- 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

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

- add linked ToC
- add table of third party software
- add rule graph
- clean up sample table description
- formalize structure for each rule description
- cross-reference rules via inputs/outputs
- clean list of references

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

In labkey_to_snakemake.py fixed the parameters so that there is 3p as well 5p polya
feature for every mate, which can be matched to the -a -g -A and -G options of cutadapt
depending on which is the sense or antisense mate the appropriate variable is populated
and the rest of variables are filled with 'XXXXXXXXXXXX' which leads to no trimming by
cutadapt. The poly-A trimming rules are fixed to contain all -a -g -A -G options.

Dominik Burri authored 5 years ago and CJHerrmann committed 5 years ago

fixed typos

updated pipeline documentation

described seqmode specific rules

adapted to updates in Snakefile

moved star_rpm and samtools index to main snakefile description

linked README in documentation and vice versa