1 files changed, 63 insertions, 0 deletions
diff --git a/node_modules/shiki/samples/nextflow.sample b/node_modules/shiki/samples/nextflow.sample
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+++ b/node_modules/shiki/samples/nextflow.sample
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+/*
+ * The following pipeline parameters specify the reference genomes
+ * and read pairs and can be provided as command line options
+ */
+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"
+ 
+workflow {
+    read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true )
+ 
+    INDEX(params.transcriptome)
+    FASTQC(read_pairs_ch)
+    QUANT(INDEX.out, read_pairs_ch)
+}
+ 
+process INDEX {
+    tag "$transcriptome.simpleName"
+ 
+    input:
+    path transcriptome
+ 
+    output:
+    path 'index'
+ 
+    script:
+    """
+    salmon index --threads $task.cpus -t $transcriptome -i index
+    """
+}
+ 
+process FASTQC {
+    tag "FASTQC on $sample_id"
+    publishDir params.outdir
+ 
+    input:
+    tuple val(sample_id), path(reads)
+ 
+    output:
+    path "fastqc_${sample_id}_logs"
+ 
+    script:
+    """
+    fastqc.sh "$sample_id" "$reads"
+    """
+}
+ 
+process QUANT {
+    tag "$pair_id"
+    publishDir params.outdir
+ 
+    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
+    """
+}
+\ No newline at end of file