Verified Commit 3de4d8de authored by Laurent Modolo's avatar Laurent Modolo
Browse files

example_marseq.nf: add illumina adaptor removal

parent 6bddba37
......@@ -4,6 +4,7 @@ nextflow.enable.dsl=2
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(
kb_protocol: "marsseq",
count_out: "quantification/"
......@@ -57,6 +58,7 @@ channel
.set { config_files }
workflow {
adaptor_removal(fastq_files)
index_fasta(fasta_files, cdna_files, gtf_files)
count(index_fasta.out.index, fastq_files, index_fasta.out.t2g, whitelist_files, config_files)
count(index_fasta.out.index, adaptor_removal.out.fastq, index_fasta.out.t2g, whitelist_files, config_files)
}
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