Verified Commit 36dac5e3 authored by Laurent Modolo's avatar Laurent Modolo
Browse files

example_marseq.nf: add vecloty example

parent 753be570
......@@ -5,18 +5,24 @@ Testing pipeline for marseq scRNASeq analysis
*/
include { adaptor_removal} from "./nf_modules/cutadapt/main.nf"
include { index_fasta; count } from "./nf_modules/kb/main.nf" addParams(
include {
index_fasta;
count;
index_fasta_velocity;
count_velocity
} from "./nf_modules/kb/main.nf" addParams(
kb_protocol: "marsseq",
count_out: "quantification/"
count_out: "quantification/",
count_velocity_out: "quantification_velocity/"
)
params.fasta = "http://ftp.ensembl.org/pub/release-94/fasta/gallus_gallus/dna/Gallus_gallus.Gallus_gallus-5.0.dna.toplevel.fa.gz"
params.cdna = "http://ftp.ensembl.org/pub/release-94/fasta/gallus_gallus/cdna/Gallus_gallus.Gallus_gallus-5.0.cdna.all.fa.gz"
params.fastq = "data/CF42_45/*/*R{1,2}.fastq.gz"
params.gtf = "http://ftp.ensembl.org/pub/release-94/gtf/gallus_gallus/Gallus_gallus.Gallus_gallus-5.0.94.gtf.gz"
params.transcript_to_gene = ""
params.whitelist = "data/expected_whitelist.txt"
params.config = "data/marseq_flexi_splitter.yaml"
params.workflow_type = "classic"
log.info "fastq files: ${params.fastq}"
log.info "fasta file : ${params.fasta}"
......@@ -32,11 +38,6 @@ channel
.ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" }
.map { it -> [it.simpleName, it]}
.set { fasta_files }
channel
.fromPath( params.cdna )
.ifEmpty { error "Cannot find any fasta files matching: ${params.cdna}" }
.map { it -> [it.simpleName, it]}
.set { cdna_files }
channel
.fromPath( params.gtf )
.ifEmpty { error "Cannot find any gtf files matching: ${params.gtf}" }
......@@ -59,6 +60,11 @@ channel
workflow {
adaptor_removal(fastq_files)
index_fasta(fasta_files, cdna_files, gtf_files)
count(index_fasta.out.index, adaptor_removal.out.fastq, index_fasta.out.t2g, whitelist_files, config_files)
if (params.workflow_type == "classic") {
index_fasta(fasta_files, gtf_files)
count(index_fasta.out.index, adaptor_removal.out.fastq, index_fasta.out.t2g, whitelist_files, config_files)
} else {
index_fasta_velocity(fasta_files, gtf_files)
count_velocity(index_fasta_velocity.out.index, adaptor_removal.out.fastq, index_fasta_velocity.out.t2g, whitelist_files, config_files)
}
}
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