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

BIOPZ-Katsantoni Maria authored 3 years ago and BIOPZ-Gypas Foivos committed 3 years ago

and are therefore not required in the rules.
- Snakefile
 star_rpm: --outWigNorm (default RPM was used)
 star_rpm: --outWigStrand (default Stranded was used)
 rename_star_rpm_for_alfa: orientation in params is redundant (Fixes #152)
- single_end.snakefile.smk
 map_genome_star: outFilterMismatchNoverLmax
 map_genome_star: outFilterScoreMinOverLread
 map_genome_star: outFilterMatchNminOverLread
 quantification_salmon: --writeUnmappedNames
- paired_end.snakefile.smk
  pe_map_genome_star: outFilterMismatchNoverLmax
  pe_map_genome_star: outFilterScoreMinOverLread
  pe_map_genome_star: outFilterMatchNminOverLread
  quantification_salmon: --writeUnmappedNames

- use of [`temp()`](https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html?highlight=temp#protected-and-temporary-files) statements in snakemake rules
  - extract_transcriptome
  - concatenate_transcriptome_and_genome
  - extract_transcripts_as_bed12
  - calculate_TIN_scores
  - star_rpm
  - rename_star_rpm_for_alfa
  - alfa_qc
  - sort_bed_4_big
  - pe_remove_adapters_cutadapt
  - pe_remove_polya_cutadapt
  - remove_adapters_cutadapt
  - remove_polya_cutadapt
- use of [`--notemp`](https://snakemake.readthedocs.io/en/stable/executing/cli.html?highlight=notemp#BEHAVIOR) in test scripts (local and slurm) for successful execution without removing temp files
  - test_alfa
  - test_create_dag_image
  - test_create_rule_graph
  - test_integration_worklow
  - test_integration_workflow_multiple_lanes
- use of [`shadow`](https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html?highlight=shadow#shadow-rules) directive in rules
  - star_rpm
  - pe_map_genome_star
  - pe_quantification_salmon
  - pe_genome_quantification_kallisto
  - map_genome_star
  - quantification_salmon
  - genome_quantification_kallisto
- See comment in #137 for setting an optional `shadow prefix`, especially useful in cluster execution
- See comment in #137 for impact of disk space savings on a real-world dataset
- correctly add snakemake `{threads}` in execution in rules
  - fastqc
  - quantification_kallisto

Fixes #137.