-
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