Add MosaiCatcher module

[weber8thomas]

This PR adds a new module for mosaicatcher counts method. Mosaicatcher counts Strand-seq reads and classifies strand states of each chromosome in each cell using a Hidden Markov Model. The software is used as a direct first step after obtaining BAM files from Strand-Seq data.

• This comment contains a description of changes (with reason)
• CHANGELOG.md has been updated

• There is example tool output for tools in the https://github.com/ewels/MultiQC_TestData repository or attached to this PR
• Code is tested and works locally (including with --lint flag)
• docs/README.md is updated with link to below
• docs/modulename.md is created
• Everything that can be represented with a plot instead of a table is a plot
• Report sections have a description and help text (with self.add_section)
• There aren't any huge tables with > 6 columns (explain reasoning if so)
• Each table column has a different colour scale to its neighbour, which relates to the data (eg. if high numbers are bad, they're red)
• Module does not do any significant computational work

[weber8thomas]

Hi @ewels ! I'm struggling to solve CI issues here with this new module, here a part of the logs:

|            report | LINT: HTML ID was a duplicate (mqc-generalstats-dragen_coverage-Aligned_reads_in_QC_coverage_region_pct-1) ## 
|            report | LINT: HTML ID was a duplicate (mqc-generalstats-dragen_coverage-Aligned_bases_in_QC_coverage_region_pct-1) ## 
|            report | LINT: HTML ID was a duplicate (mqc-generalstats-dragen_coverage-Average_alignment_coverage_over_QC_coverage_region-1) ## 
|            report | LINT: HTML ID was a duplicate (mqc-generalstats-dragen_coverage-Uniformity_of_coverage_PCT_0_2_mean_over_QC_coverage_region-1) ## 
|            report | LINT: HTML ID was a duplicate (mqc-generalstats-dragen_coverage-Mean_Median_autosomal_coverage_ratio_over_QC_coverage_region-1) ## 
|            report | LINT: HTML ID was a duplicate (mqc-generalstats-dragen_coverage-PCT_of_QC_coverage_region_with_coverage_1x_inf-1) ## 
|            report | LINT: HTML ID was a duplicate (mqc-generalstats-dragen_coverage-PCT_of_QC_coverage_region_with_coverage_10x_inf-1) ## 
|            report | LINT: HTML ID was a duplicate (mqc-generalstats-dragen_coverage-PCT_of_QC_coverage_region_with_coverage_20x_inf-1) ## 
|            report | LINT: HTML ID was a duplicate (mqc-generalstats-dragen_coverage-PCT_of_QC_coverage_region_with_coverage_50x_inf-1) ## 
|            report | LINT: HTML ID was a duplicate (mqc-generalstats-dragen_coverage-PCT_of_QC_coverage_region_with_coverage_100x_inf-1) ## 
|           multiqc | Compressing plot data
|           multiqc | Report      : full_report.html
|           multiqc | Data        : full_report_data
|           multiqc | MultiQC complete
|           multiqc | 6 flat-image plots used in the report due to large sample numbers
|           multiqc | To force interactive plots, use the '--interactive' flag. 
See the �]8;id=554880;[https://multiqc.info/docs/#flat--interactive-plots�\documentation�]8;;�\.](https://multiqc.info/docs/#flat--interactive-plots%1B\documentation%1B]8;;%1B\.)
|           multiqc | Found 22 linting errors!
LINT: >dragen/coverage_metrics.py< HTML ID was a duplicate (Aligned_reads_in_QC_coverage_region_pct-1) ## plot=table.plot(data_by_sample, own_tabl_headers, pconfig={"namespace": NAMESPACE}),
LINT: >dragen/coverage_metrics.py< HTML ID was a duplicate (Aligned_reads_in_QC_coverage_region-1) ## plot=table.plot(data_by_sample, own_tabl_headers, pconfig={"namespace": NAMESPACE}),
LINT: >dragen/coverage_metrics.py< HTML ID was a duplicate (Aligned_bases_in_QC_coverage_region_pct-1) ## plot=table.plot(data_by_sample, own_tabl_headers, pconfig={"namespace": NAMESPACE}),
LINT: >dragen/coverage_metrics.py< HTML ID was a duplicate (Aligned_bases_in_QC_coverage_region-1) ## plot=table.plot(data_by_sample, own_tabl_headers, pconfig={"namespace": NAMESPACE}),
LINT: >dragen/coverage_metrics.py< HTML ID was a duplicate (Average_alignment_coverage_over_QC_coverage_region-1) ## plot=table.plot(data_by_sample, own_tabl_headers, pconfig={"namespace": NAMESPACE}),
LINT: >dragen/coverage_metrics.py< HTML ID was a duplicate (Uniformity_of_coverage_PCT_0_2_mean_over_QC_coverage_region-1) ## plot=table.plot(data_by_sample, own_tabl_headers, pconfig={"namespace": NAMESPACE}),
LINT: >dragen/coverage_metrics.py< HTML ID was a duplicate (Average_chr_X_coverage_over_QC_coverage_region-1) ## plot=table.plot(data_by_sample, own_tabl_headers, pconfig={"namespace": NAMESPACE}),
LINT: >dragen/coverage_metrics.py< HTML ID was a duplicate (Average_chr_Y_coverage_over_QC_coverage_region-1) ## plot=table.plot(data_by_sample, own_tabl_headers, pconfig={"namespace": NAMESPACE}),
LINT: >dragen/coverage_metrics.py< HTML ID was a duplicate (Average_mitochondrial_coverage_over_QC_coverage_region-1) ## plot=table.plot(data_by_sample, own_tabl_headers, pconfig={"namespace": NAMESPACE}),
LINT: >dragen/coverage_metrics.py< HTML ID was a duplicate (Average_autosomal_coverage_over_QC_coverage_region-1) ## plot=table.plot(data_by_sample, own_tabl_headers, pconfig={"namespace": NAMESPACE}),
LINT: >dragen/coverage_metrics.py< HTML ID was a duplicate (Median_autosomal_coverage_over_QC_coverage_region-1) ## plot=table.plot(data_by_sample, own_tabl_headers, pconfig={"namespace": NAMESPACE}),
LINT: >dragen/coverage_metrics.py< HTML ID was a duplicate (Mean_Median_autosomal_coverage_ratio_over_QC_coverage_region-1) ## plot=table.plot(data_by_sample, own_tabl_headers, pconfig={"namespace": NAMESPACE}),
LINT: HTML ID was a duplicate (mqc-generalstats-dragen_coverage-Aligned_reads_in_QC_coverage_region_pct-1) ## 
LINT: HTML ID was a duplicate (mqc-generalstats-dragen_coverage-Aligned_bases_in_QC_coverage_region_pct-1) ## 
LINT: HTML ID was a duplicate (mqc-generalstats-dragen_coverage-Average_alignment_coverage_over_QC_coverage_region-1) ## 
LINT: HTML ID was a duplicate (mqc-generalstats-dragen_coverage-Uniformity_of_coverage_PCT_0_2_mean_over_QC_coverage_region-1) ## 
LINT: HTML ID was a duplicate (mqc-generalstats-dragen_coverage-Mean_Median_autosomal_coverage_ratio_over_QC_coverage_region-1) ## 
LINT: HTML ID was a duplicate (mqc-generalstats-dragen_coverage-PCT_of_QC_coverage_region_with_coverage_1x_inf-1) ## 
LINT: HTML ID was a duplicate (mqc-generalstats-dragen_coverage-PCT_of_QC_coverage_region_with_coverage_10x_inf-1) ## 
LINT: HTML ID was a duplicate (mqc-generalstats-dragen_coverage-PCT_of_QC_coverage_region_with_coverage_20x_inf-1) ## 
LINT: HTML ID was a duplicate (mqc-generalstats-dragen_coverage-PCT_of_QC_coverage_region_with_coverage_50x_inf-1) ## 
LINT: HTML ID was a duplicate (mqc-generalstats-dragen_coverage-PCT_of_QC_coverage_region_with_coverage_100x_inf-1) ## 
Error: Process completed with exit code 1.

Many thanks in advance for your help!

Thomas

[ewels]

Yeah I desperately need to merge another PR for DRAGEN to solve these - it's not your PR that's at fault.

I'm trying to implement some new back-end stuff for MultiQC before the next release. When that's done I'll try to do a PR review sprint and get that in and sorted. Apologies for the inconvenience..

[weber8thomas]

Yeah I desperately need to merge another PR for DRAGEN to solve these - it's not your PR that's at fault.

I'm trying to implement some new back-end stuff for MultiQC before the next release. When that's done I'll try to do a PR review sprint and get that in and sorted. Apologies for the inconvenience..

All fine, no worries :)

Cheers! Thomas

[vladsavelyev]

Please capitalize the column names (Cell, Mapped, etc), replace the underscores with spaces.

Should also add "namespace": "MosaiCatcher" field into the headers.

[weber8thomas]

Do you mean the title key into the nested dictionnary or the headers dict keys?

[vladsavelyev]

Should call self.ignore_samples after parsing, and if no log files are found, should raise a UserWarning - see docs and example

[weber8thomas]

Got it, done!

[vladsavelyev]

Thanks!

[vladsavelyev]

Thank you a lot for the contribution!

Left some comments.

[weber8thomas]

Hi @vladsavelyev ! :) Thanks for the reviewing! I wanted to filter out some columns to be included into the report but didn't find a good way to do it, do you have any tips on this?

[vladsavelyev]

Hey!

I wanted to filter out some columns to be included into the report but didn't find a good way to do it, do you have any tips on this?

Not sure I understand! Do you mean the general stats table, or the table generated by this module? All columns that you specify in headers will be included, and those that you label as hidden=True won't show by default unless selected in the report's UI.

[weber8thomas]

Seems to work! Let me know if I still need to modify something :)