Unverified Commit a56f79a1 authored by Chris Cheshire's avatar Chris Cheshire Committed by GitHub
Browse files

Merge pull request #48 from luslab/dev 

Release commits
parents 262b40bb 1f643373

.github/workflows/ci.yml

+40 −4
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@@ -33,9 +33,21 @@ jobs: 
          wget -qO- get.nextflow.io | bash

          sudo mv nextflow /usr/local/bin/



      - name: Run pipeline with test data

      # 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 -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

        run: |

          nextflow run ${GITHUB_WORKSPACE} -profile docker,test

          nextflow run ${GITHUB_WORKSPACE} -profile docker,test_local_zip



  ##############################

  ### LARGE INTEGRATION TEST ###

  ##############################
@@ -60,9 +72,21 @@ jobs: 
          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

      - name: Download data

        run: |

          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

        run: |

          nextflow run ${GITHUB_WORKSPACE} -profile docker,test_full_small

          nextflow run ${GITHUB_WORKSPACE} -profile docker,test_full_small_local_zip



  #####################################

  ### EDGE VERSION INTEGRATION TEST ###

  #####################################
@@ -85,9 +109,21 @@ jobs: 
          sudo mv nextflow /usr/local/bin/

          nextflow self-update



      # 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 -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

        run: |

          nextflow run ${GITHUB_WORKSPACE} -profile docker,test

          nextflow run ${GITHUB_WORKSPACE} -profile docker,test_local_zip



  ##############################

  ###      UNIT TESTS        ###

  ##############################

conf/test_full_small_local_zip.config

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params {

    config_profile_name        = 'Test profile'

    config_profile_description = 'Minimal test dataset to check pipeline function'



    // Limit resources so that this can run CI

    max_cpus   = 2

    max_memory = 6.GB

    max_time   = 6.h



    // Input data

    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet/test-GSE145187-all-small.csv'



    // Genome references

    fasta              = '/home/runner/work/cutandrun/cutandrun/hg38-chr20.fa.gz'

    bowtie2            = '/home/runner/work/cutandrun/cutandrun/hg38-chr20-bowtie2.tar.gz'

    gtf                = '/home/runner/work/cutandrun/cutandrun/hg38-chr20-genes.gtf.gz'

    gene_bed           = '/home/runner/work/cutandrun/cutandrun/hg38-chr20-genes.bed.gz'

    blacklist          = "${projectDir}/assets/blacklists/hg38-blacklist.bed"

    spikein_fasta      = '/home/runner/work/cutandrun/cutandrun/e_coli_U00096_3.fa.gz'

    spikein_bowtie2    = '/home/runner/work/cutandrun/cutandrun/e_coli_U00096_3.tar.gz'



    minimum_alignment_q_score = 10

}

conf/test_local_zip.config

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+35 −0
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/*

========================================================================================

    Nextflow config file for running minimal tests

========================================================================================

    Defines input files and everything required to run a fast and simple pipeline test.



    Use as follows:

        nextflow run nf-core/cutandrun -profile test,<docker/singularity>



----------------------------------------------------------------------------------------

*/



params {

    config_profile_name        = 'Test profile'

    config_profile_description = 'Minimal test dataset to check pipeline function'



    // Limit resources so that this can run CI

    max_cpus   = 2

    max_memory = 6.GB

    max_time   = 6.h



    // Input data

    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/samplesheet/test-GSE145187-small.csv'



    // Genome references

    fasta              = '/home/runner/work/cutandrun/cutandrun/hg38-chr20.fa.gz'

    bowtie2            = '/home/runner/work/cutandrun/cutandrun/hg38-chr20-bowtie2.tar.gz'

    gtf                = '/home/runner/work/cutandrun/cutandrun/hg38-chr20-genes.gtf.gz'

    gene_bed           = '/home/runner/work/cutandrun/cutandrun/hg38-chr20-genes.bed.gz'

    blacklist          = "${projectDir}/assets/blacklists/hg38-blacklist.bed"

    spikein_fasta      = '/home/runner/work/cutandrun/cutandrun/e_coli_U00096_3.fa.gz'

    spikein_bowtie2    = '/home/runner/work/cutandrun/cutandrun/e_coli_U00096_3.tar.gz'



    minimum_alignment_q_score = 10

}
 
 No newline at end of file

modules/local/bedtools_genomecov_scale.nf

+1 −1
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// Import generic module functions

include { initOptions; saveFiles; getSoftwareName } from './functions'

include { initOptions; saveFiles; getSoftwareName } from './common/functions'



params.options = [:]

options        = initOptions(params.options)

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