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Merge pull request #18 from TRON-Bioinformatics/ubuntu-patch
Fix conda env issues on Ubuntu
2 parents 71dff12 + 667d182 commit 8cd9e97

14 files changed

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-8
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.gitignore

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.gitlab-ci.yml

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main.nf

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modules/01_filter.nf

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@@ -9,7 +9,7 @@ process FILTER_VCF {
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memory params.memory
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tag "${name}"
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conda (params.enable_conda ? "conda-forge::libgcc-ng=10.3.0 conda-forge::gsl=2.7 bioconda::bcftools=1.15.1" : null)
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conda (params.enable_conda ? "conda-forge::libgcc-ng=14.2.0 conda-forge::gsl=2.7 bioconda::bcftools=1.15.1" : null)
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input:
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tuple val(name), file(vcf)

modules/02_normalization.nf

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@@ -9,7 +9,7 @@ process BCFTOOLS_NORM {
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memory params.memory
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tag "${name}"
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conda (params.enable_conda ? "conda-forge::libgcc-ng=10.3.0 conda-forge::gsl=2.7 bioconda::bcftools=1.15.1" : null)
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conda (params.enable_conda ? "conda-forge::libgcc-ng=14.2.0 conda-forge::gsl=2.7 bioconda::bcftools=1.15.1" : null)
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input:
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tuple val(name), file(vcf)
@@ -54,7 +54,7 @@ process REMOVE_DUPLICATES {
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tag "${name}"
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publishDir "${params.output}/${name}", mode: "copy"
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conda (params.enable_conda ? "conda-forge::libgcc-ng=10.3.0 conda-forge::gsl=2.7 bioconda::bcftools=1.15.1" : null)
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conda (params.enable_conda ? "conda-forge::libgcc-ng=14.2.0 conda-forge::gsl=2.7 bioconda::bcftools=1.15.1" : null)
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input:
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tuple val(name), file(vcf)

modules/03_summary.nf

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@@ -9,7 +9,7 @@ process SUMMARY_VCF {
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tag "${name}"
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publishDir "${params.output}/${name}/metrics", mode: "copy"
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conda (params.enable_conda ? "conda-forge::libgcc-ng=10.3.0 conda-forge::gsl=2.7 bioconda::bcftools=1.15.1" : null)
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conda (params.enable_conda ? "conda-forge::libgcc-ng=14.2.0 conda-forge::gsl=2.7 bioconda::bcftools=1.15.1" : null)
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input:
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tuple val(name), file(vcf)

modules/04_vafator.nf

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@@ -12,7 +12,7 @@ process VAFATOR {
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tag "${patient_name}"
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publishDir "${params.output}/${patient_name}", mode: "copy"
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conda (params.enable_conda ? "bioconda::vafator=2.2.0" : null)
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conda (params.enable_conda ? "bioconda::vafator=2.0.3" : null)
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input:
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tuple val(patient_name), file(vcf), val(bams), val(purities), val(clonalities)
@@ -41,7 +41,7 @@ process MULTIALLELIC_FILTER {
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tag "${name}"
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publishDir "${params.output}/${name}", mode: "copy"
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conda (params.enable_conda ? "bioconda::vafator=2.2.0" : null)
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conda (params.enable_conda ? "bioconda::vafator=2.0.3" : null)
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input:
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tuple val(name), file(vcf)

modules/06_variant_annotation.nf

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@@ -36,7 +36,7 @@ process VARIANT_ANNOTATION_BCFTOOLS {
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publishDir "${params.output}/${name}", mode: "copy"
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tag "${name}"
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conda (params.enable_conda ? "conda-forge::libgcc-ng=10.3.0 conda-forge::gsl=2.7 bioconda::bcftools=1.15.1" : null)
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conda (params.enable_conda ? "conda-forge::libgcc-ng=14.2.0 conda-forge::gsl=2.7 bioconda::bcftools=1.15.1" : null)
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input:
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tuple val(name), file(vcf)

nextflow.config

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@@ -32,7 +32,7 @@ env {
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// Capture exit codes from upstream processes when piping
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process.shell = ['/bin/bash', '-euo', 'pipefail']
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VERSION = '3.1.0'
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VERSION = '3.1.2'
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manifest {
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name = 'TRON-Bioinformatics/tronflow-vcf-postprocessing'

test/data/test_no_ad.vcf

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test/data/test_single_sample.vcf

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test/data/test_tumor_normal.vcf

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test/data/ucsc.hg19.minimal.fasta

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test/data/ucsc.hg19.minimal.fasta.fai

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