ci updates

          wget -qO- get.nextflow.io | bash

          sudo mv nextflow /usr/local/bin/

      # Work around for the unexpected end of file error that github actions seems to get when downloading compressed files during pipelie

      # execution

      # Work around for the unexpected end of file error that github actions seems to get when downloading compressed

      # files during pipelie execution

      - name: Download data

        run: |

          wget -qO- https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20.fa.gz

          wget -qO- https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-bowtie2.tar.gz

          wget -qO- https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.gtf.gz

          wget -qO- https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.bed.gz

          wget -qO- https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.fa.gz

          wget -qO- https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.tar.gz

          wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20.fa.gz

          wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-bowtie2.tar.gz

          wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.gtf.gz

          wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.bed.gz

          wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.fa.gz

          wget -q https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.tar.gz

      - name: Run pipeline with test data

      - name: Run pipeline

        run: |

          nextflow run ${GITHUB_WORKSPACE} -profile docker,test_local_zip