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nf_rnaseq
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nf_rnaseq
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#!/usr/bin/env nextflow
nextflow.enable.dsl=2
// last modified 13 October 2020
params.outdir = "."
params.genome = ""
params.verbose = false
params.single_end = false // default mode is auto-detect. NOTE: params are handed over automatically
params.fastqc_args = ''
params.fastq_screen_args = ''
params.trim_galore_args = ''
params.hisat2_args = ''
params.multiqc_args = ''
params.help = false
// Show help message and exit
if (params.help){
helpMessage()
exit 0
}
params.list_genomes = false;
if (params.list_genomes){
println ("[WORKLFOW] List genomes selected")
}
if (params.verbose){
println ("[WORKFLOW] FASTQC ARGS: " + params.fastqc_args)
println ("[WORKFLOW] FASTQ SCREEN ARGS ARE: " + params.fastq_screen_args)
println ("[WORKFLOW] TRIM GALORE ARGS: " + params.trim_galore_args)
println ("[WORKFLOW] HISAT2 ARGS ARE: " + params.hisat2_args)
println ("[WORKFLOW] MULTIQC ARGS: " + params.multiqc_args)
}
include { makeFilesChannel; getFileBaseNames } from './nf_modules/files.mod.nf'
include { getGenome } from './nf_modules/genomes.mod.nf'
include { listGenomes } from './nf_modules/genomes.mod.nf'
if (params.list_genomes){
listGenomes() // this lists all available genomes, and exits
}
genome = getGenome(params.genome)
include { FASTQC } from './nf_modules/fastqc.mod.nf'
include { FASTQC as FASTQC2 } from './nf_modules/fastqc.mod.nf'
include { FASTQ_SCREEN } from './nf_modules/fastq_screen.mod.nf'
include { TRIM_GALORE } from'./nf_modules/trim_galore.mod.nf'
include { HISAT2 } from './nf_modules/hisat2.mod.nf' params(genome: genome)
include { MULTIQC } from './nf_modules/multiqc.mod.nf'
file_ch = makeFilesChannel(args)
workflow {
main:
FASTQC (file_ch, params.outdir, params.fastqc_args, params.verbose)
FASTQ_SCREEN (file_ch, params.outdir, params.fastq_screen_args, params.verbose)
TRIM_GALORE (file_ch, params.outdir, params.trim_galore_args, params.verbose)
FASTQC2 (TRIM_GALORE.out.reads, params.outdir, params.fastqc_args, params.verbose)
HISAT2 (TRIM_GALORE.out.reads, params.outdir, params.hisat2_args, params.verbose)
// merging channels for MultiQC
multiqc_ch = FASTQC.out.report.mix(
TRIM_GALORE.out.report,
FASTQ_SCREEN.out.report.ifEmpty([]),
FASTQC2.out.report.ifEmpty([]),
HISAT2.out.stats.ifEmpty([]),
).collect()
// multiqc_ch.subscribe { println "Got: $it" }
MULTIQC (multiqc_ch, params.outdir, params.multiqc_args, params.verbose)
}
// Since workflows with very long command lines tend to fail to get rendered at all, I was experimenting with a
// minimal execution summary report so we at least know what the working directory was...
workflow.onComplete {
def msg = """\
Pipeline execution summary
---------------------------
Jobname : ${workflow.runName}
Completed at: ${workflow.complete}
Duration : ${workflow.duration}
Success : ${workflow.success}
workDir : ${workflow.workDir}
exit status : ${workflow.exitStatus}
"""
.stripIndent()
sendMail(to: "${workflow.userName}@babraham.ac.uk", subject: 'Minimal pipeline execution report', body: msg)
}
def helpMessage() {
log.info"""
>>
SYNOPSIS:
In a nutshell, this workflow runs an entire RNA-seq processing pipeline on FastQ files, including QC, contamination QC,
quality-/adapter trimming, splice -aware alignments to a genome using HISAT2, and finally generate an aggregate QC report.
The workflow is suitable for RNA-seq data, or any other form of sequencing that requires standard alignments to a genome
when you would like to use HISAT2 as the underlying aligner (in such a case you might want to consider turning off spliced
alignments). Here is a graphical representation of the workflow:
--- FastQC
--- FastQ Screen
--- Trim Galore
|
--- FastQC
--- HISAT2
--- MultiQC*
* This step runs only once ALL other jobs have completed.
All these steps are submitted as jobs to the Babraham stone compute cluster.
By default, the involved tools are run in the following way:
------------------------------------------------------------
FastQC: defaults (-q)
FastQ Screen: defaults (Bowtie 2; local mode)
Trim Galore: defaults (adapter auto-detection)
HISAT2: end-to-end mode ('--no-softclip'); '--no-unal'; for PE files: '--no-mixed --no-discordant' (concordant PE alignmnents only)
To add additional parameters to any of the programs, consider supplying tool-specific arguments (see --toolname_args="..." below).
==============================================================================================================
USAGE:
nf_rnaseq [options] --genome <genomeID> <input files>
Mandatory arguments:
====================
<input files> List of input files, e.g. '*fastq.gz' or '*fq.gz'. Files are automatically processed as
single-end (SE) or paired end (PE) files (if file pairs share the same base-name, and differ only
by a read number, e.g. 'base_name_R1.fastq.gz' and 'base_name_R2.fastq.gz' (or R3, R4). For
PE files, only Read 1 is run through FastQ Screen (as typically R1 and R2 produce nearly identical
contamination profiles). To run PE files in single-end mode, please see '--single_end' below.
--genome [str] Genome build ID to be used for the alignment, e.g. GRCh38 (latest human genome) or GRCm38
(latest mouse genome build). To list all available genomes, see '--list_genomes' below.
Tool-specific options:
======================
For all following options, please note that the format: ="your options" needs to be strictly adhered to in order to work correctly.
--fastqc_args="[str]" This option can take any number of options that are compatible with FastQC to modify its default
behaviour. For more detailed information on available options please refer to the FastQC documentation,
or run 'fastqc --help' on the command line. As an example, to run FastQC without grouping of bases when
reads are >50bp and use a specific file with non-default adapter sequences, use:
' --fastqc_args="--nogroup --adapters ./non_default_adapter_file.txt" '. [Default: None]
--fastq_screen_args="[str]" This option can take any number of options that are compatible with FastQ Screen to modify its
default behaviour. For more detailed information on available options please refer to the FastQ Screen
documentation, or run 'fastq_screen --help' on the command line. For instance, to process a bisulfite
converted library with fairly relaxed parameters, you could use:
' --fastq_screen_args="--bisulfite --score_min L,0,-0.6" '. [Default: None]
--trim_galore_args="[str]" This option can take any number of options that are compatible with Trim Galore to modify its
default trimming behaviour. For more detailed information on available options please refer
to the Trim Galore User Guide, or run 'trim_galore --help' on the command line. As an example, to trim
off the first 10bp from the 5' of R1 and 5bp of R2, use:
' --trim_galore_args="--clip_r1 10 --clip_r2 5" '. [Default: None]
--hisat2_args="[str]" This option can take any number of options that are compatible with HISAT2 to modify its
default mapping behaviour. For more detailed information on available options please refer
to the HISAT2 User Guide, or run 'hisat2 --help' on the command line. As an example, to disable
spliced alignments and tolerate a miximum fragment length of 1500 bp, use:
' --hisat2_args="--no-spliced-alignment --maxins 1500" '. [Default: None]
Other options:
==============
--outdir [str] Path to the output directory. [Default: current working directory]
--list_genomes List all genome builds that are currently available to choose from. To see this list
of available genomes with more detailed information about paths and indexes, run
the command as '--list_genomes --verbose'
--single_end Force files of a read pair to be treated as single-end files. [Default: auto-detect]
--verbose More verbose status messages. [Default: OFF]
--help Displays this help message and exits.
Workflow options:
=================
Please note the single '-' hyphen for the following options!
-resume If a pipeline workflow has been interrupted or stopped (e.g. by accidentally closing a laptop),
this option will attempt to resume the workflow at the point it got interrupted by using
Nextflow's caching mechanism. This may save a lot of time.
-bg Sends the entire workflow into the background, thus disconnecting it from the terminal session.
This option launches a daemon process (which will keep running on the headnode) that watches over
your workflow, and submits new jobs to the SLURM queue as required. Use this option for big pipeline
jobs, or whenever you do not want to watch the status progress yourself. Upon completion, the
pipeline will send you an email with the job details. This option is HIGHLY RECOMMENDED!
-process.executor=local Temporarily changes where the workflow is executed to the 'local' machine. See also Nextflow config
file for more details. [Default: slurm]
<<
""".stripIndent()
}