Create example branch

Signed-off-by: christopher-hakkaart <[email protected]>

main.nf

@@ -1,37 +1,116 @@
-#!/usr/bin/env nextflow 
+#!/usr/bin/env nextflow
 
 /*
- * Proof of concept of a RNAseq pipeline implemented with Nextflow
+ * Pipeline parameters
  */
 
+// Input data
+params.reads = "${workflow.projectDir}/data/ggal/ggal_gut_{1,2}.fq"
+
+// Reference file
+params.transcriptome = "${workflow.projectDir}/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
+
+// Output directory
+params.outdir = "results"
 
 /*
- * Default pipeline parameters. They can be overriden on the command line eg.
- * given `params.foo` specify on the run command line `--foo some_value`.
+ * Index reference transcriptome file
  */
+process INDEX {
+    tag "$transcriptome.simpleName"
+    container "community.wave.seqera.io/library/salmon:1.10.3--482593b6cd04c9b7"
+    conda "bioconda::salmon=1.10.3"
 
-params.reads = "$baseDir/data/ggal/ggal_gut_{1,2}.fq"
-params.transcriptome = "$baseDir/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
-params.outdir = "results"
-params.multiqc = "$baseDir/multiqc"
-
-log.info """\
- R N A S E Q - N F   P I P E L I N E
- ===================================
- transcriptome: ${params.transcriptome}
- reads        : ${params.reads}
- outdir       : ${params.outdir}
- """
-
-// import modules
-include { RNASEQ } from './modules/rnaseq'
-include { MULTIQC } from './modules/multiqc'
-
-/* 
- * main script flow
+    input:
+    path transcriptome
+
+    output:
+    path 'index'
+
+    script:
+    """
+    salmon index --threads $task.cpus -t $transcriptome -i index
+    """
+}
+
+/*
+ * Generate FastQC reports
  */
-workflow {
-  read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true ) 
-  RNASEQ( params.transcriptome, read_pairs_ch )
-  MULTIQC( RNASEQ.out, params.multiqc )
+process FASTQC {
+    tag "FASTQC on $sample_id"
+    publishDir params.outdir, mode:'copy'
+    container "community.wave.seqera.io/library/fastqc:0.12.1--5cfd0f3cb6760c42"
+    conda "bioconda::fastqc:0.12.1"
+
+    input:
+    tuple val(sample_id), path(reads)
+
+    output:
+    path "fastqc_${sample_id}_logs"
+
+    script:
+    """
+    mkdir fastqc_${sample_id}_logs
+    fastqc -o fastqc_${sample_id}_logs -f fastq -q ${reads}
+    """
+}
+
+/*
+ * Quantify reads
+ */
+process QUANT {
+    tag "$pair_id"
+    publishDir params.outdir, mode:'copy'
+    container "community.wave.seqera.io/library/salmon:1.10.3--482593b6cd04c9b7"
+    conda "bioconda::salmon=1.10.3"
+
+    input:
+    path index
+    tuple val(pair_id), path(reads)
+
+    output:
+    path pair_id
+
+    script:
+    """
+    salmon quant --threads $task.cpus --libType=U -i $index -1 ${reads[0]} -2 ${reads[1]} -o $pair_id
+    """
 }
+
+/*
+ * Generate MultiQC report
+ */
+process MULTIQC {
+  publishDir params.outdir, mode:'copy'
+    container "community.wave.seqera.io/library/multiqc:1.24.1--789bc3917c8666da"
+    conda "bioconda::multiqc:1.24.1"
+
+    input:
+    path '*'
+
+    output:
+    path 'multiqc_report.html'
+
+    script:
+    """
+    multiqc .
+    """
+}
+
+workflow {
+
+    // Paired reference data
+    read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true )
+
+    // Index reference transcriptome file
+    INDEX(params.transcriptome)
+
+    // Generate FastQC reports
+    FASTQC(read_pairs_ch)
+
+    // Quantify reads
+    QUANT(INDEX.out, read_pairs_ch)
+
+    // Generate MultiQC report
+    MULTIQC(QUANT.out.mix(FASTQC.out).collect())
+}