• Antonie Vietor's avatar
    Bam post analysis (#4) · 268eb612
    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: default avatarDavid Laehnemann <david.laehnemann@hhu.de>
    268eb612
cutadapt.smk 979 Bytes