Conda
See the ‘activating the conda environment’ section below to access this
software.
multiqc-1.14
MultiQC is a reporting tool that parses summary statistics from results and
log files generated by other bioinformatics tools. MultiQC doesn’t run other
tools for you - it’s designed to be placed at the end of analysis pipelines or
to be run manually when you’ve finished running your tools.
When you launch MultiQC, it recursively searches through any provided file
paths and finds files that it recognises. It parses relevant information from
these and generates a single stand-alone HTML report file. It also saves a
directory of data files with all parsed data for further downstream use.
Running multiqc
The most basic way to use is to run mutliqc . in a directory with findable
outputs.
Here is a link to the documentation for running this
software
Notice
Past installs were done using python3 -m pip install multiqc. Due to
dependency conflicts, we will be using conda for this software going forward.
Activating the conda environment
Check out a node with qrsh and run:
1
2
|
bash
source /local/cluster/conda-envs/envs/multiqc-1.14/activate.sh
|
And then run your commands as usual. To use over SGE, include the source line
above in a shell script prior to your commands, e.g.
1
2
3
4
|
$ cat run_multiqc.sh
#!/usr/bin/env bash
source /local/cluster/conda-envs/envs/multiqc-1.14/activate.sh
multiqc .
|
And then run SGE_Batch -c 'bash ./run_multiqc' -r sge.multiqc ....
Making activation easier
If you have had conda set up for a while, e.g. using the instructions in this
post, then you can
run (only necessary once):
1
2
3
|
bash
conda config --append envs_dirs /local/cluster/conda-envs/envs
conda config --append pkgs_dirs /local/cluster/conda-envs/pkgs
|
and then you can activate the env using conda activate multiqc-1.14.
Location and version
1
2
3
4
5
6
|
$ conda activate multiqc-1.14
$ which multiqc
/local/cluster/conda-envs/envs/multiqc-1.14/bin/multiqc
$ multiqc --version
multiqc, version 1.14
|
help message
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
|
$ multiqc --help
/// MultiQC 🔍 | v1.14
Usage: multiqc [OPTIONS] [ANALYSIS DIRECTORY]
MultiQC aggregates results from bioinformatics analyses across many samples
into a single report.
It searches a given directory for analysis logs and compiles a HTML report.
It's a general use tool, perfect for summarising the output from numerous
bioinformatics tools.
To run, supply with one or more directory to scan for analysis results. For
example, to run in the current working directory, use 'multiqc .'
╭─ Main options ─────────────────────────────────────────────────────────────╮
│ --force -f Overwrite any existing reports │
│ --config -c Specific config file to load, after those in │
│ MultiQC dir / home dir / working dir. │
│ (PATH) │
│ --cl-config Specify MultiQC config YAML on the command line │
│ (TEXT) │
│ --filename -n Report filename. Use 'stdout' to print to standard │
│ out. │
│ (TEXT) │
│ --outdir -o Create report in the specified output directory. │
│ (TEXT) │
│ --ignore -x Ignore analysis files (GLOB EXPRESSION) │
│ --ignore-samples Ignore sample names (GLOB EXPRESSION) │
│ --ignore-symlinks Ignore symlinked directories and files │
│ --file-list -l Supply a file containing a list of file paths to be │
│ searched, one per row │
╰────────────────────────────────────────────────────────────────────────────╯
╭─ Choosing modules to run ──────────────────────────────────────────────────╮
│ --module -m Use only this module. Can specify multiple times. │
│ (MODULE NAME) │
│ --exclude -e Do not use this module. Can specify multiple times. │
│ (MODULE NAME) │
│ --tag Use only modules which tagged with this keyword (TEXT) │
│ --view-tags View the available tags and which modules they load │
╰────────────────────────────────────────────────────────────────────────────╯
╭─ Sample handling ──────────────────────────────────────────────────────────╮
│ --dirs -d Prepend directory to sample names │
│ --dirs-depth -dd Prepend n directories to sample names. Negative │
│ number to take from start of path. │
│ (INTEGER) │
│ --fullnames -s Do not clean the sample names (leave as full file │
│ name) │
│ --fn_as_s_name Use the log filename as the sample name │
│ --replace-names TSV file to rename sample names during report │
│ generation │
│ (PATH) │
╰────────────────────────────────────────────────────────────────────────────╯
╭─ Report customisation ─────────────────────────────────────────────────────╮
│ --title -i Report title. Printed as page header, used for │
│ filename if not otherwise specified. │
│ (TEXT) │
│ --comment -b Custom comment, will be printed at the top of the │
│ report. │
│ (TEXT) │
│ --template -t Report template to use. │
│ (default|default_dev|gathered|geo|sections|simple) │
│ --sample-names TSV file containing alternative sample names for │
│ renaming buttons in the report │
│ (PATH) │
│ --sample-filters TSV file containing show/hide patterns for the │
│ report │
│ (PATH) │
│ --custom-css-file Custom CSS file to add to the final report (PATH) │
╰────────────────────────────────────────────────────────────────────────────╯
╭─ Output files ─────────────────────────────────────────────────────────────╮
│ --flat -fp Use only flat plots (static images) │
│ --interactive -ip Use only interactive plots (in-browser Javascript) │
│ --export -p Export plots as static images in addition to the │
│ report │
│ --data-dir Force the parsed data directory to be created. │
│ --no-data-dir Prevent the parsed data directory from being created. │
│ --data-format -k Output parsed data in a different format. │
│ (tsv|json|yaml) │
│ --zip-data-dir -z Compress the data directory. │
│ --no-report Do not generate a report, only export data and plots │
│ --pdf Creates PDF report with the 'simple' template. │
│ Requires Pandoc to be installed. │
╰────────────────────────────────────────────────────────────────────────────╯
╭─ MultiQC behaviour ────────────────────────────────────────────────────────╮
│ --verbose -v Increase output verbosity. (INTEGER RANGE) │
│ --quiet -q Only show log warnings │
│ --lint Use strict linting (validation) to help code │
│ development │
│ --profile-runtime Add analysis of how long MultiQC takes to run to │
│ the report │
│ --no-megaqc-upload Don't upload generated report to MegaQC, even if │
│ MegaQC options are found │
│ --no-ansi Disable coloured log output │
│ --version Show the version and exit. │
│ --help -h Show this message and exit. │
╰────────────────────────────────────────────────────────────────────────────╯
See http://multiqc.info for more details.
|
software ref: https://multiqc.info/
research ref: http://dx.doi.org/10.1093/bioinformatics/btw354