Update fake samples file: tests/samples.tsv

See merge request zavolan_group/pipelines/rnaseqpipeline!7

BIOPZ-Gypas Foivos authored 5 years ago and Alex Kanitz committed 5 years ago

- replace corrupt input files
- add script that runs locally named `run_test.sh` in the snakemake directory
- add script to CI/CD pipeline
- fix typo in `paired_end.snakefile`
- update samples.tsv with fake adapter `XXXXXXX` when we do not want to trim them

Labkey api

See merge request zavolan_group/pipelines/rnaseqpipeline!8

BIOPZ-Börsch Anastasiya authored 5 years ago and Alex Kanitz committed 5 years ago

- add usage information in file `scripts/labkey_api.md`

Added sample fastq.gz paired-end input 1000 record files, adjusted dummy sample.tsv

See merge request zavolan_group/pipelines/rnaseqpipeline!6

add continuous integration support

See merge request zavolan_group/pipelines/rnaseqpipeline!5

Subpipelines

Closes #7, #8, #16, #17, #14, and #15

See merge request zavolan_group/pipelines/rnaseqpipeline!4

Rename snakemake/paired_end.snakemake to snakemake/paired_end.snakefile. Fix wiring of rules. Add fake tests.

Clean up unused code in snakemake/Snakefile. Add 2 threads in htseq_qa (paired end mode). Add example of tsv files from LabKey.

Merge branch 'subpipelines' of https://git.scicore.unibas.ch/zavolan_group/pipelines/rnaseqpipeline into subpipelines

Add script that generates heatmap and clustermap

See merge request zavolan_group/pipelines/rnaseqpipeline!3

Add script that performs PCA analysis

Closes #20

See merge request zavolan_group/pipelines/rnaseqpipeline!2