Giter VIP home page Giter VIP logo

multiqc_sav's Introduction

Build status install with bioconda Anaconda-Server Badge Anaconda-Server Badge Anaconda-Server Badge

MultiQC_SAV is a plugin for MultiQC, leveraging the InterOp python API to generate the most used tables and graphs from the Illumina SAV

For more information about MultiQC, see http://multiqc.info

For more information about Illumina SAV, see the Illumina support page

Description

The MultiQC_SAV plugin parses the InterOp files in an Illumina Sequencer output directory and generates tables and graphs of the most important metrics

Example

An example report can be found here

Installation

This plugin can be installed using the following methods

  • using pip:
pip install --upgrade --force-reinstall git+https://github.com/MultiQC/MultiQC_SAV.git
  • using conda:
conda install -c bioconda multiqc_sav
  • using setuptools:
git clone https://github.com/MultiQC/MultiQC_SAV
cd MultiQC_SAV
python setup.py install

Usage

This plugin adds a QC module and searches for the RunInfo.xml and RunParameters.xml files. It tries to infer if all required files are present. No special params are needed.

Required files

The illumina directory should contain the following files the directory structure as dictated by the sequencer

illumina_dir
├── InterOp
│   ├── *.bin
├── RunInfo.xml
├── RunParameters.xml

Contributors

multiqc_sav's People

Contributors

matthdsm avatar

Stargazers

Mattis Knulst avatar Oliver Mazariegos avatar Laise de Moraes avatar  avatar

Watchers

 avatar

Forkers

gustaveroussy

multiqc_sav's Issues

Novaseq X plus runs

It is breaking with NovaseqXplus Runs.

Please copy this log and report it at https://github.com/MultiQC/MultiQC/issues
│ Please attach a file that triggers the error. The last file found was:
RunParameters.xml.zip
20240412_LH00557_0015_A227M7HLT4/RunParameters.xml │
│ │
│ Traceback (most recent call last): │
│ File "/MG/SHARED/APPS/ANACONDA_DIR/anaconda/envs/multiqc_sav/lib/python3.11/site-packages/multiqc/multiqc.py", line 751, in run │
│ output = mod() │
│ ^^^^^ │
│ File "/MG/SHARED/APPS/ANACONDA_DIR/anaconda/envs/multiqc_sav/lib/python3.11/site-packages/multiqc_sav/modules/sav.py", line 273, in init
│ self.imaging_qc() │
│ File "/MG/SHARED/APPS/ANACONDA_DIR/anaconda/envs/multiqc_sav/lib/python3.11/site-packages/multiqc_sav/modules/sav.py", line 635, in imaging_qc │
│ plot_data = self.parse_imaging_table(imaging) │
│ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ │
│ File "/MG/SHARED/APPS/ANACONDA_DIR/anaconda/envs/multiqc_sav/lib/python3.11/site-packages/multiqc_sav/modules/sav.py", line 706, in parse_imaging_table │
│ occ_pf[f"Lane {lane}"].append({"x": occ, "y": pf, "color": colors[lane]}) │
│ ~~~~~~^^^^^^ │
│ IndexError: list index out of range

Broken installation

Hi, I'm trying to use this plug-in, yet I have issues from installation:

  1. With pip:
$ pip install --upgrade --force-reinstall git+https://github.com/MultiQC/MultiQC_SAV.git

Collecting git+https://github.com/MultiQC/MultiQC_SAV.git
  Cloning https://github.com/MultiQC/MultiQC_SAV.git to /tmp/pip-req-build-pbmi1qf6
  Running command git clone --filter=blob:none --quiet https://github.com/MultiQC/MultiQC_SAV.git /tmp/pip-req-build-pbmi1qf6
  Resolved https://github.com/MultiQC/MultiQC_SAV.git to commit 07661ca1dd728f0871cf3f021d1c1ee325a476c2
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
ERROR: Could not find a version that satisfies the requirement interop>=1.1.23 (from multiqc-sav) (from versions: none)
ERROR: No matching distribution found for interop>=1.1.23
  1. With Conda:
$conda create -n sandbox multiqc multiqc_sav

<skip verbose installation>
Preparing transaction: done
Verifying transaction: done
Executing transaction: done

To activate this environment, use

     $ conda activate sandbox

To deactivate an active environment, use

     $ conda deactivate

No error through installation process, but :

$multiqc --view-tags | grep sav

Traceback (most recent call last):
  File "/home/tdayris/anaconda3/envs/sandbox/lib/python3.11/site-packages/multiqc/utils/plugin_hooks.py", line 14, in <module>
    hook_functions[nicename].append(entry_point.load())
    ~~~~~~~~~~~~~~^^^^^^^^^^
KeyError: 'config_loaded'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/tdayris/anaconda3/envs/sandbox/bin/multiqc", line 6, in <module>
    from multiqc.__main__ import run_multiqc
  File "/home/tdayris/anaconda3/envs/sandbox/lib/python3.11/site-packages/multiqc/__init__.py", line 16, in <module>
    from .multiqc import run
  File "/home/tdayris/anaconda3/envs/sandbox/lib/python3.11/site-packages/multiqc/multiqc.py", line 30, in <module>
    from .utils import report, plugin_hooks, megaqc, util_functions, lint_helpers, config, util_functions, log
  File "/home/tdayris/anaconda3/envs/sandbox/lib/python3.11/site-packages/multiqc/utils/plugin_hooks.py", line 16, in <module>
    hook_functions[nicename] = [entry_point.load()]
                                ^^^^^^^^^^^^^^^^^^
  File "/home/tdayris/anaconda3/envs/sandbox/lib/python3.11/site-packages/pkg_resources/__init__.py", line 2470, in load
    self.require(*args, **kwargs)
  File "/home/tdayris/anaconda3/envs/sandbox/lib/python3.11/site-packages/pkg_resources/__init__.py", line 2493, in require
    items = working_set.resolve(reqs, env, installer, extras=self.extras)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/tdayris/anaconda3/envs/sandbox/lib/python3.11/site-packages/pkg_resources/__init__.py", line 795, in resolve
    raise DistributionNotFound(req, requirers)
pkg_resources.DistributionNotFound: The 'interop>=1.1.23' distribution was not found and is required by the application

I cannot install interop, neither with pip, nor conda.

Do you have any advice or additional installation step ?

Thank you in advance

PS: If I do not include multiqc_sav plug-in, then MultiQC works perfectly well.

Error parsing dates from NextSeq 2000

Plugin version: 0.0.2
MQC version: v1.10.1

[ERROR  ]         multiqc : Oops! The 'SAV' MultiQC module broke... 
  Please copy the following traceback and report it at https://github.com/ewels/MultiQC/issues 
  If possible, please include a log file that triggers the error - the last file found was:
    /projects/demultiplex/220112_VH00559_4_AAANY2JM5/RunParameters.xml
============================================================
Module SAV raised an exception: Traceback (most recent call last):
  File "/software/bcbio/anaconda/lib/python3.6/site-packages/multiqc_sav/modules/sav.py", line 294, in set_run_info
    parsed_run_date = datetime.strftime(datetime.strptime(run_date, "%y%m%d"), "%d-%m-%Y")
  File "/software/bcbio/anaconda/lib/python3.6/_strptime.py", line 565, in _strptime_datetime
    tt, fraction = _strptime(data_string, format)
  File "/software/bcbio/anaconda/lib/python3.6/_strptime.py", line 365, in _strptime
    data_string[found.end():])
ValueError: unconverted data remains: -01-12T13:49:36Z

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/software/bcbio/anaconda/lib/python3.6/site-packages/multiqc/multiqc.py", line 594, in run
    output = mod()
  File "/software/bcbio/anaconda/lib/python3.6/site-packages/multiqc_sav/modules/sav.py", line 269, in __init__
    self.set_run_info(run_info_xml)
  File "/software/bcbio/anaconda/lib/python3.6/site-packages/multiqc_sav/modules/sav.py", line 296, in set_run_info
    parsed_run_date = datetime.strftime(datetime.strptime(run_date, "%m/%d/%Y %I:%M:%S %p"), "%d-%m-%Y")
  File "/software/bcbio/anaconda/lib/python3.6/_strptime.py", line 565, in _strptime_datetime
    tt, fraction = _strptime(data_string, format)
  File "/software/bcbio/anaconda/lib/python3.6/_strptime.py", line 362, in _strptime
    (data_string, format))
ValueError: time data '2022-01-12T13:49:36Z' does not match format '%m/%d/%Y %I:%M:%S %p'

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.