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Welcome to the YAATAP wiki!

Our team

• Felipe Vaz Peres
• Jorge Mario Munoz Pérez
• Renato Augusto Corrêa dos Santos
• Dr. rer. nat. Diego Mauricio Riaño Pachón

About our pipeline

Setup

We followed steps described in the SnakeMake SETUP page. Briefly, we created a conda environment and installed the Mambaforge Conda based distribution.

module load miniconda3
conda create -n snakemake_racs
conda install -n snakemake_racs -c conda-forge mamba

Next, we installed Snakemake with mamba in the activated environment ("snakemake_racs" in this example):

conda activate snakemake_racs
mamba install -c conda-forge -c bioconda snakemake

Files used to execute Snakemake

PART 1:

Currently, the first part of our pipeline requires two files:

• config.yaml1: configuration file that provides the path to each software used in this step.
• samples_TEST.csv: a tuple with samples (Sorghum RNA-Seq runs) to be used when testing the pipeline.
• MyAssembly_TEST/GCF_000003195.3_rna.fna: FASTA file with the Sorghum transcriptome downloaded from NCBI (under the accession GCF_000003195.3).

PART 2:

Part 2 requires two files as well:

• config.yaml2: configuration file that provides the path to each software used in this step.
• samples_TEST.csv: a tuple with samples (Sorghum RNA-Seq runs) to be used when testing the pipeline.
• parts.csv:

Actual execution of Snakemake

To save disk space, we keep a compressed version of the transcriptome in the repository (MyAssembly_TEST/GCF_000003195.3_rna.fna.gz). Make sure you decompress it (using gzip) before running the pipeline.

In our server, we execute snakemake with the screen utility:

screen

After screen was activated, all it is necessary:

module load miniconda3
conda activate snakemake_racs
snakemake -p -s Snakefile1 --cluster "qsub -q all.q -V -cwd -l h={params.server} -pe smp {threads} -l mem_free={resources.mem_free}G" --jobs 10

After running snakemake, we detach from the screen session with CTRL + A + D (see this Linuxize tutorial for more details on running screen)