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feat: make it possible to set input as files or dirs to multiqc #488
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make it possible to use the actual input from the rule as input to multiqc, instead of converting it to dirs that are then searched.
I find the variable name |
Co-authored-by: Filipe G. Vieira <fgarrettvieira@gmail.com>
good suggestion! I have updated the pull-request with variable name use_input_files_only instead of convert_file_input_to_dirs |
I think it looks goos, but could you also describe this new parameter in the |
Co-authored-by: Filipe G. Vieira <fgarrettvieira@gmail.com>
make it possible to use the actual input from the rule as input to multiqc, instead of converting it to dirs that are then searched.
Description
If multiqc search directories it's possible that unwanted files are included to the reports. This will make it possible to only use the provided files, when wanted.
For all wrappers added by this PR, I made sure that
input:
andoutput:
file paths in the resulting rule can be changed arbitrarily,threads: x
statement withx
being a reasonable default,map_reads
for a step that maps reads),environment.yaml
specifications follow the respective best practices,input:
oroutput:
),Snakefile
s and their entries are explained via comments (input:
/output:
/params:
etc.),stderr
and/orstdout
are logged correctly (log:
), depending on the wrapped tool,tempfile.gettempdir()
points to (see here; this also means that using any Pythontempfile
default behavior works),meta.yaml
contains a link to the documentation of the respective tool or command,Snakefile
s pass the linting (snakemake --lint
),Snakefile
s are formatted with snakefmt,