Main (#204)

.github/workflows/docs.yml

@@ -21,7 +21,6 @@ jobs:
       - name: build docs
         run: |
           micromamba activate dissectBCL
-          pip install .
+          pip install .[docs]
           cd docs
-          pip install -r requirements.txt
           make html

.readthedocs.yaml

@@ -12,4 +12,5 @@ python:
   install:
   - method: pip
     path: .
-  - requirements: docs/requirements.txt
+    extra_requirements:
+    - docs

contaminome.yml

@@ -85,6 +85,16 @@ prokaryotes:
    vulgarname: haemophilus
    accession: GCF_000931575.1
    taxid: 727
+  Wolbachia melanogaster symbiont:
+   URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/016/584/425/GCA_016584425.1_ASM1658442v1/GCA_016584425.1_ASM1658442v1_genomic.fna.gz
+   vulgarname: wolbachia
+   accession: GCF_016584425.1
+   taxid: 163164
+  Staphylococcus aureus:
+    URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/013/425/GCF_000013425.1_ASM1342v1/GCF_000013425.1_ASM1342v1_genomic.fna.gz
+    vulgarname: staph_aureus
+    accession: GCF_000013425.1
+    taxid: 1280
 custom:
   Severe acute respiratory syndrome coronavirus 2:
    URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/858/895/GCF_009858895.2_ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.fna.gz

pyproject.toml

@@ -22,13 +22,16 @@ dependencies = [
 ]
 [project.optional-dependencies]
 dev = [
-    "ruff",
-    "coverage",
-    "pytest",
-    "pytest-cov",
-    "pytest-datafiles"
+  "ruff",
+  "coverage",
+  "pytest",
+  "pytest-cov",
+  "pytest-datafiles"
+]
+docs = [
+  "sphinx>=7.2.6",
+  "sphinx_rtd_theme>=2.0.0"
 ]
-
 [project.scripts]
 dissect = "dissectBCL.dissect:dissect"
 wd40 = "wd40.wd40:cli"

src/tools/prep_contaminome.py

@@ -56,6 +56,8 @@
     'mycoplasma': [2148, 14, 'species'],
     'mycoplasma-hyorhinis': [2100, 14, 'species'],
     'haemophilus': [727, 14, 'species'],
+    'wolbachia': [163164, 14, 'species'],
+    'staph_aureus': [1280, 14, 'species'],
     'sars-cov2': [2697049, 7, 'species'],
     'flu-a': [335341, 7, 'species'],
     'noro': [11983, 7, 'species'],

src/wd40/wd40.py

@@ -2,11 +2,8 @@
 from rich import print
 from importlib.metadata import version
 import os
-import sys
 from dissectBCL.misc import getConf
 from wd40.release import rel as release
-from wd40.cat import catRun
-from wd40.diagnose import diagnose
 
 can_string = "[red]            ___ \n[/red]"
 can_string += "[red]           |___|--------[/red]\n"
@@ -34,7 +31,7 @@
     "wd40": [
         {
             "name": "Main commands",
-            "commands": ["rel", "cat", "diag"],
+            "commands": ["rel"],
         }
     ]
 }
@@ -103,58 +100,3 @@ def rel(ctx, flowcell):
         ctx.obj['fexBool'],
         ctx.obj['fromAddress']
     )
-
-
-@cli.command()
-@click.option(
-    "--flowcells",
-    "-f",
-    required=True,
-    help='Specify 2 flowcell folders, e.g. -f flowcell1 -f flowcell2',
-    multiple=True
-)
-@click.option(
-    "--project",
-    "-p",
-    required=True,
-    help='project folder. only 1 allowed.'
-)
-@click.option(
-    "--output",
-    "-o",
-    required=True,
-    help='folder to write output into.'
-)
-@click.pass_context
-def cat(ctx, flowcells, project, output):
-    """combine fastq files of a project sequenced on multiple flow cells."""
-    if len(flowcells) != 2:
-        sys.exit("Please specify exactly two flowcells..")
-    project = os.path.basename(project)
-    p1 = os.path.join(
-        ctx.obj['fastqDir'],
-        os.path.basename(flowcells[0]),
-        project
-    )
-    p2 = os.path.join(
-        ctx.obj['fastqDir'],
-        os.path.basename(flowcells[1]),
-        project
-    )
-    if not os.path.exists(p1):
-        sys.exit('{} not found.'.format(p1))
-    if not os.path.exists(p2):
-        sys.exit('{} not found.'.format(p2))
-    catRun(project, p1, p2, os.path.abspath(output))
-
-
-@cli.command()
-@click.argument(
-    "flowcell",
-    default='./',
-    type=click.Path(exists=True)
-)
-@click.pass_context
-def diag(ctx, flowcell):
-    """Diagnose a flowcell."""
-    diagnose(flowcell, ctx.obj['solDir'])