working example of marseq analysis

src/example_marseq.nf

+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)
+}