1. 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
  2. 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
  3. 15 Jun, 2020 1 commit
    • Antonie Vietor's avatar
      Filtering (#3) · 4607b5fc
      Antonie Vietor authored
      * trimming with cutadapt added
      
      * additions to cutadapt according to View #1, BWA added as draft
      
      * adding cutadapt comments back, bwa mem will be moved to a new branch
      
      * mapping, duplicate marking and merging
      
      * changes according View #2 added, some minor additional changes with handling cutadapt-log-files for multiqc input in common.smk were necessary
      
      * code formatting with black
      
      * changes according view #2 added and replaced directory name mapped with merged in bwa_mem output, because its bam files are only temporary and otherwise the empty mapped directory would remain after the workflow-run
      
      * rule for samtools view added
      
      * rule samtools_view added, rules for samtools_index, flagstat, idxstats and samtools_stats were created as drafts and are therefore still commented out
      
      * adding filtering rules, rule for removing orphan reads, adding rule for samtools sorting and statistics for multiqc
      
      * Higher parallelization of the stats rules by outsourcing general rules for this purpose in stats.smk and utils.smk. Statistics for multiqc input of BAM files after 'bwa_mem' and 'merge_duplicates' added.
      
      * Changes according to View #3.
      
      * refactoring _dedup
      
      * Log-path refactoring according to view #3. In multiqc-report the hovering of data points for samtools stats, flagstat and idxstats works for Chromium browser, but not for Firefox. Additional plots can be generated from the multiqc_data statistics, as described here: https://github.com/ewels/MultiQC/issues/512.
      4607b5fc
  4. 18 May, 2020 1 commit
    • Antonie Vietor's avatar
      Mapping and duplicate marking (#2) · bb5a88a1
      Antonie Vietor authored
      * trimming with cutadapt added
      
      * additions to cutadapt according to View #1, BWA added as draft
      
      * adding cutadapt comments back, bwa mem will be moved to a new branch
      
      * mapping, duplicate marking and merging
      
      * changes according View #2 added, some minor additional changes with handling cutadapt-log-files for multiqc input in common.smk were necessary
      
      * code formatting with black
      
      * changes according view #2 added and replaced directory name mapped with merged in bwa_mem output, because its bam files are only temporary and otherwise the empty mapped directory would remain after the workflow-run
      
      * view #2: output path for rule bwa_mem and input path for rule merge_bams changed
      bb5a88a1
  5. 07 May, 2020 1 commit
    • AntonieV's avatar
      trimming with cutadapt added (#1) · 3f3ed4f5
      AntonieV authored
      * trimming with cutadapt added
      
      * additions to cutadapt according to View #1, BWA added as draft
      
      * adding cutadapt comments back, bwa mem will be moved to a new branch
      3f3ed4f5
  6. 30 Apr, 2020 1 commit
  7. 29 Apr, 2020 1 commit
  8. 28 Apr, 2020 1 commit
  9. 22 Apr, 2020 1 commit
  10. 15 Apr, 2020 2 commits