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

Replace zpca container from zavolab to biocontainers.

See merge request !81

Use biocontainers images for star, gffread, salmon, kallisto, cutadapt, samtools, fastqc, alfa, bedtools, bedgraphtobigwig. Change container from bash to ubuntu. Fixes #149

Use biocontainers images for star, gffread, salmon, kallisto, cutadapt, samtools, fastqc, alfa, bedtools, bedgraphtobigwig. Change container from bash to ubuntu. Fixes #149

feat: enable user to configure CLI params per rule

See merge request !83

Remove default arguments from rules

See merge request !80