- Jun 11, 2020
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Dominik Burri authored
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- Apr 27, 2020
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Alex Kanitz authored
- clean up command line interface - improve descriptions - add consistent structure - remove or merge superfluous CLI arguments - set defaults - update test calls - update docs - when importing data from LabKey, table is saved to 'samples.tsv.labkey' in same directory as Snakemake sample table - allow user to specify environment variables and relative paths in input table and on CLI - relative paths in the input table are interpreted with respect to the directory containing the input table - relative paths will are interpreted with respect to the current working directory; this is to achieve portability with respect to tests but is discouraged in production because its behavior is not very predictable from the user's perspective; consequently a warning is thrown - set STAR index size to read length - 1 - remove `gtf_filtered` and `tr_fasta_filtered` and update Snakefiles and test sample tables accordingly - rename some MultiQC report-related parameters and update Snakefiles and test config files accordingly - add logging - add docstrings to module and all functions - add typing definitions to all functions - restructure and comment code to improve readability - linters `flake8` and `mypy` pass
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* Sequencing mode-related changes: * allowed sequencing modes in Snakemake input table changed from `paired_end` and `single_end` to `pe` and `se`, respectively * remove sequencing mode from output paths for each rule * corresponding wild cards removed entirely from all rules that do not depend on sequencing mode (currently all rules that are defined in the main `Snakefile` in the project root directory) * where absolutely necessary, sequencing mode is added as part of output file or directory instead * remove dependency of sequencing mode for rule for `FastQC`; now runs separately for each strand * Changes related to MultiQC and output file/directory structure * moving and renaming outputs for MultiQC is no longer required * code to create MultiQC custom config externalized into script `scripts/rhea_multiqc_config.py` * add MultiQC output files with deterministic output to md5 sum checks performed during execution of `tests/test_integration_workflow/test.{local,slurm}.sh` * output filenames for each rule now follow this general structure: `samples/{sample_name}/{rule}/{output_file}` * change log directory structure matches results directory structure * Miscellaneous changes * consistent, PEP8-compliant formatting in most parts, including Snakemake files, where allowed * remove rule `extract_decoys_salmon`; equivalent file `chrName.txt` produced by `star_index` is used instead * add rule `start` which copies sample data to the results directory and enforces uniform naming * refactoring of ALFA rules and modification of the CI/CD test to ensure compatibility
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- Mar 20, 2020
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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.
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- Mar 19, 2020
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- Mar 18, 2020
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- Mar 17, 2020
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- Mar 13, 2020
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BIOPZ-Katsantoni Maria authored
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- Mar 12, 2020
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Dominik Burri authored
- 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
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- Mar 06, 2020
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BIOPZ-Gypas Foivos authored
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.
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- Feb 21, 2020
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Alex Kanitz authored
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- 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
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- Feb 20, 2020
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Alex Kanitz authored
- 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)
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- Feb 17, 2020
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- add rule for input preparation (GTF to BED12) - add rule for TIN score calculation - update rule graph and DAG image - update Slurm cluster config
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- Feb 14, 2020
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Alex Kanitz authored
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- Feb 08, 2020
- Feb 07, 2020
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Alex Kanitz authored
- remove log files and add '.snakemake' directories to '.gitignore' - update wrong link in 'README.md' - delete superfluous script documentation 'scripts/labkey_api.md' - add Snakemake-specific file extension '.smk' to subworkflows - remove non-deterministic workflow output from md5 sums
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- Jan 24, 2020
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BIOPZ-Gypas Foivos authored
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- 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
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- Dec 20, 2019
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BIOPZ-Gypas Foivos authored
Rename snakemake/paired_end.snakemake to snakemake/paired_end.snakefile. Fix wiring of rules. Add fake tests.
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BIOPZ-Gypas Foivos authored
Clean up unused code in snakemake/Snakefile. Add 2 threads in htseq_qa (paired end mode). Add example of tsv files from LabKey.
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BIOPZ-Gypas Foivos authored
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BIOPZ-Katsantoni Maria authored
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