From 6bddba3750a87ec04b3d338f78c5e5a143bc46cf Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 28 May 2021 16:37:13 +0200
Subject: [PATCH] working example of marseq analysis
---
src/example_marseq.nf | 62 +++++++++++++++++++++++++++++++++++++++++++
1 file changed, 62 insertions(+)
create mode 100644 src/example_marseq.nf
diff --git a/src/example_marseq.nf b/src/example_marseq.nf
new file mode 100644
index 00000000..8b8068a9
--- /dev/null
+++ b/src/example_marseq.nf
@@ -0,0 +1,62 @@
+nextflow.enable.dsl=2
+
+/*
+Testing pipeline for marseq scRNASeq analysis
+*/
+
+include { index_fasta; count } from "./nf_modules/kb/main.nf" addParams(
+ kb_protocol: "marsseq",
+ count_out: "quantification/"
+)
+
+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"
+
+log.info "fastq files: ${params.fastq}"
+log.info "fasta file : ${params.fasta}"
+log.info "gtf file : ${params.gtf}"
+log.info "transcript_to_gene file : ${params.transcript_to_gene}"
+log.info "whitelist file : ${params.whitelist}"
+
+channel
+ .fromFilePairs( params.fastq, size: -1)
+ .set { fastq_files }
+channel
+ .fromPath( params.fasta )
+ .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}" }
+ .map { it -> [it.simpleName, it]}
+ .set { gtf_files }
+if (params.whitelist == "") {
+ channel.empty()
+ .set { whitelist_files }
+} else {
+ channel
+ .fromPath( params.whitelist )
+ .map { it -> [it.simpleName, it]}
+ .set { whitelist_files }
+}
+channel
+ .fromPath( params.config )
+ .ifEmpty { error "Cannot find any config files matching: ${params.config}" }
+ .map { it -> [it.simpleName, it]}
+ .set { config_files }
+
+workflow {
+ index_fasta(fasta_files, cdna_files, gtf_files)
+ count(index_fasta.out.index, fastq_files, index_fasta.out.t2g, whitelist_files, config_files)
+}
--
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