diff --git a/CHANGELOG.md b/CHANGELOG.md index 9d6e98f019..c3e1412a8c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,17 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## dev + +### Changed + +- [#1087](https://github.com/nf-core/sarek/pull/1087) - Back to dev +- [#1087](https://github.com/nf-core/sarek/pull/1087) - Minor modules update + +### Fixed + +- [#1087](https://github.com/nf-core/sarek/pull/1087) - Fix wrong default memory in GATK4_CREATESEQUENCEDICTIONARY [#1085](https://github.com/nf-core/sarek/pull/1085) + ## [3.2.1](https://github.com/nf-core/sarek/releases/tag/3.2.1) - Pierikjaure Pierikjaure is a previous spelling of Bierikjávrre. diff --git a/modules.json b/modules.json index 3e59e23517..97eb570c13 100644 --- a/modules.json +++ b/modules.json @@ -198,7 +198,7 @@ }, "gatk4/createsequencedictionary": { "branch": "master", - "git_sha": "2df2a11d5b12f2a73bca74f103691bc35d83c5fd", + "git_sha": "541811d779026c5d395925895fa5ed35e7216cc0", "installed_by": ["modules"] }, "gatk4/estimatelibrarycomplexity": { @@ -213,7 +213,7 @@ }, "gatk4/filtervarianttranches": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "541811d779026c5d395925895fa5ed35e7216cc0", "installed_by": ["modules"] }, "gatk4/gatherbqsrreports": { @@ -263,7 +263,7 @@ }, "gatk4/markduplicatesspark": { "branch": "master", - "git_sha": "4b7d4863a5883b76e6bff13b6e52468fab090c5b", + "git_sha": "541811d779026c5d395925895fa5ed35e7216cc0", "installed_by": ["modules"] }, "gatk4/mergemutectstats": { diff --git a/modules/nf-core/gatk4/createsequencedictionary/main.nf b/modules/nf-core/gatk4/createsequencedictionary/main.nf index 41abb235c6..15a86beab3 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/main.nf +++ b/modules/nf-core/gatk4/createsequencedictionary/main.nf @@ -20,7 +20,7 @@ process GATK4_CREATESEQUENCEDICTIONARY { script: def args = task.ext.args ?: '' - def avail_mem = 6 + def avail_mem = 6144 if (!task.memory) { log.info '[GATK CreateSequenceDictionary] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.' } else { diff --git a/modules/nf-core/gatk4/filtervarianttranches/main.nf b/modules/nf-core/gatk4/filtervarianttranches/main.nf index f72e64cc7d..be232ab4bb 100644 --- a/modules/nf-core/gatk4/filtervarianttranches/main.nf +++ b/modules/nf-core/gatk4/filtervarianttranches/main.nf @@ -27,8 +27,8 @@ process GATK4_FILTERVARIANTTRANCHES { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def resources = resources.collect{"--resource $it"}.join(' ') + def avail_mem = 3072 if (!task.memory) { log.info '[GATK FilterVariantTranches] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' diff --git a/modules/nf-core/gatk4/filtervarianttranches/meta.yml b/modules/nf-core/gatk4/filtervarianttranches/meta.yml index 72cf9f319f..4152a65c1f 100644 --- a/modules/nf-core/gatk4/filtervarianttranches/meta.yml +++ b/modules/nf-core/gatk4/filtervarianttranches/meta.yml @@ -3,15 +3,17 @@ description: Apply tranche filtering keywords: - gatk4 - filtervarianttranches - + - tranche_filtering tools: - "gatk4": - description: Genome Analysis Toolkit (GATK4) + description: | + Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools + with a primary focus on variant discovery and genotyping. Its powerful processing engine + and high-performance computing features make it capable of taking on projects of any size. homepage: https://gatk.broadinstitute.org/hc/en-us - documentation: https://gatk.broadinstitute.org/hc/en-us - tool_dev_url: https://github.com/broadinstitute/gatk - doi: "10.1158/1538-7445.AM2017-3590" - licence: ["BSD-3-clause"] + documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360051308071-FilterVariantTranches + doi: 10.1158/1538-7445.AM2017-3590 + licence: ["Apache-2.0"] input: - meta: diff --git a/modules/nf-core/gatk4/markduplicatesspark/main.nf b/modules/nf-core/gatk4/markduplicatesspark/main.nf index f64fbfd521..f51d598f86 100644 --- a/modules/nf-core/gatk4/markduplicatesspark/main.nf +++ b/modules/nf-core/gatk4/markduplicatesspark/main.nf @@ -25,7 +25,6 @@ process GATK4_MARKDUPLICATES_SPARK { prefix = task.ext.prefix ?: "${meta.id}" def input_list = bam.collect{"--input $it"}.join(' ') - def avail_mem = 3072 if (!task.memory) { log.info '[GATK MarkDuplicatesSpark] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' diff --git a/nextflow.config b/nextflow.config index 8d0dd50a29..dafabcfca1 100644 --- a/nextflow.config +++ b/nextflow.config @@ -323,7 +323,7 @@ manifest { description = """An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '3.2.1' + version = '3.3dev' doi = '10.12688/f1000research.16665.2, 10.5281/zenodo.4063683' } diff --git a/tests/test_joint_germline.yml b/tests/test_joint_germline.yml index 2b6821f9fe..dc0b60fa36 100644 --- a/tests/test_joint_germline.yml +++ b/tests/test_joint_germline.yml @@ -13,13 +13,13 @@ - path: results/preprocessing/recalibrated/test/test.recal.cram.crai should_exist: false - path: results/reports/bcftools/haplotypecaller/joint_variant_calling/joint_germline.bcftools_stats.txt - md5sum: 404d1208df301a6726f5543245625ef3 + # Not stable enough - path: results/reports/vcftools/haplotypecaller/joint_variant_calling/joint_germline.FILTER.summary - md5sum: 87a84b5f8ac3d3cbeeef7d60afcdbfe7 + # Not stable enough - path: results/reports/vcftools/haplotypecaller/joint_variant_calling/joint_germline.TsTv.count - md5sum: 974f6922981c87bb017b124aa009f654 + # Not stable enough - path: results/reports/vcftools/haplotypecaller/joint_variant_calling/joint_germline.TsTv.qual - md5sum: 1e34357e5848c318f8c2c7d3b041d229 + # Not stable enough - path: results/variant_calling/haplotypecaller/joint_variant_calling/joint_germline.vcf.gz # binary changes md5sums on reruns - path: results/variant_calling/haplotypecaller/joint_variant_calling/joint_germline.vcf.gz.tbi