From 9a3ffbde2e464d10084bba93c141c82b8e383c02 Mon Sep 17 00:00:00 2001 From: AmstlerStephan Date: Fri, 8 Mar 2024 10:45:31 +0100 Subject: [PATCH 1/4] adapt freebayes variant calling flags --- config/test.config | 2 +- lib/processes/variant_calling/freebayes.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/config/test.config b/config/test.config index 7154282..ae4e5c6 100644 --- a/config/test.config +++ b/config/test.config @@ -10,7 +10,7 @@ params { help = false version = false - debug = true + debug = false input = "$baseDir/data/fastq_pass/" output = "umi-pipeline-nf_test-run" diff --git a/lib/processes/variant_calling/freebayes.nf b/lib/processes/variant_calling/freebayes.nf index ed41f44..6087c38 100644 --- a/lib/processes/variant_calling/freebayes.nf +++ b/lib/processes/variant_calling/freebayes.nf @@ -12,6 +12,6 @@ process FREEBAYES { script: """ - freebayes -f ${reference} -F 0.009 -p 80 ${bam} | vcfallelicprimitives -kg >${type}.vcf + freebayes -f ${reference} -F 0.009 -p 80 ${bam} | vcfallelicprimitives -k >${type}.vcf """ } From 30f9bd1660aae0389e6cf6e5f5042f6f6ac0b2f9 Mon Sep 17 00:00:00 2001 From: AmstlerStephan Date: Fri, 8 Mar 2024 15:40:25 +0100 Subject: [PATCH 2/4] Update README.md Add link to paper --- README.md | 4 ++-- config/test.config | 2 +- env/environment.yml | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index c9f514a..200a99c 100644 --- a/README.md +++ b/README.md @@ -50,12 +50,12 @@ nextflow run genepi/umi-pipeline-nf -r v0.2.0 -profile test,docker 3.1 Download and adapt the config/custom.config with paths to your data (relative and absolute paths possible). ```bash -nextflow run genepi/umi-pipeline-nf -r v0.2.0 -c -profile docker +nextflow run genepi/umi-pipeline-nf -r v0.2.0 -c -profile custom, ``` ## Citation -If you use the pipeline please cite our Paper: +If you use the pipeline please cite [our Paper](https://www.biorxiv.org/content/10.1101/2024.03.01.582741v1): Amstler S, Streiter G, Pfurtscheller C, Forer L, Di Maio S, Weissensteiner H, Paulweber B, Schoenherr S, Kronenberg F, Coassin S. Nanopore sequencing with unique molecular identifiers enables accurate mutation analysis and haplotyping in the complex Lipoprotein(a) KIV-2 VNTR. bioRxiv. 2024. doi: 10.1101/2024.03.01.582741. diff --git a/config/test.config b/config/test.config index 7154282..ae4e5c6 100644 --- a/config/test.config +++ b/config/test.config @@ -10,7 +10,7 @@ params { help = false version = false - debug = true + debug = false input = "$baseDir/data/fastq_pass/" output = "umi-pipeline-nf_test-run" diff --git a/env/environment.yml b/env/environment.yml index bec01d1..2264dae 100644 --- a/env/environment.yml +++ b/env/environment.yml @@ -11,7 +11,7 @@ dependencies: - seqtk=1.3 - lofreq=2.1.5 - freebayes=1.3.2 - - vcflib + - vcflib=1.0.0 - bedtools=2.30.0 - vsearch=2.21.2 - openjdk=11.0.9 From ace9534d05ecafd6dc7f0b3c7cfec1e6074c163d Mon Sep 17 00:00:00 2001 From: AmstlerStephan Date: Fri, 8 Mar 2024 15:42:07 +0100 Subject: [PATCH 3/4] adjust freebayes process --- lib/processes/variant_calling/freebayes.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/processes/variant_calling/freebayes.nf b/lib/processes/variant_calling/freebayes.nf index 6087c38..ed41f44 100644 --- a/lib/processes/variant_calling/freebayes.nf +++ b/lib/processes/variant_calling/freebayes.nf @@ -12,6 +12,6 @@ process FREEBAYES { script: """ - freebayes -f ${reference} -F 0.009 -p 80 ${bam} | vcfallelicprimitives -k >${type}.vcf + freebayes -f ${reference} -F 0.009 -p 80 ${bam} | vcfallelicprimitives -kg >${type}.vcf """ } From 0b0f4b4ef4536d643cf011a9ff2204219ea1e642 Mon Sep 17 00:00:00 2001 From: AmstlerStephan Date: Fri, 8 Mar 2024 15:55:17 +0100 Subject: [PATCH 4/4] prepare release 0.2.1 --- README.md | 4 ++-- nextflow.config | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 200a99c..33f6bd1 100644 --- a/README.md +++ b/README.md @@ -43,14 +43,14 @@ Umi-pipeline-nf orignates from a snakemake-based analysis pipeline ([pipeline-um 2. Download the pipeline and test it on a [minimal dataset](data/info.txt) with a single command. ```bash -nextflow run genepi/umi-pipeline-nf -r v0.2.0 -profile test,docker +nextflow run genepi/umi-pipeline-nf -r v0.2.1 -profile test,docker ``` 3. Start running your own analysis! 3.1 Download and adapt the config/custom.config with paths to your data (relative and absolute paths possible). ```bash -nextflow run genepi/umi-pipeline-nf -r v0.2.0 -c -profile custom, +nextflow run genepi/umi-pipeline-nf -r v0.2.1 -c -profile custom, ``` ## Citation diff --git a/nextflow.config b/nextflow.config index cfc065e..a3bd23b 100644 --- a/nextflow.config +++ b/nextflow.config @@ -1,7 +1,7 @@ // NEXTFLOW MANIFEST manifest { name = 'umi-pipeline-nf' - version = '0.2.0' + version = '0.2.1' description = 'Nextflow pipeline to analyze umi amplicon data' author = 'Stephan Amstler' homePage = 'https://github.com/AmstlerStephan/umi-pipeline-nf.git' @@ -67,7 +67,7 @@ params { // Load base.config by default for all pipelines includeConfig "${baseDir}/config/base.config" -process.container = 'quay.io/genepi/umi-pipeline-nf:v0.2.0' +process.container = 'quay.io/genepi/umi-pipeline-nf:v0.2.1' profiles {