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Alex Kanitz authored
`README.md` file describes - aim and background of the project (including the workflow DAG representation) - how to install requirements (including setting up a `conda` environment for the project) - how to execute the workflow run integration test - how to run the workflow on your own samples (including how to auto-generate required params from LabKey metadata) Additional minor changes: - minor changes in various test and related files, including updates of paths - root directory now includes subdirectory `runs/` for a user's workflow runs (contents not version-controlled)
Alex Kanitz authored`README.md` file describes - aim and background of the project (including the workflow DAG representation) - how to install requirements (including setting up a `conda` environment for the project) - how to execute the workflow run integration test - how to run the workflow on your own samples (including how to auto-generate required params from LabKey metadata) Additional minor changes: - minor changes in various test and related files, including updates of paths - root directory now includes subdirectory `runs/` for a user's workflow runs (contents not version-controlled)
config.yaml 1.29 KiB
---
##############################################################################
### Annotation
##############################################################################
organism: "Homo_sapiens"
annotation: "../prepare_annotation/results/annotation.gtf"
genome: "../prepare_annotation/results/genome.fa"
annotation_filtered: "../prepare_annotation/results/filtered_transcripts.gtf"
STAR_index: "../prepare_annotation/results/STAR_index/"
other_RNAs_sequence: "../prepare_annotation/other.fa"
other_RNAs_index: "../prepare_annotation/results/other_RNAs_sequence.idx"
salmon_index: "../prepare_annotation/results/filtered_transcripts_salmon.idx/"
##############################################################################
### Output and log directories
##############################################################################
database_path: "/some/path"
STAR_idx_folder: "STAR_indices"
output_dir: "results"
star_indexes: "results"
salmon_indexes: "results"
kallisto_indexes: "results"
local_log: "logs/local_log"
cluster_log: "logs/cluster_log"
##############################################################################
### Sample info
##############################################################################
samples: "samples.tsv"
...