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  • v1.0.0
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Created with Raphaël 2.2.017Jun17Jan17Dec25Nov22Sep2117161514109831Aug305429Jul2322117Jun1431May30Apr28222112Mar428Feb23191242128Jan24221918Dec18Aug11Mar5Feb31Jan3029108718Dec17166Nov9Oct732130Sep272624109653230Aug292829Jul251525Jun31May292726Apr252422Mar2119151211125Feb222119181512876530Jan2944Jun28Apr2715Jan2Oct30Sep18Aug1430Jun27730May27Apr25hg38 and minimal snakemake startbranch_enorabranch_enorasep script and logs for Run and Tagscript+data+gitignore+space removed from config[dwnspg] in snakefilemerging mastertesttestAdding scripts to mastermaster metamaster metaAdding the tss yml conda env fileAdding the anme of conda env in the installation to avoid confusionetting the gitkeep fiel for keeping logs as a directory in the repoAdding a gitkeep to have logs staying in the dirAdding SEACR1.4dev version as working version. Changing arguments for SEACRseacrseacrAdding SEACR v4 that correct some bugs especially when no peaks are foundUpdating config filesignormsignormCorrecting and testing BIGWIGCompareTring new way to get bigwig input using already scaled bigwigRemoving some commentsspikeinspikeinCorrecting samtools stats raw and going back to q value for macs2Spike-in computation is going through with proper calculationAdding SEACR in the main envSmall multiQC changesMerge branch 'master' of https://gitlab.univ-nantes.fr/foucal-a/full-chipseqTesting new featuresUpdate README.mdAdding some threads to a long stepCorrecting down_sample rules to work with samtools statsRemoving samtools flagstats info in the multiQC since its useless. Replacing it with samtools statsqcqcMerge branch 'master' of https://gitlab.univ-nantes.fr/foucal-a/full-chipseq into seacrProper handling of SEACR QC. Still some errors due to SEACR removal of temp files. Snakemake just need to be rerunAdd LICENSEAdding some multiQC output to count peaksAdding seacr command. Errors if not pics are detected, thats from the seacr softMerge branch 'master' of https://gitlab.univ-nantes.fr/foucal-a/full-chipseqine working version of the pipeline, with still peak_calling being tough to parametrize for CUT&RUNAdding two flagstat metrics, before and after filteringCommenting some printing statementUpdating TODOGoing back to shiftsize modellingReadding hub commands using normal bigwigNo more errors. Still weird peaks calling results, due to perhaps difficulty for macs to estimate fragment length with CUT&RUn dataUpdating the multibigwig command to focus on chr1 to cut computing time. Also removing useless grouping per samples, since all deptools plots are now in the multiQCCommenting cutrunsamples since not used yet and adding some check if there is no control at all in the samples