docs: GitHub migration notice

See merge request !105

Update documentation

See merge request !104

Add temp directories for ALFA

See merge request !103

Feature/samtools sort after STAR

See merge request !101

Change alfa output folder names

See merge request !102

docs: remove old labkey section

See merge request !100

ci: clean old comments

See merge request !99

Remove sample specific options and use them as rule specific.

See merge request !98

Collapse directionality params in sample table

See merge request !93

feat: add Snakemake profiles

See merge request !97

Minor fixes to surround parameter argument in multiqc preparation with quotes

See merge request !96

Bump snakemake version that fixes the reported time in snakemake report.

See merge request !95

Config validation and add author information. Closes #174 and #78.

See merge request !91

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.

Added author name and author email as optional fields in `tests/input_files/config.yaml`, and added it into the multiqc report.

Cutadapt set -m=1 to avoid empty reads

See merge request !92

Fix paths to Snakefile for slurm test scripts

See merge request !90

Conda support in ZARP

See merge request !89

Add biocontainers image for multiqc-plugins

See merge request !88

Add biocontainers image for tin-score-calculation

See merge request !87

Add biocontainers image for merge_kallisto.R

See merge request !86