on verbosity #11
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rekado
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Apr 7, 2022
* added rendercite rules to snakemake adapted snakefile and rendercite to communicate with report_scripts * dummy Kraken and Krona output files - to test rendersite updated timecourse page to be in nav_bar * moved two report scripts of vic into report_scripts/ added qc-report and its params to rendersite generation * added rule to snakefile and from .rmd to .Rmd * changed test file to new sample csv file * modified _settings and suppressed warnings added snakemake rules for rendersite and commented out the ones which are not needed any more * renamed variantreport inserted variantreport to communicate with snakefile and generaterenderFiles. Also added the rule to the snakefile * changed test paths in files and added plot snippets from rafael deletet vep file because old changed settings file so timecourse can read in the params and added test_vep file added bubble figure try deleted commented lines for pull request * adapted st reports are generated via render_site removed commented lines for pull request * added krona to kraken report * deleted krona report, this will be handled by kraken2_report changed name of kraken2-report to taxonomic classification added index.rmd * changed paste0 to file.path() Co-authored-by: Dohmen <jan.dohmen@googlemail.com>
rekado
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Apr 7, 2022
* prep for develop_mode * change to development mode * switch magic 13 to proper column name * adding function "dedupeMuts" for collapsing rows in sigmut dataframe * split chunk "processa_and_match_snvs_to_signature_mutations" in chunk for processing the sigmut dataframe and filtering the variant dataframe * adding procedure for deduplicating the sigmut dataframe and grouping the variant names per mutation * change "left_join" so the variant dataframe is now joined with the deduplicated version of the sigmut dataframe * fixed typo in line 312 * change "getIdentCols" function to the refined function "dedupe" * adapting chunk "collapse_identicals" to use "dedupe" function * adapting chunk "getting_unique_muts_bulk", match.df is already unique now and doesn't need that extra "distinct()" step anymore * fix typo in line 375 * comment development chunks again * Dev rendersite (#11) * added rendercite rules to snakemake adapted snakefile and rendercite to communicate with report_scripts * dummy Kraken and Krona output files - to test rendersite updated timecourse page to be in nav_bar * moved two report scripts of vic into report_scripts/ added qc-report and its params to rendersite generation * added rule to snakefile and from .rmd to .Rmd * changed test file to new sample csv file * modified _settings and suppressed warnings added snakemake rules for rendersite and commented out the ones which are not needed any more * renamed variantreport inserted variantreport to communicate with snakefile and generaterenderFiles. Also added the rule to the snakefile * changed test paths in files and added plot snippets from rafael deletet vep file because old changed settings file so timecourse can read in the params and added test_vep file added bubble figure try deleted commented lines for pull request * adapted st reports are generated via render_site removed commented lines for pull request * added krona to kraken report * deleted krona report, this will be handled by kraken2_report changed name of kraken2-report to taxonomic classification added index.rmd * changed paste0 to file.path() Co-authored-by: Dohmen <jan.dohmen@googlemail.com> * changing structure, adding metadata * adapting to renderStie structure * it's still a mixed structure with some development-testing parts left adapted snakefile and rendercite to communicate with report_scripts * dummy Kraken and Krona output files - to test rendersite updated timecourse page to be in nav_bar * moved two report scripts of vic into report_scripts/ added qc-report and its params to rendersite generation * added rule to snakefile and from .rmd to .Rmd * changed test file to new sample csv file * modified _settings and suppressed warnings added snakemake rules for rendersite and commented out the ones which are not needed any more * renamed variantreport inserted variantreport to communicate with snakefile and generaterenderFiles. Also added the rule to the snakefile * changed test paths in files and added plot snippets from rafael deletet vep file because old changed settings file so timecourse can read in the params and added test_vep file added bubble figure try deleted commented lines for pull request * adapted st reports are generated via render_site removed commented lines for pull request * added krona to kraken report * deleted krona report, this will be handled by kraken2_report changed name of kraken2-report to taxonomic classification added index.rmd * changed paste0 to file.path() Co-authored-by: Dohmen <jan.dohmen@googlemail.com> * uncomment test env * comment renderSite env * uncomment test env * adding "dedupeMuts" again I lost the function in the recent merging process * adding start of writing var_output * adding sample name var * adding comment for input args * adding skeleton for output.csv dataframe skeleton and first functions are added for creating the variant_output. * adding variable for csv output directory * writing data_variant_plot.csv added part for writing the csv file which is used to plot the variant abundance. * switching off/commenting dev chunks * remove redundant "samplename" samplename variable changed to sample_name since it was already defined earlier * adding csv-writing part again Idk why but for some reason it got lost during the merging process * prep for develop_mode * change to development mode * switch magic 13 to proper column name * adding function "dedupeMuts" for collapsing rows in sigmut dataframe * split chunk "processa_and_match_snvs_to_signature_mutations" in chunk for processing the sigmut dataframe and filtering the variant dataframe * adding procedure for deduplicating the sigmut dataframe and grouping the variant names per mutation * change "left_join" so the variant dataframe is now joined with the deduplicated version of the sigmut dataframe * fixed typo in line 312 * change "getIdentCols" function to the refined function "dedupe" * adapting chunk "collapse_identicals" to use "dedupe" function * adapting chunk "getting_unique_muts_bulk", match.df is already unique now and doesn't need that extra "distinct()" step anymore * fix typo in line 375 * adapting to renderStie structure * it's still a mixed structure with some development-testing parts left adapted snakefile and rendercite to communicate with report_scripts * dummy Kraken and Krona output files - to test rendersite updated timecourse page to be in nav_bar * moved two report scripts of vic into report_scripts/ added qc-report and its params to rendersite generation * added rule to snakefile and from .rmd to .Rmd * changed test file to new sample csv file * modified _settings and suppressed warnings added snakemake rules for rendersite and commented out the ones which are not needed any more * renamed variantreport inserted variantreport to communicate with snakefile and generaterenderFiles. Also added the rule to the snakefile * changed test paths in files and added plot snippets from rafael deletet vep file because old changed settings file so timecourse can read in the params and added test_vep file added bubble figure try deleted commented lines for pull request * adapted st reports are generated via render_site removed commented lines for pull request * added krona to kraken report * deleted krona report, this will be handled by kraken2_report changed name of kraken2-report to taxonomic classification added index.rmd * changed paste0 to file.path() Co-authored-by: Dohmen <jan.dohmen@googlemail.com> * comment renderSite env * adding "dedupeMuts" again I lost the function in the recent merging process * adding start of writing var_output * adding sample name var * adding comment for input args * adding skeleton for output.csv dataframe skeleton and first functions are added for creating the variant_output. * adding variable for csv output directory * writing data_variant_plot.csv added part for writing the csv file which is used to plot the variant abundance. * switching off/commenting dev chunks * remove redundant "samplename" samplename variable changed to sample_name since it was already defined earlier * adding csv-writing part again Idk why but for some reason it got lost during the merging process Co-authored-by: mirifax <45397751+mirifax@users.noreply.github.com> Co-authored-by: Dohmen <jan.dohmen@googlemail.com>
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In some of the pipelines we already have some verbosity options included, see BIMSBbioinfo/pigx_bsseq#107.
Here we added the snakemake commands
--printshellcmdsand--verbosedirectly as arguments.As Rekado actually pointed out there are different levels of verbosity, a nice example is shown here how it could be done and what the levels mean.
Maybe at some point we could decide on the different levels,
but I would like to already propose a structure, with lower numbers meaning lower verbosity:
e.g.
--printshellcmds--verboseThe text was updated successfully, but these errors were encountered: