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.
<Subcommands>
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.
<Others>
--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 =========
====================
RECIPE DESCRIPTION
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[ ...]]]
<Required>
pipeline : See 'seqliner list' for a list of available pipelines
<Optional>
-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
<Notes>
--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
OR:
>> 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.
To do.