From 19e8481a9080630af612b05cdc109686b6b09d22 Mon Sep 17 00:00:00 2001 From: Shaun Regenbaum Date: Wed, 28 Aug 2024 14:20:38 +0300 Subject: [PATCH] its not working and everything is a mess --- subworkflows/nf-core/ensemblvep_annotate.nf | 2 +- subworkflows/nf-core/snpeff_annotate.nf | 2 +- workflows/rnavar.nf | 5 +---- 3 files changed, 3 insertions(+), 6 deletions(-) diff --git a/subworkflows/nf-core/ensemblvep_annotate.nf b/subworkflows/nf-core/ensemblvep_annotate.nf index 13dffee4..e61381b1 100644 --- a/subworkflows/nf-core/ensemblvep_annotate.nf +++ b/subworkflows/nf-core/ensemblvep_annotate.nf @@ -2,7 +2,7 @@ // Run VEP to annotate VCF files // -include { ENSEMBLVEP } from '../../modules/nf-core/modules/ensemblvep/main' +include { ENSEMBLVEP_VEP } from '../../modules/nf-core/modules/ensemblvep/vep/main' include { TABIX_BGZIPTABIX } from '../../modules/nf-core/modules/tabix/bgziptabix/main' workflow ENSEMBLVEP_ANNOTATE { diff --git a/subworkflows/nf-core/snpeff_annotate.nf b/subworkflows/nf-core/snpeff_annotate.nf index 9a8b65bc..f9758e2d 100644 --- a/subworkflows/nf-core/snpeff_annotate.nf +++ b/subworkflows/nf-core/snpeff_annotate.nf @@ -2,7 +2,7 @@ // Run snpEff to annotate VCF files // -include { SNPEFF } from '../../modules/nf-core/modules/snpeff/main' +include { SNPEFF_SNPEFF } from '../../modules/nf-core/modules/snpeff/snpeff/main' include { TABIX_BGZIPTABIX } from '../../modules/nf-core/modules/tabix/bgziptabix/main' workflow SNPEFF_ANNOTATE { diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index 8a68110a..89f16801 100644 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -71,7 +71,6 @@ include { GATK4_INDEXFEATUREFILE } from '../modules/nf-core/modules/gatk4 include { GATK4_VARIANTFILTRATION } from '../modules/nf-core/modules/gatk4/variantfiltration/main' include { SAMTOOLS_INDEX } from '../modules/nf-core/modules/samtools/index/main' include { TABIX_TABIX as TABIX } from '../modules/nf-core/modules/tabix/tabix/main' -include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/modules/custom/dumpsoftwareversions/main' /* ======================================================================================== @@ -80,7 +79,7 @@ include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/modules/custo */ include { ALIGN_STAR } from '../subworkflows/nf-core/align_star' // Align reads to genome and sort and index the alignment file -include { STAR_GENOMEGENERATE } from '../subworkflows/nf-core/genomegenerate' // Generate genome index for STAR +include { STAR_GENOMEGENERATE } from '../modules/nf-core/modules/star/genomegenerate/main' //addParams(options: params.star_index_options) include { MARKDUPLICATES } from '../subworkflows/nf-core/markduplicates' // Mark duplicates in the BAM file include { SPLITNCIGAR } from '../subworkflows/nf-core/splitncigar' // Splits reads that contain Ns in their cigar string include { RECALIBRATE } from '../subworkflows/nf-core/recalibrate' // Estimate and correct systematic bias @@ -446,8 +445,6 @@ workflow RNAVAR { } ch_version_yaml = Channel.empty() - CUSTOM_DUMPSOFTWAREVERSIONS (ch_versions.unique().collectFile(name: 'collated_versions.yml')) - ch_version_yaml = CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect() // // MODULE: MultiQC