switch working directory back to fastq/

add precommit
remove requirements (useless)

.pre-commit-config.yaml

@@ -0,0 +1,33 @@
+
+files: '\.(py|rst|sh)$'
+fail_fast: false
+
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.2.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+    #-   id: check-executables-have-shebangs
+    -   id: check-ast
+
+-   repo: https://github.com/pycqa/flake8
+    rev: 6.1.0
+    hooks:
+    -   id: flake8
+        args: ["-j8", "--ignore=E203,E501,W503,E722", "--max-line-length=120", "--exit-zero"]
+
+-   repo: https://github.com/psf/black
+    rev: 22.10.0
+    hooks:
+    -   id: black
+        args: ["--line-length=120"]
+        exclude: E501
+
+-   repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        args: ["--profile", "black"] # solves conflicts between black and isort
+

sequana_pipelines/demultiplex/main.py

@@ -10,18 +10,18 @@
 #  documentation: http://sequana.readthedocs.io
 #
 ##############################################################################
-import sys
 import os
+import sys
 
-import rich_click as click
 import click_completion
+import rich_click as click
 
 click_completion.init()
 
 NAME = "demultiplex"
 
-from sequana_pipetools.options import *
 from sequana_pipetools import SequanaManager
+from sequana_pipetools.options import *
 
 help = init_click(
     NAME,
@@ -32,7 +32,7 @@
 
 
 @click.command(context_settings=help)
-@include_options_from(ClickSnakemakeOptions, working_directory=NAME)
+@include_options_from(ClickSnakemakeOptions, working_directory="fastq")
 @include_options_from(ClickSlurmOptions)
 @include_options_from(ClickInputOptions, add_input_readtag=False)
 @include_options_from(ClickGeneralOptions)
@@ -96,7 +96,7 @@
     default=False,
     is_flag=True,
     show_default=True,
-    help="""Set options to--minimum-trimmed-read-length 15 --mask-short-adapter-reads 15 
+    help="""Set options to--minimum-trimmed-read-length 15 --mask-short-adapter-reads 15
 and do not merge lanes""",
 )
 @click.option(
@@ -190,7 +190,7 @@ def main(**options):
             logger.critical(err)
             logger.critical(
                 """Your sample sheet seems to be incorrect. Before running the pipeline you will have to fix it. You may use 'sequana samplesheet --quick-fix'"""
-                )
+            )
 
     # finalise the command and save it; copy the snakemake. update the config
     # file and save it.