diff --git a/scripts/rnaseq_pipeline/modules/rnaseq-flow.nf b/scripts/rnaseq_pipeline/modules/rnaseq-flow.nf
deleted file mode 100644
index 1ed405e..0000000
--- a/scripts/rnaseq_pipeline/modules/rnaseq-flow.nf
+++ /dev/null
@@ -1,20 +0,0 @@
-/*
- * include requires tasks
- */
-include { INDEX; QUANT; FASTQC; MULTIQC  } from './rnaseq-tasks.nf'
-
-/*
- * define the data analysis workflow
- */
-workflow RNASEQFLOW {
-    // required inputs
-    take:
-      transcriptome
-      read_files
-    // workflow implementation
-    main:
-      INDEX(transcriptome)
-      QUANT(INDEX.out, read_files)
-      FASTQC(read_files)
-      MULTIQC( QUANT.out.mix(FASTQC.out).collect() )
-}
diff --git a/scripts/rnaseq_pipeline/modules/rnaseq-tasks.nf b/scripts/rnaseq_pipeline/modules/rnaseq-tasks.nf
deleted file mode 100644
index b064430..0000000
--- a/scripts/rnaseq_pipeline/modules/rnaseq-tasks.nf
+++ /dev/null
@@ -1,76 +0,0 @@
-params.outdir = 'results'
-
-/*
- * define the `index` process that create a binary index
- * given the transcriptome file
- */
-process INDEX {
-
-    input:
-    path transcriptome
-
-    output:
-    path 'index'
-
-    script:
-    """
-    salmon index --threads $task.cpus -t $transcriptome -i index
-    """
-}
-
-/*
- * Run Salmon to perform the quantification of expression using
- * the index and the matched read files
- */
-process QUANT {
-
-    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
-    """
-}
-
-/*
- * Run fastQC to check quality of reads files
- */
-process FASTQC {
-    tag "FASTQC on $sample_id"
-
-    input:
-    tuple val(sample_id), path(reads)
-
-    output:
-    path("fastqc_${sample_id}_logs")
-
-    script:
-    """
-    mkdir fastqc_${sample_id}_logs
-    fastqc -o fastqc_${sample_id}_logs -f fastq -q ${reads}
-    """
-}
-
-/*
- * Create a report using multiQC for the quantification
- * and fastqc processes
- */
-process MULTIQC {
-    publishDir params.outdir, mode:'copy'
-
-    input:
-    path('*')
-
-    output:
-    path('multiqc_report.html')
-
-    script:
-    """
-    multiqc .
-    """
-}