Hide empty rows in General Statistics table when opening html file #835
Comments
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Hi @pancheto, Many thanks for the nice suggestion: such a module-wide hiding of columns should certainly be feasible. The automatic hiding of empty rows / columns should happen already, I'll take a look into reproducing and fixing this behaviour. Note that I have a work-in-progress branch for the new merging functionality that needs testing and finishing here: #576 - you're welcome to have a play around with that code if you would like. I'm pretty busy travelling for the next few weeks but will get to this as soon as I can 👍 Phil |
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I have the same problem: I'm hiding all FastQC related columns by default, but empty rows are displayed when opening the html report. If I check and uncheck a FastQC column using Configure Columns in the web UI the empty rows become hidden. I'm using v1.7. I'll try playing around with the code and see if I can find a solution. |
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Sorry, double-post from #541 (comment) Hi @pancheto, It took me over a year, but I finally implemented your request! 🎉 This now works: table_columns_visible:
FastQC: FalseUpdated docs: https://multiqc.info/docs/#hiding-columns Let me know if you find any problems, and thanks for the suggestion 👍 Phil |
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@matrulda - just replicated the bug you found. Looking into it now, pretty sure I know what's going on.. |
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Ok, fixed in 045407a - should now behave as expected on page load. Tricky bug, thanks for reporting! Let me know how you get on with the new code. |
it would be great to see this last option, but using MultiQC v1.8, although I can perfectly use this: table_columns_visible:
fastp:
pct_duplication: False
after_filtering_q30_rate: False
after_filtering_q30_bases: False
after_filtering_gc_content: False
pct_surviving: False
pct_adapter: False
FastQC:
percent_duplicates: False
percent_gc: False
avg_sequence_length: False
percent_fails: False
total_sequences: Falseunfortunately this is not working: table_columns_visible:
fastp: False
FastQC: Falsein fact, I get the following error: Traceback (most recent call last):
File "/myhome/ngs/software/MultiQC-1.8/BUILD_FT/bin/multiqc", line 11, in <module>
load_entry_point('multiqc==1.8', 'console_scripts', 'multiqc')()
File "/mnt/netapp1/Optcesga_FT2_RHEL7/easybuild-cesga/software/Compiler/gcccore/6.4.0/setuptools/40.4.3-python-3.7.0/lib/python3.7/site-packages/setuptools-40.4.3-py3.7.egg/pkg_resources/__init__.py", line 484, in load_entry_point
File "/mnt/netapp1/Optcesga_FT2_RHEL7/easybuild-cesga/software/Compiler/gcccore/6.4.0/setuptools/40.4.3-python-3.7.0/lib/python3.7/site-packages/setuptools-40.4.3-py3.7.egg/pkg_resources/__init__.py", line 2714, in load_entry_point
File "/mnt/netapp1/Optcesga_FT2_RHEL7/easybuild-cesga/software/Compiler/gcccore/6.4.0/setuptools/40.4.3-python-3.7.0/lib/python3.7/site-packages/setuptools-40.4.3-py3.7.egg/pkg_resources/__init__.py", line 2332, in load
File "/mnt/netapp1/Optcesga_FT2_RHEL7/easybuild-cesga/software/Compiler/gcccore/6.4.0/setuptools/40.4.3-python-3.7.0/lib/python3.7/site-packages/setuptools-40.4.3-py3.7.egg/pkg_resources/__init__.py", line 2338, in resolve
File "/myhome/ngs/software/MultiQC-1.8/BUILD_FT/lib/python3.7/site-packages/multiqc-1.8-py3.7.egg/multiqc/__main__.py", line 44, in <module>
multiqc.run_cli(prog_name='multiqc')
File "/myhome/ngs/software/MultiQC-1.8/BUILD_FT/lib/python3.7/site-packages/Click-7.0-py3.7.egg/click/core.py", line 764, in __call__
return self.main(*args, **kwargs)
File "/myhome/ngs/software/MultiQC-1.8/BUILD_FT/lib/python3.7/site-packages/Click-7.0-py3.7.egg/click/core.py", line 717, in main
rv = self.invoke(ctx)
File "/myhome/ngs/software/MultiQC-1.8/BUILD_FT/lib/python3.7/site-packages/Click-7.0-py3.7.egg/click/core.py", line 956, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/myhome/ngs/software/MultiQC-1.8/BUILD_FT/lib/python3.7/site-packages/Click-7.0-py3.7.egg/click/core.py", line 555, in invoke
return callback(*args, **kwargs)
File "/myhome/ngs/software/MultiQC-1.8/BUILD_FT/lib/python3.7/site-packages/multiqc-1.8-py3.7.egg/multiqc/multiqc.py", line 238, in run_cli
kwargs=kwargs
File "/myhome/ngs/software/MultiQC-1.8/BUILD_FT/lib/python3.7/site-packages/multiqc-1.8-py3.7.egg/multiqc/multiqc.py", line 303, in run
config.mqc_load_userconfig(config_file)
File "/myhome/ngs/software/MultiQC-1.8/BUILD_FT/lib/python3.7/site-packages/multiqc-1.8-py3.7.egg/multiqc/utils/config.py", line 113, in mqc_load_userconfig
mqc_load_config(p)
File "/myhome/ngs/software/MultiQC-1.8/BUILD_FT/lib/python3.7/site-packages/multiqc-1.8-py3.7.egg/multiqc/utils/config.py", line 123, in mqc_load_config
mqc_add_config(new_config, yaml_config)
File "/myhome/ngs/software/MultiQC-1.8/BUILD_FT/lib/python3.7/site-packages/multiqc-1.8-py3.7.egg/multiqc/utils/config.py", line 179, in mqc_add_config
update({c: v})
File "/myhome/ngs/software/MultiQC-1.8/BUILD_FT/lib/python3.7/site-packages/multiqc-1.8-py3.7.egg/multiqc/utils/config.py", line 210, in update
return update_dict(globals(), u)
File "/myhome/ngs/software/MultiQC-1.8/BUILD_FT/lib/python3.7/site-packages/multiqc-1.8-py3.7.egg/multiqc/utils/config.py", line 217, in update_dict
d[key] = update_dict(d.get(key, {}), val)
File "/myhome/ngs/software/MultiQC-1.8/BUILD_FT/lib/python3.7/site-packages/multiqc-1.8-py3.7.egg/multiqc/utils/config.py", line 217, in update_dict
d[key] = update_dict(d.get(key, {}), val)
File "/myhome/ngs/software/MultiQC-1.8/BUILD_FT/lib/python3.7/site-packages/multiqc-1.8-py3.7.egg/multiqc/utils/config.py", line 219, in update_dict
d[key] = u[key]
TypeError: 'bool' object does not support item assignment |
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Hi @jamigo - please try to avoid posting at the end of old closed issues, as it's very tricky to keep track of these notifications. Instead it's better to make a new issue and refer to any other old relevant issues. I'll move your comment into a new issue now 👍 |
Description of bug:
I've came across a possible solution for this issue described here #541, although it's not working properly right now. let me describe it:
what I have
starting from fastq files and ending up with bam and vcf files, one ends up too with fastq associated reports and also with bam and vcf associated reports. the first ones are listed in General Statistics table with suffixes (
_L00\d_R\d_001typically), and the last ones are listed without them. e.g., as you well said, a first sample_name line and subsequent sample_name lines per lane and direction.what I thought
what happens if I hide all fastq related columns from the General Statistics table by default through the multiqc_config.yaml file? the data would be still there, but only the main sample lines with whole sample information would be visible, and the rest of columns would be accessible on demand through the Configure Columns button.
what I found out
if you hide all fastq related columns from the General Statistics table by default the fastq related empty rows keep being displayed by default, although single a touch on any checkbox in the Configure Columns section updates these columns to be displayed only if a fastq related column is selected, or to be hidden otherwise.
what I request
I know that this behaviour is not the same thing as merging fastq data into main sample data as this issue started, which would be much more complicated indeed, but being able to hide already empty rows by default could be enough for most of us. also, being able to hide all columns from a section instead of having to write down all columns' ids in the configuration file would be a great plus.
current example
MultiQC run details (please complete the following):
multiqc -f --no-data-dir -c multiqc_config.yaml .The text was updated successfully, but these errors were encountered: