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

- log and, if workflow is executed on cluster, cluster log directories are explicitly created in `Snakefile`
- location of main log directory can be configured in `config.yaml` (field `log_dir`, previously: `local_log`; requires change in script `labkey_to_snakemake.py` as well as subworkflows as field name is hard-coded there)
- location of cluster log directory can be configured in `cluster.json` (in field `__default__` -> `out`)
- `config.yaml` and `cluster.json` in `tests/input_files` are set such that a directory `logs/` is created in the directory where Snakemake is run (i.e., the directory of each test); cluster logs are stored in a subdirectory `logs/cluster`
- removes instructions to explicitly create log directories from docs and all test scripts
- cleans up main `Snakefile` (apart from Snakemake-specific syntax, now passes `flake8` linter test)

fix broken links in docs

See merge request zavolan_group/pipelines/rnaseqpipeline!27

install dependencies via Conda

Closes #56

See merge request zavolan_group/pipelines/rnaseqpipeline!24

- add 3 separate Conda environment files for installing
  - essential dependencies without Singularity (most users)
  - essential dependencies including Singularity (root users on Linux only)
  - non-essential dependencies (required for tests etc.)
- install Python dependencies via `pip` _within_ Conda environment to avoid #56
- update Conda-based installation instructions
  - describe usage of different environment files
  - add supported OS versions (macOS not yet added, because only installation works)
- update CI config to use same setup (based on Miniconda Docker image)

run tests in verbose mode

Closes #68

See merge request zavolan_group/pipelines/rnaseqpipeline!26

- trap call functionalized through cleanup() function
- function added to all test scripts
- function prints out exit status of last command before trap
- flag `--verbose` added to Snakemake calls in all test scripts
- script tests rename to follow naming convention 'test_script_<script_name>_<script_run_mode>

TIN score calculation added

See merge request zavolan_group/pipelines/rnaseqpipeline!25

BIOPZ-Bak Maciej authored 5 years ago and Alex Kanitz committed 5 years ago

- add rule for input preparation (GTF to BED12)
- add rule for TIN score calculation
- update rule graph and DAG image
- update Slurm cluster config

get Snakemake input from LabKey API

Closes #47

See merge request zavolan_group/pipelines/rnaseqpipeline!23

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

- add script that prepares Snakemake input files 'samples.tsv' and 'config.yaml' from LabKey table
- script either connects to API directly (with '--remote' and related options) or processes a tab-separated LabKey dump file
- add tests for both use cases
- common input files for tests now in 'tests/input_files'
- update all other tests to account for new file locations
- update documentation

repo follows recommended structure

Closes #31

See merge request zavolan_group/pipelines/rnaseqpipeline!22

hot fix integration test script

See merge request zavolan_group/pipelines/rnaseqpipeline!21

LabKey-like input to Snakmake input

See merge request zavolan_group/pipelines/rnaseqpipeline!20

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

- separate organism genome architecture (different input folder)
- change MD5 checksums to match the new output

update install instructions

See merge request zavolan_group/pipelines/rnaseqpipeline!17