Arriba & star nf dvpt

src/arriba_fusion.nf

@@ -112,6 +112,10 @@ Channel
  ****************************************************************
 */
 
+include { fastp } from './nf_modules/fastp/main.nf'
+include { fastqc_fastq as fastqc_raw } from fastqc_mod addParams(fastqc_fastq_out: "$params.project/01_fastqc_raw/")
+include { fastqc_fastq as fastqc_preprocessed } from fastqc_mod addParams(fastqc_fastq_out: "$params.project/02_fastqc_preprocessed/")
+include { multiqc } from './nf_modules/multiqc/main.nf' addParams(multiqc_out: "$params.project/QC/")
 include { arriba } from "./nf_modules/arriba/main.nf"
 
 /*
@@ -122,6 +126,23 @@ include { arriba } from "./nf_modules/arriba/main.nf"
 
 workflow {
 
+  if(params.bam == ""){
+    fastp()
+    fastqc_raw()
+    fastqc_preprocessed()
+    multiqc()
+    .mix(
+      fastqc_preprocessed.out.report
+      ).collect()
+    index_fasta()
+    mapping_fastq()
+    filter_bam_quality()
+    sort_bam()
+    index_bam()
+  }
+
+
+
   //###################### ARRIBA FUSION ########################
 
   arriba(fastq_files, gtf, genome)

src/star_fusion.nf

@@ -25,7 +25,8 @@ def helpMessage() {
       nextflow ./src/star_fusion.nf -c ./src/nextflow.config -profile singularity
 
     Mandatory arguments:
-      --project [path]                Path to the project folder containing fastq folder. Results are saved in this folder.
+      --project [path]                Path to the project folder. Results are saved in this folder.
+      --fastq [path]                  Path to fastq folder.
       -profile [str]                  Configuration profile to use.
                                       Available: docker, singularity, podman, psmn, ccin2p3
 
@@ -57,7 +58,7 @@ if (params.help || params.h) {
 */
  
 params.project = ""
-params.fastq = "${params.project}/fastq"
+params.fastq = "${project}/fastq/*R{1,2}.fastq.gz"
 
 /*
 if (params.genome)          { params.genome = path(params.genome, checkIfExists: true) } else { exit 1, "No genome specified." }