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saramonzonsaramonzon
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Added profiles to nextflow.config. Docker, singularity and standard working. Added help and cool info stuff to main.nf
1 parent f4853fa commit 0ea2655

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+1485
-14
lines changed

‎Dockerfile

+2-1
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@@ -19,4 +19,5 @@ RUN scif install /opt/bcftools_v1.9_centos7.scif
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ENV PATH=${PATH}:/scif/apps/bcftools/bin
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# SciF Entrypoint
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ENTRYPOINT ["scif"]
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# Disabled because of compatibility with nextflow.
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#ENTRYPOINT ["scif"]

‎conf/base.config

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/*
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* -------------------------------------------------
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* Nextflow base config file
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* -------------------------------------------------
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* A 'blank slate' config file, appropriate for general
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* use on most high performace compute environments.
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* Assumes that all software is installed and available
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* on the PATH. Runs in `local` mode - all jobs will be
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* run on the logged in environment.
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*/
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// TO-DO. Prepare configuration for local execution. Define mem, cpus, etc.

‎conf/docker.config

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/*
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* -------------------------------------------------
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* Nextflow config file for use with Docker
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* -------------------------------------------------
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* Defines basic usage limits and docker image id.
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* Imported under the default 'docker' Nextflow
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* profile in nextflow.config
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*/
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docker {
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enabled = true
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}
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process {
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container = 'nextflow-scif'
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executor = 'local'
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// To define
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//cpus = 8
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/* $executor.cpus*/
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//memory = 20G
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/* $executor.memory*/
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//time = 48.h
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}

‎conf/singularity.config

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/*
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* -------------------------------------------------
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* Nextflow config file for use with Singularity
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* -------------------------------------------------
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* Defines basic usage limits and docker image id.
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* Imported under the default 'docker' Nextflow
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* profile in nextflow.config
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*/
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singularity {
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enabled = true
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}
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process {
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// Path to container
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container = './nextflow-scif.simg'
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executor = 'local'
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// To define
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//cpus = 8
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/* $executor.cpus*/
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//memory = 20G
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/* $executor.memory*/
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//time = 48.h
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}

‎main.nf

+73-8
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@@ -1,15 +1,60 @@
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/*
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========================================================================================
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N E X T F L O W B A S I C W O R K F L O W
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========================================================================================
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#### Homepage / Documentation
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https://github.com/BU-ISCIII/nextflow-scif
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@#### Authors
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S. Monzon <[email protected]>
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## Based on nf-core pipelines
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# https://github.com/nf-core
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----------------------------------------------------------------------------------------
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----------------------------------------------------------------------------------------
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Pipeline overview:
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- 1: BWA indexing of reference genome.
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- 2: BWA mapping against indexed genome.
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- 3: Samtools sorting and indexing.
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- 4: Variant calling using bcftools
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----------------------------------------------------------------------------------------
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*/
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def helpMessage() {
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log.info"""
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=========================================
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BU-ISCIII/nextflow-scif DEMO PIPELINE v${version}
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=========================================
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Usage:
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The typical command for running the pipeline is as follows:
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nextflow run BU-ISCIII/nextflow-scif -profile standard
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Pipeline arguments:
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--reads Path to input data (must be surrounded with quotes).
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--genome Path to reference genome.
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--outdir Output dir.
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--help show this message.
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-profile Hardware config to use. standard/docker/singularity. Default: standard.
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""".stripIndent()
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}
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// Pipeline version
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version = '0.1'
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// Show help message
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params.help = false
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if (params.help){
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helpMessage()
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exit 0
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}
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// Default parameters
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params.reads = "$baseDir/data/samples/*.fastq"
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params.genome = "$baseDir/data/genome.fa"
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params.outdir = 'results'
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log.info """\
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VARIANT CALLING TOY PIPELINE
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=============================
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genome: ${params.genome}
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reads : ${params.reads}
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outdir: ${params.outdir}
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"""
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.stripIndent()
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/*
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* the reference genome file
@@ -24,6 +69,23 @@ Channel
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.ifEmpty { error "Cannot find any reads matching: ${params.reads}" }
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.set { reads }
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// Header log info
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log.info "========================================================="
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log.info " BU-ISCIII/nextflow-scif : basic nf workflow"
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log.info "========================================================="
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def summary = [:]
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summary['Reads'] = params.reads
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summary['Reference genome'] = params.genome
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summary['Results dir'] = params.outdir
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log.info summary.collect { k,v -> "${k.padRight(21)}: $v" }.join("\n")
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log.info "===================================="
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// Posible software version and profile checks (p.e check if standar profile is used in hpc server)
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// if().....
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/*
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* Step 1. Builds the genome index required by the mapping process
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*/
@@ -104,4 +166,7 @@ process variantCalling {
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workflow.onComplete {
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println ( workflow.success ? "Done!" : "Oops .. something went wrong" )
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// E-mail and html reporting configuration.
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}

‎nextflow.config

+80-2
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@@ -1,2 +1,80 @@
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process.container = '/home/smonzon/Documents/desarrollo/builder/nexflow-scif.img'
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singularity.enabled = true
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/*
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* -------------------------------------------------
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* Nextflow config file
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* -------------------------------------------------
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* Default config options for all environments.
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* Cluster-specific config options should be saved
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* in the conf folder and imported under a profile
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* name here.
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*/
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manifest {
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homePage = 'https://github.com/BU-ISCIII/nextflow-scif'
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description = 'This is a template project for develop and deploy nextflow pipelines with container and scif integration'
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mainScript = 'main.nf'
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}
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// Global default params, used in configs
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params {
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version = '0.1' //Pipeline version
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nf_required_version = '0.27.6' //Minimum version of Nextflow required
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reads="$baseDir/data/samples/*.fastq"
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genome="$baseDir/data/genome.fa"
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outdir='results'
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}
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profiles {
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standard {
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includeConfig 'conf/base.config'
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}
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docker {
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includeConfig 'conf/docker.config'
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}
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singularity {
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includeConfig 'conf/singularity.config'
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}
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hpc_isciii {
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// TODO. with modules.
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}
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testing {
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// TODO
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}
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aws {
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// TO DO
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}
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none {
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// Don't load any config (for use with custom home configs)
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}
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}
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// Capture exit codes from upstream processes when piping
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process.shell = ['/bin/bash', '-euo', 'pipefail']
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// By default output execution reports
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timeline {
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enabled = true
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file = "${params.outdir}/timeline.html"
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}
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report {
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enabled = true
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file = "${params.outdir}/report.html"
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}
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trace {
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enabled = true
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file = "${params.outdir}/trace.txt"
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}
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dag {
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enabled = true
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file = "${params.outdir}/DAG.svg"
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}
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‎results/DAG.dot

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digraph DAG {
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p0 [shape=point,label="",fixedsize=true,width=0.1,xlabel="Channel.fromFilePairs"];
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p1 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="ifEmpty"];
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p0 -> p1;
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p1 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="ifEmpty"];
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p5 [label="mapping"];
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p1 -> p5 [label="reads"];
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p2 [shape=point,label="",fixedsize=true,width=0.1];
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p3 [label="makeBWAindex"];
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p2 -> p3 [label="fasta"];
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p3 [label="makeBWAindex"];
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p5 [label="mapping"];
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p3 -> p5 [label="bwa_index"];
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p4 [shape=point,label="",fixedsize=true,width=0.1];
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p5 [label="mapping"];
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p4 -> p5 [label="fasta"];
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p5 [label="mapping"];
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p6 [label="samtools"];
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p5 -> p6 [label="bwa_bam"];
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p6 [label="samtools"];
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p9 [label="variantCalling"];
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p6 -> p9 [label="bam_for_bcftools"];
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p6 [label="samtools"];
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p9 [label="variantCalling"];
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p6 -> p9 [label="bai_for_bcftools"];
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p6 [label="samtools"];
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p7 [shape=point];
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p6 -> p7 [label="samtools_stats"];
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p8 [shape=point,label="",fixedsize=true,width=0.1];
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p9 [label="variantCalling"];
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p8 -> p9 [label="genome"];
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p9 [label="variantCalling"];
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p10 [shape=point];
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p9 -> p10 [label="vcf_file"];
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}

‎results/report.html

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