Merge pull request #16 from cokelaer/main

switch working directory back to fastq/
sequana · Dec 6, 2023 · 47da7fa · 47da7fa
2 parents 666f61e + 014ed35
commit 47da7fa
Show file tree

Hide file tree

Showing 5 changed files with 61 additions and 30 deletions.
diff --git a/.pre-commit-config.yaml b/.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
+
diff --git a/README.rst b/README.rst
@@ -99,14 +99,14 @@ Details
 .. image:: https://raw.githubusercontent.com/sequana/demultiplex/master/sequana_pipelines/demultiplex/dag.png
 
 This pipeline runs bcl2fastq 2.20 and creates a set of diagnostics plots to help
-deciphering common issues such as missing index and sample sheet errors. 
+deciphering common issues such as missing index and sample sheet errors.
 
 
 Rules and configuration details
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 Here is the `latest documented configuration file <https://raw.githubusercontent.com/sequana/demultiplex/master/sequana_pipelines/demultiplex/config.yaml>`_
-to be used with the pipeline. Each rule used in the pipeline may have a section in the configuration file. 
+to be used with the pipeline. Each rule used in the pipeline may have a section in the configuration file.
 
 
 
@@ -116,8 +116,9 @@ Changelog
 ========= =======================================================================
 Version   Description
 ========= =======================================================================
+1.5.1     * swictch working directory to fastq instead of demultiplex(regression)
 1.5.0     * Uses click and new sequana_pipetools, add multiqc
-1.4.0     * Implement demultiplexing of single cell ATAC seq data with 
+1.4.0     * Implement demultiplexing of single cell ATAC seq data with
             cellranger.
 1.3.1     * use sequana_wrappers version in the config file
 1.3.0     * use latest sequana-wrappers to benefit and graphivz apptainer
@@ -129,8 +130,8 @@ Version   Description
 1.1.0     * Uses new sequana-wrappers repository
 1.0.5     * Fix regression bug to cope with new snakemake API
           * Compatibility with sequanix GUI
-1.0.4     * Better HTML report with updated images. 
-          * validate the SampleSheet when using sequana_demultiplex and/or the 
+1.0.4     * Better HTML report with updated images.
+          * validate the SampleSheet when using sequana_demultiplex and/or the
             pipeline
           * Add error handler from sequana_pipetools
           * save all undetermined barcodes (not just first 20)
@@ -139,7 +140,7 @@ Version   Description
             it can be used in Sequanix
 1.0.3     * remove check_samplesheet and fix_samplesheet modules now in sequana
           * check sample sheet but do not fail. Instead, informing users that
-            there is an error and suggest to use 'sequana samplesheet 
+            there is an error and suggest to use 'sequana samplesheet
             --quick-fix'
 1.0.2     Use 'sequana samplesheet --check ' command instead of deprecated
           sequana_check_sample_sheet command
@@ -152,40 +153,40 @@ Version   Description
           * The --ignore-missing-bcls option is changed into
             --no-ignore-missing-bcls so as to ignore missing bcls by default
             keep this option as a flag and keep same behaviour
-          * Fix HTML syntax 
+          * Fix HTML syntax
 1.0.0     * stable version pinned on sequana libraries
-0.9.11    * fix label in plot_summary, 
+0.9.11    * fix label in plot_summary,
           * add new plot to show reads per sample + undetermined
-          * add two tools one to check the samplesheet called 
-            sequana_sample_sheet and one called sequana_fix_samplesheet. The 
+          * add two tools one to check the samplesheet called
+            sequana_sample_sheet and one called sequana_fix_samplesheet. The
             former is now inside the pipeline as well and when creating the
             pipeline
           * set --write_reverse_complement to False by default
           * remove the --ignore-missing-control which is deprecated anyway
 0.9.10    * implement the new option --from-project, add missing MANIFEST
-0.9.9     * simplification of the pipeline to use sequana 0.8.4 to speed up 
+0.9.9     * simplification of the pipeline to use sequana 0.8.4 to speed up
             the --help calls.
-          * include a summary HTML report 
+          * include a summary HTML report
 0.9.8     * fix typos
 0.9.7     * Use new release of sequana_pipetools
           * set matplotlib backend to agg
           * include a simple HTML report
 0.9.6     * Handle different RunParameter.xml name (NextSeq vs HiSeq)
-0.9.5     * Fix a regression bug due to new sequana release. We do not check 
+0.9.5     * Fix a regression bug due to new sequana release. We do not check
             the input file (fastq) since this is not a sequence analysis
             pipeline
           * Check whether it is a NextSeq run. If so, merging-strategy must be
             set to 'merge'. Can be bypassed using --force
-0.9.4     * Check the presence of the bcl input directory and samplesheet. 
-          * More help in the --help message. 
+0.9.4     * Check the presence of the bcl input directory and samplesheet.
+          * More help in the --help message.
           * add  --sample-sheet option to replace --samplesheet option
           * Fix the schema file
           * Check for presence of RunParameters.xml and provide information
             if merging-stratgy is set to None whereas it is a NextSeq run
 0.9.3     Fix regression bug
-0.9.2     remove warning due to relative paths. 
-0.9.1     Make the merging options compulsory. Users must tell whether they 
-          want to merge the lanes or not. This avoid to do the merging or not 
+0.9.2     remove warning due to relative paths.
+0.9.1     Make the merging options compulsory. Users must tell whether they
+          want to merge the lanes or not. This avoid to do the merging or not
           whereas the inverse was expected.
 0.8.6     Uses 64G/biomics queue and 16 cores on a SLURM scheduler
 ========= =======================================================================
@@ -195,7 +196,6 @@ Version   Description
 Contribute & Code of Conduct
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-To contribute to this project, please take a look at the 
-`Contributing Guidelines <https://github.com/sequana/sequana/blob/master/CONTRIBUTING.rst>`_ first. Please note that this project is released with a 
+To contribute to this project, please take a look at the
+`Contributing Guidelines <https://github.com/sequana/sequana/blob/master/CONTRIBUTING.rst>`_ first. Please note that this project is released with a
 `Code of Conduct <https://github.com/sequana/sequana/blob/master/CONDUCT.md>`_. By contributing to this project, you agree to abide by its terms.
-
diff --git a/pyproject.toml b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "sequana-demultiplex"
-version = "1.5.0"
+version = "1.5.1"
 description = "Pipeline that runs bcl2fastq and ease demultiplexing of Sequencing data"
 authors = ["Sequana Team"]
 license = "BSD-3"

diff --git a/requirements.txt b/requirements.txt
diff --git a/sequana_pipelines/demultiplex/main.py b/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.