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Created with Raphaël 2.2.09Sep26Aug252423201921Jul161514131211Jun28May1211715Apr25Mar26Feb1116Oct25Jun2318171512111028Apr25Mar2422212019181713127624Feb2120181715149874324Jan10720Dec1319Feb18Merge branch 'migration-notice' into 'dev'devdevdocs: GitHub migration noticeMerge branch 'update_documentation' into 'dev'Update documentationMerge branch 'feature/temp-dirs-for-alfa' into 'dev'Add temp directories for ALFAMerge branch 'feature/samtools-sort' into 'dev'Feature/samtools sort after STARMerge branch 'alfa_output_names' into 'dev'Change alfa output folder namesMerge branch 'docs-fix-labkey' into 'dev'docs: remove old labkey sectionMerge branch 'cifix' into 'dev'ci: clean old commentsMerge branch 'restructure_sample_table' into 'dev'Remove sample specific options and use them as rule specific.Merge branch 'simplify_directionality' into 'dev'Collapse directionality params in sample tableMerge branch 'profiles' into 'dev'feat: add Snakemake profilesMerge branch 'minor_fixes' into 'dev'Merge branch 'buxfix/fix-time-in-snakemake-report' into 'dev'Bump snakemake version that fixes the reported time in snakemake report.surround params in multiqc prepration; fixes #180Bump version of tin-score-calculation from 0.4 to 0.5. Fixes #179Bump version of tin-score-calculation from 0.4 to 0.5Merge branch 'input_validation' into 'dev'Validation of configuration file with a json schema `resources/config_schema.json` using the snakemake utility **validate**. The schema includes all the fields from `tests/input_files/config.yaml`, assigns certain fields as required and forbids the use of additional fields. All of the optional fields include default values, taken from the config above, except `rule_config` which has no default.Merge branch 'cutadapt_min_len' into 'dev'Cutadapt set -m=1 to avoid empty readsproperly raise TypeError and rephrase error message.separate empty and erroneous optional field.correct error to create empty optional dict.Report missing required keys, restructure rule config handling.Merge branch 'dev' into input_validationMerge branch 'bug/snakemake-report-with-slurm-run' into 'dev'adjust all config files and test cases to new optional field.Fix paths to Snakefile for slurm test scripstvalidate config on required and optional fields #174add author information (#78)