Merge pull request #857 from nf-core/dev

release 3.1.1
nf-core · Nov 21, 2022 · 96749f7 · 96749f7
2 parents 0b7f0e2 + 578aacf
commit 96749f7
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diff --git a/.github/RELEASE_CHECKLIST.md b/.github/RELEASE_CHECKLIST.md
@@ -12,6 +12,8 @@
 4. Sync `dev` and checkout a new branch for the release
 5. Bump version:
    - `nf-core bump-version . <VERSION>`
+   - edit `docs/images/sarek_indices_subway.svg`
+   - generate a new `docs/images/sarek_indices_subway.png`
    - edit `docs/images/sarek_subway.svg`
    - generate a new `docs/images/sarek_subway.png`
    - edit `docs/images/sarek_workflow.svg`
@@ -28,6 +30,8 @@
     - `git checkout upstream/master -- CHANGELOG.md`
 14. Add a new `Unreleased` section in `CHANGELOG.md` for the `dev` version
 15. Checkout figures from `master`
+    - `git checkout upstream/master -- docs/images/sarek_indices_subway.svg`
+    - `git checkout upstream/master -- docs/images/sarek_indices_subway.png`
     - `git checkout upstream/master -- docs/images/sarek_subway.svg`
     - `git checkout upstream/master -- docs/images/sarek_subway.png`
     - `git checkout upstream/master -- docs/images/sarek_workflow.svg`

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,29 @@ 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).
 
+## [3.1.1](https://github.com/nf-core/sarek/releases/tag/3.1.1) - Lilla Luleälven
+
+Lilla Luleälven river's main affluent is Rapaätno.
+
+### Added
+
+- [#856](https://github.com/nf-core/sarek/pull/856) - Add annotation for `R64-1-1` and `UMD3.1`
+
+### Changed
+
+- [#855](https://github.com/nf-core/sarek/pull/855) - Speed up duplicate marking by using `samtools` for CRAM conversion
+- [#858](https://github.com/nf-core/sarek/pull/858) - Prepare release `3.1.1`
+
+### Fixed
+
+- [#851](https://github.com/nf-core/sarek/pull/851) - Fix `schema` definition `None` for `cf_chrom_len`
+
+### Deprecated
+
+### Removed
+
+### Dependencies
+
 ## [3.1](https://github.com/nf-core/sarek/releases/tag/3.1) - Rapaätno
 
 Rapaätno is the river you can see from the Skierfe mountain.

diff --git a/conf/igenomes.config b/conf/igenomes.config
@@ -138,6 +138,13 @@ params {
             bwa                   = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/version0.6.0/"
             fasta                 = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa"
             readme                = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt"
+            snpeff_db             = 'UMD3.1.75'
+            snpeff_genome         = 'UMD3.1'
+            snpeff_version        = '5.1'
+            vep_cache_version     = 94
+            vep_genome            = 'UMD3.1'
+            vep_species           = 'bos_taurus'
+            vep_version           = '106.1'
         }
         'WBcel235' {
             bwa                   = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/version0.6.0/"
@@ -214,6 +221,13 @@ params {
         'R64-1-1' {
             bwa                   = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0/"
             fasta                 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa"
+            snpeff_db             = 'R64-1-1.105'
+            snpeff_genome         = 'R64-1-1'
+            snpeff_version        = '5.1'
+            vep_cache_version     = 106
+            vep_genome            = 'R64-1-1'
+            vep_species           = 'saccharomyces_cerevisiae'
+            vep_version           = '106.1'
         }
         'EF2' {
             bwa                   = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/version0.6.0/"

diff --git a/conf/modules/markduplicates.config b/conf/modules/markduplicates.config
@@ -57,7 +57,7 @@ process {
     }
 
     withName: 'GATK4_MARKDUPLICATES' {
-        ext.args         = '-REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true'
+        ext.args         = '-REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT'
         ext.prefix       = { "${meta.id}.md.cram" }
         ext.when         = { !(params.skip_tools && params.skip_tools.split(',').contains('markduplicates')) }
         publishDir       = [

diff --git a/docs/images/sarek_indices_subway.png b/docs/images/sarek_indices_subway.png
diff --git a/docs/images/sarek_indices_subway.svg b/docs/images/sarek_indices_subway.svg
diff --git a/docs/images/sarek_subway.png b/docs/images/sarek_subway.png
diff --git a/docs/images/sarek_subway.svg b/docs/images/sarek_subway.svg
diff --git a/docs/images/sarek_workflow.png b/docs/images/sarek_workflow.png
diff --git a/docs/images/sarek_workflow.svg b/docs/images/sarek_workflow.svg
diff --git a/modules.json b/modules.json
@@ -197,7 +197,8 @@
                     },
                     "gatk4/markduplicates": {
                         "branch": "master",
-                        "git_sha": "7578005a576f3ac1b0d4f10c037dde34cdedfb67"
+                        "git_sha": "7578005a576f3ac1b0d4f10c037dde34cdedfb67",
+                        "patch": "modules/nf-core/gatk4/markduplicates/gatk4-markduplicates.diff"
                     },
                     "gatk4/markduplicatesspark": {
                         "branch": "master",

diff --git a/modules/nf-core/gatk4/markduplicates/gatk4-markduplicates.diff b/modules/nf-core/gatk4/markduplicates/gatk4-markduplicates.diff