From eee35443b37dfe83cad32b57b7cec311bf08afc9 Mon Sep 17 00:00:00 2001 From: Anders Sune Pedersen Date: Tue, 6 Sep 2022 16:17:35 +0200 Subject: [PATCH 1/5] Require haptotypecaller for joint-germline-genotype-calling --- workflows/sarek.nf | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/workflows/sarek.nf b/workflows/sarek.nf index 45016870af..49662803a3 100644 --- a/workflows/sarek.nf +++ b/workflows/sarek.nf @@ -114,6 +114,10 @@ if(!params.dbsnp && !params.known_indels){ } } +if (params.joint_germline && (!params.tools || !params.tools.split(',').contains('haplotypecaller'))){ + log.error "The Haplotypecaller should be specified as one of the tools when doing joint germline variant calling. (The Haplotypecaller could be specified by adding `--tools haplotypecaller` to the nextflow command.) " + exit 1 +} if (params.joint_germline && (!params.dbsnp || !params.known_indels || !params.known_snps || params.no_intervals)){ log.warn "If Haplotypecaller is specified, without `--dbsnp`, `--known_snps`, `--known_indels` or the associated resource labels (ie `known_snps_vqsr`), no variant recalibration will be done. For recalibration you must provide all of these resources.\nFor more information see VariantRecalibration: https://gatk.broadinstitute.org/hc/en-us/articles/5358906115227-VariantRecalibrator \nJoint germline variant calling also requires intervals in order to genotype the samples. As a result, if `--no_intervals` is set to `true` the joint germline variant calling will not be performed." } From d792f466ac97b41ed2b623acf57c93bcd7e20a9d Mon Sep 17 00:00:00 2001 From: Anders Sune Pedersen Date: Thu, 8 Sep 2022 21:03:21 +0200 Subject: [PATCH 2/5] Updating the usage-doc. The pipeline no longer support input in the form of a list of csv-files. --- docs/usage.md | 6 ------ 1 file changed, 6 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index c8a817441a..3216dbbac5 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -44,12 +44,6 @@ If multiple samples IDs are specified in the CSV file, Sarek will consider all f Output from Variant Calling and/or Annotation will be in a specific directory for each sample and tool configuration (or normal/tumor pair if applicable). -Multiple CSV files can be specified if the path is enclosed in quotes. - -```bash ---input '[path to sample sheet file(s)]' -``` - ### Overview: Samplesheet Columns | Column | Description | From f3cd5f6a4713c52db91a709fba9e35255a3d4a69 Mon Sep 17 00:00:00 2001 From: Anders Sune Pedersen Date: Thu, 8 Sep 2022 22:00:55 +0200 Subject: [PATCH 3/5] Updating changelog --- CHANGELOG.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index ef92f79859..28ed1067bc 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -28,6 +28,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#733](https://github.com/nf-core/sarek/pull/733) - Add description for params.cf_chrom_len - [#734](https://github.com/nf-core/sarek/pull/734) - nf-core modules update -a - [#736](https://github.com/nf-core/sarek/pull/736) - More extensive CI for default test +- [#742](https://github.com/nf-core/sarek/pull/742) - Requiring the Hyplotypecaller to be specified as one of the tools for joint germline genotyping. ### Fixed @@ -47,6 +48,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Deprecated ### Removed +- [#742](https://github.com/nf-core/sarek/pull/742) - Removed some lines from the usage-doc as Sarek no longer support input supplied as a list of multiple csv-files. + ## [3.0.1](https://github.com/nf-core/sarek/releases/tag/3.0.1) - Saiva From d007f01feeed2100e901b27c5ae802baba936c09 Mon Sep 17 00:00:00 2001 From: "Maxime U. Garcia" Date: Fri, 9 Sep 2022 08:46:15 +0200 Subject: [PATCH 4/5] Update CHANGELOG.md --- CHANGELOG.md | 1 - 1 file changed, 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 28ed1067bc..ac572fd3c3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -50,7 +50,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Removed - [#742](https://github.com/nf-core/sarek/pull/742) - Removed some lines from the usage-doc as Sarek no longer support input supplied as a list of multiple csv-files. - ## [3.0.1](https://github.com/nf-core/sarek/releases/tag/3.0.1) - Saiva Saiva is a lake in the Sarek national park, just below the Skierfe mountain. From 0c2fb2d3e913873c241fce00c9a8bdcd9e8daef4 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 9 Sep 2022 07:07:59 +0000 Subject: [PATCH 5/5] [automated] Fix linting with Prettier --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index ac572fd3c3..64516f3702 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -48,6 +48,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Deprecated ### Removed + - [#742](https://github.com/nf-core/sarek/pull/742) - Removed some lines from the usage-doc as Sarek no longer support input supplied as a list of multiple csv-files. ## [3.0.1](https://github.com/nf-core/sarek/releases/tag/3.0.1) - Saiva