Unverified Commit 56bd5dba authored by Chris Cheshire's avatar Chris Cheshire Committed by GitHub
Browse files

Merge pull request #38 from luslab/dev 

Concensus peaks now only run on samples with more than one replicate
parents e2152bec b5f35004

conf/test.config

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@@ -32,5 +32,4 @@ 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

    skip_upset_plots          = true

}
 
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conf/test_no_igg.config

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@@ -33,5 +33,4 @@ params { 


    minimum_alignment_q_score = 10

    igg_control               = false

    skip_upset_plots          = true

}

conf/test_tech_reps.config

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@@ -32,5 +32,4 @@ 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

    skip_upset_plots          = true

}
 
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subworkflows/local/consensus_peaks.nf

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@@ -16,7 +16,7 @@ include { PLOT_CONSENSUS_PEAKS } from "../../modules/local/plot_consensus_peaks" 
workflow CONSENSUS_PEAKS {



    take:

    bed //  channel: [ val(meta), [ bed ] ]

    bed //  channel: [ val(meta), [ bed ], count]



    main:
@@ -26,7 +26,7 @@ workflow CONSENSUS_PEAKS { 
    // Merge peaks

    BEDTOOLS_MERGE ( SORT.out.file )



    // Optionally filter peaks on minimum replicate consensus and produce plot

    // Filter peaks on minimum replicate consensus

    AWK ( BEDTOOLS_MERGE.out.bed )



    // Plot consensus peak sets

tests/test_verify_output_only_peak_calling.yml

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- name: test_verify_output_only_peak_calling

  command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true -c tests/config/nextflow.config

  command: nextflow run main.nf -profile docker,test_full_small --only_peak_calling true --skip_fastqc true -c tests/config/nextflow.config

  tags:

    - verify_output

    - verify_output_peak_calling

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