diff --git a/conf/test.config b/conf/test.config index 550e42d..00bbe3b 100644 --- a/conf/test.config +++ b/conf/test.config @@ -27,7 +27,7 @@ params { //Germlinecnvcaller options gcnv_scatter_content = 2 - gcnv_ploidy_priors = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/gatk/contig_ploidy_priors_table.tsv" + gcnv_ploidy_priors = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/gatk/contig_ploidy_priors_table.tsv" // Small reference genome genome = null diff --git a/nextflow.config b/nextflow.config index e355fd0..d51a0aa 100644 --- a/nextflow.config +++ b/nextflow.config @@ -28,7 +28,7 @@ params { gcnv_scatter_content = 5000 gcnv_segmental_duplications = null - // Germlinecnvcaller options + // Gens options gens_bin_length = 100 // CNVkit options diff --git a/subworkflows/local/gens_pon.nf b/subworkflows/local/gens_pon.nf index 8dc2ec2..1bf8e57 100644 --- a/subworkflows/local/gens_pon.nf +++ b/subworkflows/local/gens_pon.nf @@ -1,9 +1,9 @@ include { GATK4_COLLECTREADCOUNTS } from '../../modules/nf-core/gatk4/collectreadcounts/main' +include { GATK4_CREATEREADCOUNTPANELOFNORMALS } from '../../modules/nf-core/gatk4/createreadcountpanelofnormals/main' include { GATK4_PREPROCESSINTERVALS } from '../../modules/nf-core/gatk4/preprocessintervals/main' include { PICARD_CREATESEQUENCEDICTIONARY } from '../../modules/nf-core/picard/createsequencedictionary/main' include { SAMTOOLS_FAIDX } from '../../modules/nf-core/samtools/faidx/main' include { SAMTOOLS_INDEX } from '../../modules/nf-core/samtools/index/main' -include { GATK4_CREATEREADCOUNTPANELOFNORMALS } from '../../modules/nf-core/gatk4/createreadcountpanelofnormals/main' workflow GENS_PON { take: @@ -80,12 +80,12 @@ workflow GENS_PON { GATK4_CREATEREADCOUNTPANELOFNORMALS (ch_readcounts_out) - ch_versions = ch_versions.mix(SAMTOOLS_FAIDX.out.versions) - ch_versions = ch_versions.mix(PICARD_CREATESEQUENCEDICTIONARY.out.versions) - ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first()) - ch_versions = ch_versions.mix(GATK4_PREPROCESSINTERVALS.out.versions) ch_versions = ch_versions.mix(GATK4_COLLECTREADCOUNTS.out.versions.first()) ch_versions = ch_versions.mix(GATK4_CREATEREADCOUNTPANELOFNORMALS.out.versions.first()) + ch_versions = ch_versions.mix(GATK4_PREPROCESSINTERVALS.out.versions) + ch_versions = ch_versions.mix(PICARD_CREATESEQUENCEDICTIONARY.out.versions) + ch_versions = ch_versions.mix(SAMTOOLS_FAIDX.out.versions) + ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first()) emit: genspon = GATK4_CREATEREADCOUNTPANELOFNORMALS.out.pon