Commit 3d5a4eb3 authored by Chris Cheshire's avatar Chris Cheshire
Browse files

WIP

parent 99f041a9

.github/workflows/ci.yml

+2 −2
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@@ -152,8 +152,8 @@ jobs: 
      matrix:

        nxf_version: ['21.10.3', '']

        tags:

          - params

          - samplesheet

          - test_params

          - test_samplesheet

          - verify_output_save_ref

          - verify_output_only_input

          - verify_output_save_merged

conf/test_no_igg.config

+1 −1
Original line number Diff line number Diff line
@@ -32,5 +32,5 @@ params { 
    spikein_bowtie2    = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.tar.gz'



    minimum_alignment_q_score = 10

    igg_control               = false

    use_control               = false

}

modules/local/python/samplesheet_check.nf

+1 −1
Original line number Diff line number Diff line
@@ -17,7 +17,7 @@ process SAMPLESHEET_CHECK { 


    script:

    """

    check_samplesheet.py $samplesheet samplesheet.valid.csv $params.igg_control

    check_samplesheet.py $samplesheet samplesheet.valid.csv $params.use_control



    cat <<-END_VERSIONS > versions.yml

    "${task.process}":

nextflow.config

+1 −1
Original line number Diff line number Diff line
@@ -66,7 +66,7 @@ params { 
    peakcaller                 = null



    // SEACR Peak Calling

    igg_control                = true

    use_control                = true

    peak_threshold             = 0.05

    replicate_threshold        = 1

    only_peak_calling          = false

tests/test_param_check.yml

+2 −2
Original line number Diff line number Diff line 
- name: test_param_check_custom_genome_blacklist

  command: nextflow run main.nf -profile docker,test_fasta_only --only_input true --gtf https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.gtf.gz --blacklist ./assets/blacklists/hg38-blacklist.bed -c tests/config/nextflow.config

  tags:

    - params

    - test_params

    - params_customgenome

    - params_customgenome_blacklist



- name: test_param_check_custom_genome_noblacklist

  command: nextflow run main.nf -profile docker,test_fasta_only --only_input true --gtf https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.gtf.gz -c tests/config/nextflow.config

  tags:

    - params

    - test_params

    - params_customgenome

    - params_customgenome_noblacklist

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