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.

MultiQC plugins for TIN scores and ALFA
See merge request !79

PCA analysis on genes and transcripts TPM for kallisto and salmon

See merge request !77

- Delete unused files scripts/fg_extract_transcripts.py, scripts/heatmap_and_clustermap.py, scripts/perform_PCA.py
- Add rules (pca_kallisto, pca_salmon) that run zpca (https://github.com/zavolanlab/zpca) on genes and transcripts TPM tables from kallisto and salmon.
- The output is wired to multiqc_report but the plots are not visualized to multiqc. Update documentation.
- Update dag and rulegraph.
Fixes #140 #142

docs: revised terminology for non-experts

See merge request !73

Merge kallisto

See merge request !75

BIOPZ-Iborra de Toledo Paula authored 4 years ago and BIOPZ-Gypas Foivos committed 4 years ago

The rules rely on https://github.com/zavolanlab/merge_kallisto
Update info in pipeline_documentation.md

Cluster.json was updated

See merge request !74

feat: add support for multi-lane samples

See merge request !71

BIOPZ-Katsantoni Maria authored 4 years ago and Alex Kanitz committed 4 years ago

fix: Renamed samples_concat.tsv to samples.multiple_lanes.tsv. Renamed rows with split with the same name as the other test samples, so that I do not change the tests (md5 and sunch). Removed the one lane samples. Created config that uses this tsv file

refactor: rename LabKey/input table column

See merge request !70

Add Snakemake report

See merge request !64

docs: rename project/workflow

See merge request !69

fix(prepare_inputs): support relative paths

See merge request !68

Salmon argument fix

See merge request !67

BIOPZ-Katsantoni Maria authored 4 years ago and BIOPZ-Gypas Foivos committed 4 years ago

fix: added arguments for fragment size mean and sd required for the salmon quantification approach in single-end mode

Gtf2bed update

See merge request !65