Commit 268b68ba authored by Chris Cheshire's avatar Chris Cheshire
Browse files

Updated blacklists for test configs

parent bed913cc

conf/test.config

+1 −1
Original line number Diff line number Diff line
@@ -27,7 +27,7 @@ params { 
    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"

    blacklist          = "${projectDir}/assets/blacklists/hg38-blacklist.bed"

    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'

conf/test_full.config

+6 −0
Original line number Diff line number Diff line
@@ -16,5 +16,11 @@ params { 


    genome = 'GRCh38'

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



    // // Genome references

    // blacklist          = "${projectDir}/assets/blacklists/hg38-blacklist.bed"

    // 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

conf/test_full_small.config

+1 −1
Original line number Diff line number Diff line
@@ -15,7 +15,7 @@ params { 
    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"

    blacklist          = "${projectDir}/assets/blacklists/hg38-blacklist.bed"

    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'

conf/test_no_igg.config

+1 −1
Original line number Diff line number Diff line
@@ -27,7 +27,7 @@ params { 
    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"

    blacklist          = "${projectDir}/assets/blacklists/hg38-blacklist.bed"

    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'

conf/test_tech_reps.config

+1 −1
Original line number Diff line number Diff line
@@ -27,7 +27,7 @@ params { 
    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"

    blacklist          = "${projectDir}/assets/blacklists/hg38-blacklist.bed"

    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'

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