1. 06 Jul, 2021 1 commit
  2. 24 Jun, 2021 1 commit
  3. 23 Jun, 2021 1 commit
  4. 16 Jun, 2021 2 commits
  5. 04 Jun, 2021 1 commit
    • Antonie Vietor's avatar
      Consensus peak analysis (#6) · 1345df8a
      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 ...
      1345df8a
  6. 21 Oct, 2020 1 commit
    • 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
  7. 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 a...
      268eb612