utils/listInputDir

Description

List the contents of a directory and parse contained fastq files

Type

nextflow_script

License

MIT

Links

Repository

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
r1_output: "$id.$key.r1_output._*"  
r2_output: "$id.$key.r2_output._*"  
lane: "$id.$key.lane._*"  
sample: "$id.$key.sample"  
sample_id: "$id.$key.sample_id"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/htrnaseq.git \  
  -revision v0.14.7 \  
  -main-script target/nextflow/utils/listInputDir/main.nf \  
  -params-file params.yaml

Arguments

Name	Type & Properties	Description
--input -i	file required	Path to the directory containing fastq files
--pools	string multiple	Pool names to include. By default all pools are selected for analysis.
--r1_output	file multiple output	Path to read 1 fastq/fasta file
--r2_output	file multiple output	Path to read 2 fastq/fasta file
--lane	string multiple output	Lane nr
--sample	string output	Sample nr
--sample_id	string output	Sample name

Name

Type & Properties

--input

-i

file

required

--pools

string

multiple

--r1_output

file

multiple

output

--r2_output

file

multiple

output

--lane

string

multiple

output

--sample

string

output

--sample_id

string

output