Indrops analysis pipeline at BioCore@CRG
The pipeline is based on the DropEST tool: https://github.com/hms-dbmi/dropEst
The parameters are listed when using nextflow run indrop.nf --help
command.
nextflow run indrop.nf --help
N E X T F L O W ~ version 19.07.0
Launching `indrop.nf` [gigantic_ride] - revision: 17bd0ef49f
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BIOCORE@CRG indropSEQ - N F ~ version 1.0
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pairs : {PATH}/*R{1,2,3,4}.fastq.gz
genome : {PATH}/anno/test.fa.gz
annotation : {PATH}/anno/gencode.v28.annotation.gtf
config : {PATH}/conf/indrop_v3.xml
barcode_list : {PATH}/conf/indrop_v3_barcodes.txt
email : yourmail@yourdomain
mtgenes : {PATH}/anno/mitoc_genes.txt
version : 3_4
library_tag : AGATATAA
output (output folder) : output_v3
You can change them either by using the command line:
nextflow run indrop.nf --pairs "data/{1,2}.fastq.gz" --version 1-2 > log
or changing the params.file You can use the nextflow options for sending the execution in background (-bg) or resuming a failed one (-resume).
nextflow run indrop.nf --pairs "data/{1,2}.fastq.gz" --version 1-2 -bg -resume > log
Parameter version: "V1-2"
Parameter version: "V3_3"
Parameter version: "V3_4"
The parameter library_tag is only needed with version V3_4