Nextflow RNA-seq Pipeline (rna_nf)

Conda environment

To create the 'rna' conda environment for Nextflow

conda env create -f environment.yml -p [path_and_environment name]

In the environment.yml, the environment name, conda channels and packages with or without restriction of versions.

Include this environment path in ~/.condarc, that is

envs_dirs:
  - /hpc/users/liuy22/LOAD/rna/py2_conda_env

Make sure conda is loaded via module load ananconda or miniconda in HPC, or locally available.

Conda integration in Nextflow

In the Nextflow configuration, include 'conda' in the 'process' scope as the following. This ablates specification in 'processes' of the Nextflow script.

process {
	conda = '/home/yiyuan/Data/Nextflow/py2_conda_env/rna'
}

Nextflow configuration file (*.config)

Parameter file (*.yml)

Local usage

As in the call_nf.sh, to run the RNA-seq pipeline locally,

nextflow rna.nf -c rna_local.config -params-file project_local.yml

or with more complexity,

nextflow rna.nf \
	-c rna_local.config \
	-params-file project_local.yml \
	-with-trace \
	-with-timeline \
	-with-dag flowchart.html

HPC usage

To be continued.