parallel_map

Description

Map wells in batch, using STAR
Spliced Transcripts Alignment to a Reference (C) Alexander Dobin
https://github.com/alexdobin/STAR

Type

bash_script

License

MIT

Links

Repository

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
limitBAMsortRAM: [ "10000000000" ]  
runThreadN: [ 1 ]  
output: "$id.$key.output._*"  
joblog: "$id.$key.joblog"  
id: "run"  
publish_dir: "output/"  
EOM

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

Input arguments

Name	Type & Properties	Description
--input_r1	file required multiple	Input FASTQ files for the forward reads. All FASTQ file names must start with the prefix '{well_id}_R1', where 'well_id' can be found as the sequence identifier in the barcodes FASTA file (see 'barcodesFasta' argument). For each FASTQ file, a matching FASTQ file for the reverse reads must be provided to the 'input_r2' argument, meaning that their 'well_id' prefix must match. The number of items provided for 'input_r1' must be equal to the number of items for 'input_r2'.
--input_r2	file required multiple	Input FASTQ files for the reverse reads. All FASTQ file names must start with the prefix '{well_id}_R2', where 'well_id' can be found as the sequence identifier in the barcodes FASTA file (see 'barcodesFasta' argument). For each FASTQ file, a matching FASTQ file for the reverse reads must be provided to the 'input_r1' argument, meaning that their 'well_id' prefix must match. The number of items provided for 'input_r1' must be equal to the number of items for 'input_r2'.
--genomeDir	file required	Reference genome to match to. Can be generated from genomic FASTA sequences and a genome annotation by using STAR with '--runMode genomeGenerate'.
--barcodesFasta	file required	FASTA file where each entry specifies a unique barcode sequence present at the start of the forward input reads (input_r1). The IDs of each barcode (the start of the FASTA headers up until the first whitespace character) must match with the start of one input FASTQ pair.

Name

Type & Properties

--input_r1

file

required

multiple

--input_r2

file

required

multiple

--genomeDir

file

required

--barcodesFasta

file

required

Barcode arguments

Name	Type & Properties	Description
--umiLength	integer required	Length of the Unique Molecular Identifiers (UMI). The UMI are expected to be located after the barcodes in the forwards reads.
--limitBAMsortRAM	string

Name

Type & Properties

--umiLength

integer

required

--limitBAMsortRAM

string

Runtime arguments

Name	Type & Properties	Description
--runThreadN	integer	Number of threads to use for a single STAR execution.

Name

Type & Properties

--runThreadN

integer

Output arguments

Name	Type & Properties	Description
--output	file required multiple output	A list of output folders which are the result of using STAR to map each input FASTQ pair STAR to the reference genome. The order of the items DO NOT match with the order of the entries in the barcodes FASTA file or the input FASTQ pairs.
--joblog	file output	Where to store the log file listing all the jobs.

Name

Type & Properties

--output

file

required

multiple

output

--joblog

file

output