1. 09 Sep, 2020 1 commit
    • 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