stub \
-          --sample_sheet .tests/pairs.tsv \
-          --fastq_input ".tests/*R{1,2}_001.fastq.gz" \
-          --vc --cnv --sv --gl --qc \
-          --split_regions 2 \
-          --genome hg38 \
-          --outdir output_tn_fqs \
-          --intervals .tests/interval.bed \
-          -preview
+          logan run \
+            -profile ci_stub \
+            --mode local \
+            --sample_sheet .tests/pairs.tsv \
+            --fastq_input ".tests/*R{1,2}_001.fastq.gz" \
+            --vc --cnv --sv --gl --qc \
+            --split_regions 2 \
+            --genome hg38 \
+            --outdir output_tn_fqs \
+            --intervals .tests/interval.bed \
+            -preview

CHANGELOG.md

@@ -1,5 +1,8 @@
 ## LOGAN development version
 
+- Improve help message for `logan run`. (#97, @kelly-sovacool)
+  - the default `--mode` is now `slurm`.
+
 # LOGAN 0.3.0
 
 - LOGAN now depends on ccbr_tools v0.4 for updated jobby & spooker utilities. (#95, @kelly-sovacool)

bin/hello-world.py

@@ -12,4 +12,4 @@ def main():
 
 
 if __name__ == "__main__":
-    main(sys.argv)
+    main(sys.argv)

bin/logan

@@ -4,4 +4,4 @@
 
 TOOLDIR=$(realpath $(dirname $(dirname ${BASH_SOURCE})))
 
-${TOOLDIR}/main.py "$@"
+${TOOLDIR}/main.py "$@"

bin/make_freec_exome_paired.pl

@@ -47,4 +47,4 @@
 print C "makePileup = $makePileup\n";
 print C "fastaFile = $fastaFile\n";
 print C "minimalCoveragePerPosition = 10\n";
-print C "SNPfile = $SNPfile";
+print C "SNPfile = $SNPfile";

bin/reformat_bed.py

@@ -82,4 +82,4 @@
                 # freec_bed.write(freec_bed_output)
 
                 ### Update loop variables
-                last_start = curr_cols[1]
+                last_start = curr_cols[1]

main.py

@@ -0,0 +1,16 @@
+#!/usr/bin/env python
+import os
+import re
+import sys
+
+# add script directory to the path to allow logan CLI to work out-of-the-box
+# without the need to install it via pip first
+SCRIPT_DIR = os.path.join(os.path.dirname(os.path.abspath(__file__)), "src")
+sys.path.append(SCRIPT_DIR)
+from src.__main__ import main
+
+if (
+    __name__ == "__main__"
+):  # this block is adapted from the executable file created by `pip install`
+    sys.argv[0] = re.sub(r"(-script\.pyw|\.exe)?$", "", sys.argv[0])
+    sys.exit(main())

src/__main__.py

@@ -52,18 +52,21 @@ def cli():
 
 
 help_msg_extra = """
+\b
+Nextflow options:
+-profile <profile>    Nextflow profile to use (e.g. test)
+-params-file <file>   Nextflow params file to use (e.g. assets/params.yml)
+-preview              Preview the processes that will run without executing them
+
 \b
 EXAMPLES:
 Execute with slurm:
-    logan run ... --mode slurm
+  logan run --output path/to/outdir --mode slurm
 Preview the processes that will run:
-    logan run ... --mode local -preview
+  logan run --output path/to/outdir --mode local -preview
 Add nextflow args (anything supported by `nextflow run`):
-    logan run ... -work-dir path/to/workDir
-Run with a specific installation of logan:
-    logan run --main path/to/logan/main.nf ...
-Run with a specific tag, branch, or commit from GitHub:
-    logan run --main CCBR/LOGAN -r v0.1.0 ...
+  logan run --output path/to/outdir --mode slurm -profile test
+  logan run --output path/to/outdir --mode slurm -profile test -params-file assets/params.yml
 """
 
 
@@ -82,6 +85,7 @@ def cli():
     type=str,
     default=repo_base("main.nf"),
     show_default=True,
+    hidden=True,
 )
 @click.option(
     "--output",
@@ -95,7 +99,7 @@ def cli():
     "_mode",
     help="Run mode (slurm, local)",
     type=str,
-    default="local",
+    default="slurm",
     show_default=True,
 )
 @click.option(
@@ -109,7 +113,12 @@ def cli():
 )
 @click.argument("nextflow_args", nargs=-1)
 def run(main_path, output, _mode, force_all, **kwargs):
-    """Run the workflow"""
+    """
+    Run the workflow
+    
+    Note: you must first run `logan init --output <output_dir>` to initialize
+    the output directory.
+    """
     if (  # this is the only acceptable github repo option for logan
         main_path != "CCBR/LOGAN"
     ):