Bam post analysis (#4)
* 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>
.github/workflows/main.yaml
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.gitignore
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.gitmodules
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.test/config/config.yaml
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.test/config/samples.tsv
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.test/config/units.tsv
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workflow/envs/curl.yaml
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workflow/envs/gawk.yaml
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workflow/envs/perl.yaml
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