Commit 49e7daa9 authored by Chris Cheshire's avatar Chris Cheshire
Browse files

removed flow test configs

parent fe8034e7

conf/igg_flow_tests/test_all_exp_one_igg_small.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/luslab/test-datasets/cutandrun/samplesheet/test-GSE145187-allexp-1igg-small.csv'



    // Genome references

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

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

    gtf                = 'https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.gtf.gz'

    gene_bed           = 'https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.bed.gz'

    blacklist          = "${projectDir}/assets/blacklists/GRCh37-blacklist.bed"

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

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



    minimum_alignment_q_score = 10

}

conf/igg_flow_tests/test_one_exp_all_igg_small.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/luslab/test-datasets/cutandrun/samplesheet/test-GSE145187-1exp-alligg-small.csv'



    // Genome references

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

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

    gtf                = 'https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.gtf.gz'

    gene_bed           = 'https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.bed.gz'

    blacklist          = "${projectDir}/assets/blacklists/GRCh37-blacklist.bed"

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

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



    minimum_alignment_q_score = 10

}

conf/igg_flow_tests/test_some_exp_all_igg_small.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/luslab/test-datasets/cutandrun/samplesheet/test-GSE145187-varyingexp-alligg-small.csv'



    // Genome references

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

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

    gtf                = 'https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.gtf.gz'

    gene_bed           = 'https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/reference/genomes/hg38-chr20-genes.bed.gz'

    blacklist          = "${projectDir}/assets/blacklists/GRCh37-blacklist.bed"

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

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



    minimum_alignment_q_score = 10

}

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