parallel_map
Description
Map wells in batch, using STAR
Spliced Transcripts Alignment to a Reference (C) Alexander Dobin
https://github.com/alexdobin/STAR
Input arguments
Name | Type & Properties | Description |
|---|---|---|
--input_r1 | file required multiple | |
--input_r2 | file required multiple | |
--genomeDir | file required | STAR reference directory |
--barcodes | string required multiple | The barcodes/wells to process |
Barcode arguments
Name | Type & Properties | Description |
|---|---|---|
--wellBarcodesLength | integer required | The length of the well barcodes |
--umiLength | integer required | The length of the UMIs |
--limitBAMsortRAM | string |
Runtime arguments
Name | Type & Properties | Description |
|---|---|---|
--runThreadN | integer | Number of threads to use for a single STAR execution. |
Output arguments
Name | Type & Properties | Description |
|---|---|---|
--output | file required multiple output | Location of the output folders, 1 folder per barcode. The value used for this argument must contain a '*', which will be replaced with the barcode to form the final output location for that barcode. |
--joblog | file output | Where to store the log file listing all the jobs. |
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 v0.1.0 \
-main-script target/nextflow/parallel_map/main.nf \
-params-file params.yaml Relationships
Used by
1 relationships
Current component
parallel_maphtrnaseq v0.1.0
Uses
0 relationships
No component dependencies found.