Commit 2cf98e67 authored by Chris Cheshire's avatar Chris Cheshire
Browse files

Switched over all configs to main nf-core test data repo

parent 23fc5e97

conf/test.config

+7 −7
Original line number Diff line number Diff line
@@ -20,16 +20,16 @@ params { 
    max_time   = 6.h



    // Input data

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

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

    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'

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

    gene_bed           = 'https://raw.githubusercontent.com/nf-core/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'

    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

    skip_upset_plots          = true

conf/test_full.config

+1 −1
Original line number Diff line number Diff line
@@ -15,6 +15,6 @@ params { 
    config_profile_description = 'Full test dataset to check pipeline function'



    genome = 'GRCh38'

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

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

    minimum_alignment_q_score = 10

}
 
 No newline at end of file

conf/test_full_small.config

+7 −7
Original line number Diff line number Diff line
@@ -8,16 +8,16 @@ params { 
    max_time   = 6.h



    // Input data

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

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

    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'

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

    gene_bed           = 'https://raw.githubusercontent.com/nf-core/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'

    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

}

conf/test_no_igg.config

+7 −7
Original line number Diff line number Diff line
@@ -20,16 +20,16 @@ params { 
    max_time   = 6.h



    // Input data

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

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

    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'

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

    gene_bed           = 'https://raw.githubusercontent.com/nf-core/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'

    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

    igg_control               = false

conf/test_tech_reps.config

+7 −7
Original line number Diff line number Diff line
@@ -20,16 +20,16 @@ params { 
    max_time   = 6.h



    // Input data

    input = 'https://raw.githubusercontent.com/luslab/test-datasets/cutandrun/samplesheet/test-GSE145187-small-tech-reps.csv'

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

    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'

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

    gene_bed           = 'https://raw.githubusercontent.com/nf-core/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'

    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

    skip_upset_plots          = true

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