• Antonie Vietor's avatar
    Peak analysis v2 (#5) · bc1ebc47
    Antonie Vietor authored
    * preseq and picard collectalignmentsummarymetrics added
    
    * changed PICARD COLLECTALIGNMENTSUMMARYMETRICS to PICARD COLLECTMULTIPLEMETRICS and integrated the new wrapper as a temporary script
    
    * integration of next steps with temporary use of future wrappers as scripts
    
    * wrapper integration for collectmultiplemetrics and genomecov, rule to create an igv-file from bigWig files
    
    * deeptools and phantompeakqualtools integration
    
    * phantompeakqualtools, headers and multiqc integration
    
    * draft for integration of additional plots from phantompeakqualtools data into multiqc
    
    * Changes according view #4
    
    * Cross-correlation plots are grouped now. Changes in the description of the plots.
    
    * change to newer wrapper versions n all rules and code cleanup
    
    * Changes according to view #4, temporary matplotlib dependency to multiqc added, github actions added
    
    * github actions
    
    * test config and test data
    
    * changes according to PR #4
    
    * update config
    
    * more logs added
    
    * lint: Mixed rules and functions in same snakefile -> moved a part of the rule_all input to common.smk, input functions for rule_all added
    
    * undo the changes of the last commit
    
    * moved all function from Snakefile to common.smk
    
    * --cache flag added for github actions
    
    * --cache flag added for github actions
    
    * snakemake_output_cache location added
    
    * test snakemake_output_cache location
    
    * another test snakemake_output_cache location
    
    * another test snakemake_output_cache location
    
    * set cache in github actions
    
    * fix: dependencies in pysam resulted in ContextualVersionConflict in multiqc
    
    * test: set cache location in github actions
    
    * removed config files in .test from gitignore
    
    * pysam depenencies and changes for github actions
    
    * directory for ngs-test-data added
    
    * gitmodules
    
    * config
    
    * test submodules
    
    * test submodules
    
    * config added
    
    * directory for snakemake output cache changed
    
    * cache location removed
    
    * creating directory for snakemake output cache in github actions
    
    * test cache directory with mkdir and chmod
    
    * code cleanup github actions
    
    * code cleanup github actions
    
    * conda-forge channel added to pysam env
    
    * conda-forge channel added to pysam env
    
    * rule phantompeak added in a script instead of a shell command via Rscript
    
    * testing on saccharomyces cerevisiae data set with deactivated preseq_lc_extrap rule
    
    * r-base environment added to rule phantompeak_correlation
    
    * changed genome data back to human, added rule for downloading single chromosomes from the reference genome (to generate smaller test data)
    
    * rule preseq_lc_extrap activated again, changed genome data back to human, added rule for downloading single chromosomes from the reference genome (to generate smaller test data)
    
    * adopt changes from bam_post_analysis branch, control grouping for samples and input rule to get sample-control combinations
    
    * minimal cleanup
    
    * adjustment of the plot_fingerprint: input function, matching of each treatment sample to its control sample for common output, integration of the JSD calculation, new wildcard for the control samples
    
    * changes on wildcard handling for controls
    
    * rule for macs2 callpeak added
    
    * rule for bedtools intersect added, drafts for multiqc peaks count added
    
    * broad and narrow option handling via config, additional rule for narrow peaks output, peaks count and frip score for multiqc, peaks for igv
    
    * adaptation and integration of plot scripts for results from homer and macs2 analysis, script for plot_peaks_count and it's integration in snakemake-report, integraion of older plots in snakemake-report
    
    * changes for linter
    
    * changes for linter
    
    * changes for linter
    
    * changes for linter
    
    * changes for linter
    
    * changes on input functions and on params parsing for rules plot_macs_qc and plot_homrer_annotatepeaks, peaks wildcard added to all outputs
    
    * test for the behavior of the linter
    
    * test for the behavior of the linter
    
    * changes for the linter
    
    * test for the linter
    
    * refactoring the config variable, restoring the input functions
    
    * plot for FRiP score and some reports added, plot for annotatepeaks summary as draft added
    
    * plot for homer annotatepeaks summary and report description, changes on frip score and peak count plots, changes according to PR #5
    
    * some code cleanup
    
    * changes for PR #5 added
    
    * code cleanup
    bc1ebc47
common.smk 11.5 KB