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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) * Add some TODOs for later * reflect that compute_matrix requests two threads in the extra params * also cache bwa_index, as this can take quite some time Co-authored-by: David Laehnemann <david.laehnemann@hhu.de>