nf_trim_galore

#!/usr/bin/env nextflow
nextflow.enable.dsl=2

// Last modified 13 October 2020

params.outdir = "."
params.verbose = false
params.trim_galore_args = ''
params.single_end = false  // default mode is auto-detect. NOTE: params are handed over automatically 

params.help = false
// Show help message and exit
if (params.help){
    helpMessage()
    exit 0
}

if (params.verbose){
    println ("[WORKFLOW] TRIM GALORE ARGS: "      + params.trim_galore_args)
}

include { makeFilesChannel; getFileBaseNames } from './nf_modules/files.mod.nf'
include { TRIM_GALORE }                            from './nf_modules/trim_galore.mod.nf'

file_ch = makeFilesChannel(args)

workflow {

    main:
        TRIM_GALORE(file_ch, params.outdir, params.trim_galore_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
        ---------------------------
        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:
    
    This workflow takes in a list of filenames (in FastQ format), and runs the files through Trim Galore for adapter- and
    quality trimming (on the Babraham stone compute cluster).

    If called as is, this Trim Galore workflow auto-detects the library type (single-end (SE)/ paired-end (PE)), the sequencing 
    adapter used and selects Phred 20 as the default quality cutoff. To modify this default trimming behaviour, please specify
    additional tool-specific arguments that are compatible with Trim Galore (see '--trim_galore_args' below).


              ==============================================================================================================


    USAGE:
    
    nf_trim_galore [options] <input files>
    
    Mandatory arguments:
    ====================

      <input files>                   List of input files, e.g. '*fastq.gz' or '*fq.gz'. In theory, files will automatically be
                                      processed as SE or PE files (if file pairs share the same base-name, and differ only by a
                                      different read number, e.g. 'base_name_R1.fastq.gz' and 'base_name_R2.fastq.gz' (or R3, R4).
                                      To run PE files in single-end mode, please see '--single_end' below.

    Tool-specific options:
    ======================

      --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 (https://github.com/FelixKrueger/TrimGalore/tree/master/Docs),
                                      or run 'trim_galore --help' on the command line. As an example, to trim off the first 10bp
                                      from the 5' of R1, and run FastQC on the files after trimming, use: 
                                      ' --trim_galore_args="--clip_R1 10 --fastqc" '. Please note that the format 
                                      ="your options" needs to be strictly adhered to in order to work correctly. [Default: None]

    Other Options:
    ==============

      --outdir [str]                  Path to the output directory. [Default: current working directory]

      --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 the nextflow.config
                                      file for more details. [Default: slurm] 
    

    <<
    """.stripIndent()

}