Seqliner QuickStart


Once you or your site admin have made Seqliner available in your system (see Installation Guide), simply type seqliner to get the list of commands:

>> seqliner

seqliner: A toolkit for effective use and management of bioinformatics pipelines.


  list           lists available pipelines
  run            runs a pipeline
  config         creates a config template where pipeline parameters can be customized.
  dev            more tools for developers.
  admin          tools for administering pipelines and resources.


  --version      get version

To browse the list of available pipelines and recipes, type seqliner list. Listing options can be obtained via seqliner list --help:

>> seqliner list

== Pipelines =======
===== amplicon ===============================================================
    Desc: Amplicon pipeline. Performs alignment (Primal Aligner) & Variant
          Calling (VarScan),
  Inputs: <dir, fasta>   Sample directory containing fastq pair(s), fasta file
 Outputs: <vcf,bam,...> Variant call by VarScan, bam files from PrimalAligner
          and more.

===== germline ===============================================================
    Desc: Germline pipeline. Performs alignment, duplicate marking, indel
          realignment, base quality recalibration, performance summary,
          variant calling.
   Input: <dir>   Sample directory containing fastq pair(s)
 Outputs: <vcf,bam,...> Variant call by GATK, performance summary, bam files
          and more.

===== somatic ================================================================


== Recipes =========
        hg19 : Defines reference and data resources for HG19
        mm10 : Defines reference for MM10 (TODO: known snps & known indels)
   idt_borca : Defines IDT_BORCA target regions
     nimb_v3 : Defines NimbleGen Exome V3 target regions
  agilent_v4 : Defines Agilent SureSelect Human Exome V4 target regions
   pairedEnd : Data is paired-end.
   singleEnd : Data is single-end.

From the description above, you should be able to work out A) the intended use of the pipelines, B) expected inputs, and C) relevant recipes. If you can’t, make a complaint to the pipeline developers!!

Once you know what pipeline and recipes to use, you are ready to run a pipeline. Just type seqliner run to get a description of the syntax:

>>seqliner run

USAGE: seqliner run <pipeline> [options] [input1[ input2[ ...]]]

 pipeline : See 'seqliner list' for a list of available pipelines

     -r : Comma separated recipes (e.g. hg19,SureSelectHuExomeV4)
     -o : Output directory [default: current working dir]
     -c : Custom config (see 'seqliner config'). Settings in this file will
          override recipes (if overlaps) and site config.
     -d : Custom script directory
     -p : Additional parameter(s) required by pipeline; comma separated
          key-value pairs (e.g. RUN_ID=001,SAMPLE_LABEL=003).
     -t : RESOURCE ROOT. Default root directory for resource files unless full
          path is specified

 --rerun  : Use 'seqliner run --rerun <params-log.groovy>' to perform a rerun
            using previously supplied arguments
 -f false : inputs will be converted to full path by default. Use '-f false'
            to suppress
 -q true  : seqliner will use bpipe built-in qsub handler (default: false)

For example, to analyse a germline sample that has been target-enriched using the Agilent SureSelect Human All Exon v4 capture, we will be using the “germline” pipeline and the “hg19” and “agilent_v4” recipes, which were all described when we typed seqliner list above. Now, we use seqliner run as follows:

>> seqliner run germline -r hg19,agilent_v4 -o myOutDir /path/to/germline/fastq/dir

If you are running this in a compute cluster environment, either use -q or do a normal job submission:

>> seqliner run germline -q -r hg19,agilent_v4 -o myOutDir /path/to/germline/fastq/dir


>> echo "cd $PWD; seqliner run germline -r hg19,agilent_v4 -o myOutDir /path/to/germline/fastq/dir" | qsub -l walltime=48:00:00,mem=16GB

To customise pipelines and/or use custom configurations (e.g. for a custom capture panel), one of the -c / -d / -p parameters can be used. Full documentation is available in Seqliner Configuration Hierarchy.

We also recommend reading and understand the Roles concept underlying the design of Seqliner.

Installation Guide

To do.