This PR updates the preprocessing pipepile so that we dynamically use the outputs of preceding rules as input for the rules. This minimizes the need to copy paste paths around and makes it more clear from which rule the input comes.
Testing
Clone the repo and checkout this branch run the preprocessing pipelines, they should all run without problems.
git checkout feature/snakemake-dynamic-rulescd example/preprocesswget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_44/GRCh38.primary_assembly.genome.fa.gz -P workdir/reference (if you don't have it)
gzip -d workdir/reference/GRCh38.primary_assembly.genome.fa.gz
Run the pipeline with qc
snakemake -j 1 --snakefile ../../pipelines/preprocess_with_qc.snakefile --configfile ../../pipelines/config/deeprvat_preprocess_config.yaml
Run the pipeline without qc
snakemake -j 1 --snakefile ../../pipelines/preprocess_no_qc.snakefile --configfile ../../pipelines/config/deeprvat_preprocess_config.yaml
What
This PR updates the preprocessing pipepile so that we dynamically use the outputs of preceding rules as input for the rules. This minimizes the need to copy paste paths around and makes it more clear from which rule the input comes.
Testing
Clone the repo and checkout this branch run the preprocessing pipelines, they should all run without problems.
git checkout feature/snakemake-dynamic-rulescd example/preprocesswget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_44/GRCh38.primary_assembly.genome.fa.gz -P workdir/reference(if you don't have it)gzip -d workdir/reference/GRCh38.primary_assembly.genome.fa.gzRun the pipeline with qc
snakemake -j 1 --snakefile ../../pipelines/preprocess_with_qc.snakefile --configfile ../../pipelines/config/deeprvat_preprocess_config.yamlRun the pipeline without qc
snakemake -j 1 --snakefile ../../pipelines/preprocess_no_qc.snakefile --configfile ../../pipelines/config/deeprvat_preprocess_config.yaml