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Created with Raphaël 2.2.09Sep26Aug252423201921Jul1615141311Jun28May1211715Apr25Mar26Feb1116Oct25Jun2318171512111028Apr25Mar2422212019181713127624Feb2120181715149874324Jan10720Dec1319Feb18Merge 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 readsMerge branch 'bug/snakemake-report-with-slurm-run' into 'dev'Fix paths to Snakefile for slurm test scripstMerge branch 'feature/conda-support' into 'dev'Add conda support in ZARPMerge branch 'feature/biocontainers_zavolan-multiqc-plugins' into 'dev'Add biocontainers image for multiqc-pluginsMerge branch 'feature/biocontainers_tin-score-calculation' into 'dev'Add biocontainers image for tin-score-calculationMerge branch 'feature/biocontainers_merge_kallisto' into 'dev'Add biocontainers image for merge_kallisto.R