Step 0:
curl -fsSL get.nextflow.io | bash
And add NXF_HOME to your .bashrc in case the space in your home directory is restricted:
export NXF_HOME=/path/to/.nextflow
Step1: Run test
The pipeline is preconfigured with test data. INorder to tst whether the pipeline runs through call vc_pipe without command line parameters:
./nextflow run PlantandFoodResearch/VariantAnalysis/align.nf [--help]
If the pipeline does not run through, look into teh log file:
.nextflow.log
and contact the app steward (helge.dzierzon@plantandfood.co.nz).
Step 2: Configure file and sample IDs
This is the test data design.config. Adapt to your needs.
sample,file,rep,read,experiment,date,comments
HW1,kiwitest.1.R1.fq.gz,1,R1,kiwitest,2016-01-01,This is crap
HW1,kiwitest.1.R2.fq.gz,1,R2,kiwitest,2016-01-01,This is crap
HW2,kiwitest.2.R1.fq.gz,2,R1,kiwitest,2016-01-01,This is crap
HW2,kiwitest.2.R2.fq.gz,2,R2,kiwitest,2016-01-01,This is crap
Step 3: Run the pipeline
Options:
output_dir: publish directory for results ["./"]
inpu_dir: Directory that contains the raw reads ["$baseDir/KiwiTestData"]
genome: Reference genome file (*.fasta) ["$baseDir/KiwiTestData/kiwitest.fasta"]
config: Location of config file ["$baseDir/design.config"]
$baseDir = $HOME/.nextflow/assets/hdzierz/VariantAnalysisFB
Typical run with the test data copied to $HOME/KiwiTestData
./nextflow run PlantandFoodResearch/VariantAnalysis/align.nf --input_dir '$HOME/KiwiTestData/' --genome '$HOME/KiwiTestData/kiwitest.fasta'