Added support for missing genome blacklist files

params {

    config_profile_name        = 'Test profile'

    config_profile_description = 'Minimal test dataset to check pipeline function with custom genome files except fasta and bt index'

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

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

    spikein_fasta      = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.fa.gz'

    spikein_bowtie2    = 'https://raw.githubusercontent.com/nf-core/test-datasets/cutandrun/reference/genomes/e_coli_U00096_3.tar.gz'

    minimum_alignment_q_score = 10

}

 No newline at end of file

            "==================================================================================="

    }

    //

    // Print a warning if not blacklist detected

    //

    private static void blacklistWarn(log) {

        log.warn "=============================================================================\n" +

            "  No genome blacklist file specified, switching to dummy empty file...\n" +

            "==================================================================================="

    }

}

    local           { includeConfig "conf/local.config"           } // Sets up compute resources for local computing run

    test            { includeConfig "conf/test.config"            } // Runs a single sample with an IgG control

    test_fasta_only { includeConfig "conf/test_fasta_only.config" } // Runs a single sample with an IgG control but with no extra genome files just as bed files and black lists

    test_tech_reps  { includeConfig "conf/test_tech_reps.config"  } // Runs a single sample with two technical replicates and an IgG control

    test_full_small { includeConfig "conf/test_full_small.config" } // Runs a full experimental configuration but with a small dataset

    test_no_igg     { includeConfig "conf/test_no_igg.config"     } // Runs a single sample with NO IgG control

- 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/GRCh37-blacklist.bed -c tests/config/nextflow.config

  tags:

    - 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

    - params_customgenome

    - params_customgenome_noblacklist

 No newline at end of file

// Check mandatory parameters that cannot be checked in the groovy lib as we want a channel for them

if (params.input)     { ch_input     = file(params.input)     } else { exit 1, "Input samplesheet not specified!"     }

if (params.blacklist) { ch_blacklist = file(params.blacklist) } else { exit 1, "Genome blacklist file not specified!" }

ch_blacklist = Channel.empty()

if (params.blacklist) {

    ch_blacklist = file(params.blacklist)

}

else {

    ch_blacklist = file("$projectDir/assets/dummy_file.txt", checkIfExists: true)

    WorkflowCutandrun.blacklistWarn(log)

}

// Save AWS IGenomes file containing annotation version

def anno_readme = params.genomes[ params.genome ]?.readme