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If a process fails, you can fix the error and rerun the previous command using -resume and it will pick up where it failed. The key here is that all of the processes are run in the work directory and are given unique hash numbers.

Here is a more comprehensive structure of the files generated. This script produces a work directory which is default for all nextflow scripts and an out_dir directory which can be specified with -outdir (see help above) WARN: Task runtime metrics are not reported when using macOS without a container engine Launching `isugifNF/blast` - revision: ef0477a498 This nextflow script happens to have a test dataset to show it is functioning properly and is perfect to show how nextflow operates. chunkSize Number of fasta records to use when splitting the query fasta file threads Number of CPUs to use during blast job outfileName Prefix name for BLAST output options Additional options for BLAST command outdir Output directory to place final BLAST output Can use multiple (comma separated)Īvailable: test, condo, ceres, local, nova dbName Prefix name of the BLAST database dbDir BLAST database directory (full path required) genome Genome from which BLAST databases will be generated query Query fasta file of sequences you wish to BLAST Nextflow run main.nf -query QUERY.fasta -dbDir "blastDatabaseDirectory" -dbName "blastPrefixName" -profile local Nextflow run main.nf -query QUERY.fasta -genome GENOME.fasta -profile local The typical command for running the pipeline is as follows:

Launching `isugifNF/blast` - revision: 11f393fd09 Stream oriented – promotes programming approach extending Unix pipes model.Continuous checkpoints – each chunk and process it goes through is checkpointed.Unified parallelism – can process chunks through the entire pipeline (QC -> align -> call snps).

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Portable – can run locally, Slurm, SGE, PBS, and cloud (Google, Kubernetes and AWS).

Reproducibility – supports Docker and Singularity containers.

Fast protyping – let’s you write a computational pipeline from smaller tasks.

Nextflow is its own DSL (Domain Specific Language) that extends a language called groovy which is an extension of Java that has language feature similarity to Python, Ruby and Smalltalk. Nextflow is a workflow framework that can be used by a bioinformatician to integrate all of her/his/their bash/python/perl/other scripts into a one cohesive pipeline that are portable, reproducible, scalable and checkpointed.

Basic nextflow commands to run a workflow.

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Install the client, select your protobuf files and start making requests No extra steps or configuration needed. BloomRPC aim to give the simplest and efficient developer experience for exploring and querying your GRPC services. Inspired by Postman and GraphQL Playground.

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How to have the workflow Use the blast database I provide The missing GUI Client for GRPC services. How to have the workflow create the blast database for me These steps are taken from those found on the Singularity website. The environment that Singularity creates is often called a "container".įor the JEDI project, we will be using VirtualBox and Vagrant to create an Ubuntu (version 16.04) operating system that is then populated with the specific tools (compilers, ecbuild, etc.) using Singularity. Once a virtual machine is up and running, Singularity is used to create a specific environment (software tools, libraries, etc.) within that operating system. The combination of VirtualBox and Vagrant running a specific operating system, constitute an object commonly called a "virtual machine". The second is Vagrant which is a manager for configuring a specific operating system using the features of VirtualBox. The first is VirtualBox which extends your Mac to be able to run a large set of different operating systems (windows, linux, etc).

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Singularity requires two other pieces of software to put the whole container system together. usr/bin/ruby -e "$(curl -fsSL )" # install brew tools # The following command uses a bourne shell syntax so if you experience problems, try running it from a bash shell.