najlabioinfo/nextflowtuto repository overview

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⁠docker-nextflow-one-container: How

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⁠I/ Install

⁠1. CONDA

⁠1.a). Pull CONDA image

docker pull continuumio/anaconda3

⁠1.b). Launch CONDA image

docker run -i -t continuumio/anaconda3 /bin/bash

⁠1.c). Check conda version

conda --version

⁠1.d). Start a Jupyter Notebook server and interact with Anaconda via your browser

docker run -i -t -p 8888:8888 continuumio/anaconda3 /bin/bash -c "/opt/conda/bin/conda install jupyter -y --quiet && mkdir /opt/notebooks && /opt/conda/bin/jupyter notebook --notebook-dir=/opt/notebooks --ip='*' --port=8888 --no-browser"

⁠2. NEXTFLOW

⁠2.a). Install nextflow / Will update conda too

conda install -c bioconda nextflow 

⁠2.b). Check conda version again

conda --version

⁠2.c). Check nextflow version

nextflow -v

⁠2.c). Important folders generated

ls /home/najlabioinfo/hack17-tutorial/.nextflow

⁠3. Salmon

⁠3.a). Install salmon // for tutorial (nf-hack17-tutorial)

conda install -c bioconda salmon 

⁠3.b). Check salmon version

salmon -v

⁠4. FastQC

⁠4.a). Install FastQC // for tutorial (nf-hack17-tutorial)

conda install -c bioconda fastqc 

⁠4.b). Check fastqc version

fastqc -v

⁠4. MultiQC

⁠4.a). Install MultiQC // for tutorial (nf-hack17-tutorial)

conda install -c bioconda -c conda-forge multiqc

⁠4.b). Check multiqc version

multiqc -v

⁠5. Slurm

⁠5.a). Install SLURM // for tutorial (rnaSeq_byBABS)

apt-get install sbatch

⁠5.b). Check slurm version

slurm  -v

⁠5.c). Install sbatch // for tutorial (rnaSeq_byBABS)

• sbatch is used to submit a job script for later execution. The script will typically contain one or more srun commands to launch parallel tasks.

apt-get install sbatch

⁠5.d). sbatch slurm version

sbatch --version

⁠5.e). Edit slum config file slurm.conf

 vi /etc/slurm-llnl/slurm.conf

⁠6. TUTO:: Run Nextflow workflow from one container

⁠6.a). Pull The nextflow ready docker image

docker pull najlabioinfo/nextflowtuto:latest

⁠6.b). RUN The nextflow ready docker image

docker run -i -t -p 8888:8888 bhntools/nextflowtuto:latest /bin/bash 

⁠6.c). Go to the tuto repository

cd /home/najlabioinfo/Tuto/nf-hack17-tutorial

⁠6.d). Run nextflow

nextflow run script6.nf -resume -with-report

⁠7. Clean work

nextflow clean -f -k

⁠8. Note

• The Tuto repository contain others tutorials (rntoy,rnaseq-nf) and new-nextflow-project-template, but it's for running with multiple docker containers.

⁠V/ Refereces:

• https://anaconda.org/bioconda/multiqc-bcbio⁠
• https://hub.docker.com/r/continuumio/anaconda3⁠
• https://github.com/nextflow-io/awesome-nextflow/⁠
• https://github.com/nextflow-io/nextflow⁠
• https://github.com/nextflow-io/nf-hack17-tutorial⁠
• https://github.com/crickbabs/rnaSeq_byBABS⁠
• https://github.com/czbiohub/nextflow-tutorial-2019⁠
• https://slurm.schedmd.com/quickstart.html⁠