Usage

Complete black-box

Use: bash /path/to/rna-count-salmon/run.sh. You'll see, it's magic. On GR's Flamingo, just copy paste:

bash -i /mnt/beegfs/pipelines/rna-count-salmon/pipeline/rna-count-salmon/run.sh

Wow! Such a pipeline! Many time to wait! Good time for a coffee break!

Automatic (Gencode's GRCh38)

You have red and followed the one-line-for-all installation command, and have a dedicated environment for this pipeline. We want to activate it, and launch the analysis.

You have your reads in a directory (whatever its name is) within your current working directory ? You want to count your reads over GRCh38 from Gencode ? You're ready for the grand tour!

conda activate rna-count-salmon
python3 ${RNA_COUNT_LAUNCHER} flamingo --fastqdir /path/to/reads/directory/

Yes dear, that's all. You wanted a single-line launcher ? You have it.

Semi-Automatic (Change your reference genome)

You have red and followed the one-line-for-all command, and have a dedicated environment for this pipeline. We want to activate it, and launch the analysis.

You have your reads in a directory (whatever its name is) within your current working directory ? However, the GRCh38 sequence and annotation does not fulfill your needs ? We still have something for you:

conda activate rna-count-salmon
FASTA="/path/to/sequence.fasta"
GTF="/path/to/annotation.gtf"
export FASTA GTF
python3 ${RNA_COUNT_LAUNCHER} flamingo --fastqdir /path/to/reads/directory/

You made it!

Manual (Full custom analysis)

You have red and followed the one-line-for-all command, and have a dedicated environment for this pipeline. We want to activate it, and launch the analysis.

The pipeline is shipped with a launcher:

conda activate rna-count-salmon
python3 ${RNA_COUNT_LAUNCHER} --help

Four options are available:

Subcommand	Purpose
config	Prepare your config file
design	Prepare your design file
snakemake	Run the pipeline with YOUR parameters
report	Build a report based on your previous run
flamingo	Ignore this. It is here for automated pipeline launch.

At each step, use --help to have a dedicated list of options, alongside with examples.