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To catch up, just use stage Anna's pre-made files:
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After saving this file, remove the previous MultiQC outputs and re-run the program:
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To catch up, just use Anna's pre-made files:
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Now run multiqc again:
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cd $SCRATCH/byteclub/multiqc/02_bowtie rm -rf mqc_report* multiqc . |
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To catch up, just use Anna's pre-made files:
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After making this config file modification, you can now run multiqc again:
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# Titles to use for the report.
title: "ATAC-Seq QC Reports"
subtitle: null
intro_text: "MultiQC reports for Igor's ATAC-Seq proof-of-concept project."
report_header_info:
- Sequenced by: 'GSAF'
- Job: 'JA17277'
- Run: 'SA17121'
- Setup: '2x150'
# Change the output filenames
output_fn_name: mqc_report.html
data_dir_name: mqc_report_data
# Ignore these files / directories / paths when searching for reports
fn_ignore_files:
- '*.dupinfo.txt'
# Modules that should come at the top of the report
top_modules:
- 'generalstats'
- 'fastqc'
- 'samtools'
- 'picard' |
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To catch up, just use Anna's pre-made files:
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After making this config file modification, you can now run multiqc again:
...
Producing a report like this: . ftphttp://gapdhweb.corral.icmbtacc.utexas.edu/misciyer/byteclub/multiqc/05_section_order.mqc_report.changed_section_order.htmlhtml, with a section order that more closely follows workflow processing steps.
About MultiQC custom data
When MultiQC does not know about data produced by a program it doesn't know about, it has a mechanisms for adding custom report sections. The simple way to do this is declaratively, (i.e., via configuation parameters) as described below. (You can also write a Python module for very fine-grained control, but that is a lot more work.)
To add a section for custom data:
- Format the data appropriately
- MultiQC supports a number of data file formats (yaml, comma-separated values, etc.)
- I recommend using simple tab-delimited text files, with MultiQC's preferred .tsv extension.
- data can be provided as one file per sample (where the sample name is part of the file name)
- or as a single table-like file containing data for all samples
- MultiQC supports a number of data file formats (yaml, comma-separated values, etc.)
- Add two required custom data section entries in the multiqc_config.yaml configuration file
- a sp (search path) section for finding report data
- specifying a wildcard pattern, if data is supplied as one file per sample
- or a single file name for a consolidated data file
- each report has a user-named section under a single custom_data section.
- the required id attribute must be unique, and ties the custom_data, sp and custom_content sections
- other important attributes include description, file_format, and plot_type.
- a pconfig sub-section contains plot configuration options
- a sp (search path) section for finding report data
- Specify the ordering of the custom report section (optional)
- add a custom_content section order list entry
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# Titles to use for the report.
title: "ATAC-Seq QC Reports"
subtitle: null
intro_text: "MultiQC reports for Igor's ATAC-Seq proof-of-concept project."
report_header_info:
- Sequenced by: 'GSAF'
- Job: 'JA17277'
- Run: 'SA17121'
- Setup: '2x150'
# Change the output filenames
output_fn_name: mqc_report.html
data_dir_name: mqc_report_data
# Ignore these files / directories / paths when searching for reports
fn_ignore_files:
- '*.dupinfo.txt'
# Modules that should come at the top of the report
top_modules:
- 'generalstats'
- 'fastqc'
- 'samtools'
- 'picard'
# --------------------------------
# Custom data
# --------------------------------
custom_content:
order:
- bowtie2_isize_section
custom_data:
bowtie2_isize:
id: 'bowtie2_isize_section'
section_name: 'Bowtie2 insert size'
description: 'distribution for alignments (bowtie2 --local -X2000 --no-mixed --no-discordant)'
file_format: 'tsv'
plot_type: 'linegraph'
pconfig:
id: 'bowtie2_isize_plot'
title: 'Insert sizes for proper pairs'
xlab: 'Insert size'
ylab: 'Count'
sp:
bowtie2_isize_section:
fn: '*.bowtie2_isizes.tsv'ylab: 'Count'
sp:
bowtie2_isize_section:
fn: '*.bowtie2_isizes.tsv' |
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To catch up, just use Anna's pre-made files:
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Then the usual...
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cd ~/playtime/multiqc/atacseq; rm -rf mqc_report*; multiqc . |
Resulting in a report that includes our inset size distribution data the custom data section we configured: xxx. : ftp://gapdh.icmb.utexas.edu/misc/multiqc/06.mqc_report.custom_linegraph.html
...