Fix log file names

Closes #96

See merge request zavolan_group/pipelines/rhea!48

Update cluster.json

See merge request zavolan_group/pipelines/rnaseqpipeline!47

Changed adapter trimming parameters to fix overtrimming issues

Closes #92

See merge request zavolan_group/pipelines/rnaseqpipeline!46

fixed snakemake subworkflow typos/bugs

Closes #84

See merge request zavolan_group/pipelines/rnaseqpipeline!45

Documentation of pipeline steps

Closes #60 and #57

See merge request zavolan_group/pipelines/rnaseqpipeline!44

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

add TIN score merge and plot steps

See merge request zavolan_group/pipelines/rnaseqpipeline!43

Alfa integration

See merge request zavolan_group/pipelines/rnaseqpipeline!41

moved input_files into top-layer test directory for consistency.

corrected removal of test files

corrected md5sum for config.yaml

remove unnecessary file

- renaming bedgraph
- creating ALFA qc plots

removed conda dependence, moved import statement.

included ALFA in finish rule, corrected annotation.gtf and config.yaml, created new .svg

Simplify star_rpm & index_genomic_alignment_samtools.

See merge request zavolan_group/pipelines/rnaseqpipeline!38

Merged paired end and single end rules for star_rpm and index_genomic_alignment_samtools. Fixed wiring of calculate tin score: bam should be input and not params.

Replace cufflinks image with gffread image

Closes #85

See merge request zavolan_group/pipelines/rnaseqpipeline!37

Generate gene and transcript count tables from salmon

Closes #51

See merge request zavolan_group/pipelines/rnaseqpipeline!33

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

- compile Salmon gene and transcript count summary tables across all samples in workflow run
- add `pandas` to `install/environment.dev.yml`
- update rule graph and DAG images

Use minified docker images

Closes #67

See merge request zavolan_group/pipelines/rnaseqpipeline!32

Rule to collect all TPM values from Salmon added

See merge request zavolan_group/pipelines/rnaseqpipeline!30

BIOPZ-Iborra de Toledo Paula authored 5 years ago and Alex Kanitz committed 5 years ago

-  Remove files with non-deterministic output from `tests/test_integration_workflow/expected_output.files`
-  Update MD5 sums in `tests/test_integration_workflow/expected_output.md5`
-  Update new workflow DAG and rule graph images

Handle polyA processing in input preparation script

Closes #37

See merge request zavolan_group/pipelines/rnaseqpipeline!31

BIOPZ-Katsantoni Maria authored 5 years ago and Alex Kanitz committed 5 years ago

- fixes some functions in `labkey_to_snakemake.py`
- add optional argument for trimming polyA tails; they are trimmed as follows:
  - if mate is sense, oligo-A is added to sample table for `cutadapt` rule to trim
  - if mate is antisense, oligo-T is added to sample table for `cutadapt` rule to trim
  - if option is set to `--trim_polya`, oligo-X stretch is added to sample table and `cutadapt` will not trim

create log directories in Snakefile

Closes #70

See merge request zavolan_group/pipelines/rnaseqpipeline!28