Merge pull request #1244 from nf-core/dev

Candidate release 3.3.1
nf-core · Sep 18, 2023 · 59026dc · 59026dc
2 parents 1a263a2 + 8785be8
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diff --git a/.nf-core.yml b/.nf-core.yml
@@ -10,6 +10,5 @@ lint:
     - docs/images/nf-core-sarek_logo_light.png
     - lib/NfcoreTemplate.groovy
     - lib/NfcoreSchema.groovy
-  schema_params: False
   template_strings: False
   multiqc_config: False
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,32 @@ 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).
 
+## [3.3.1](https://github.com/nf-core/sarek/releases/tag/3.3.1) - Biellorippjávrre
+
+A lake near the Rapaselet delta.
+
+### Added
+
+- [#1231](https://github.com/nf-core/sarek/pull/1231) - Back to dev
+
+### Changed
+
+- [#1242](https://github.com/nf-core/sarek/pull/1242) - Simplify sentieon nf-core test license usage
+- [#1243](https://github.com/nf-core/sarek/pull/1243) - Improve json schema usage for input
+
+### Fixed
+
+- [#1232](https://github.com/nf-core/sarek/pull/1232) - Fix Zenodo IDs in manifest
+- [#1236](https://github.com/nf-core/sarek/pull/1236) - Fix annotation cache folder verification when no annotation
+- [#1240](https://github.com/nf-core/sarek/pull/1240) - Disable JVM Hotspot in all modules/gatk4 ([#1030](https://github.com/nf-core/sarek/issues/1030))
+- [#1241](https://github.com/nf-core/sarek/pull/1241) - Fix axis text of controlfreec plots closing [#921](https://github.com/nf-core/sarek/issues/921)
+
+### Dependencies
+
+| Dependency    | Old version | New version |
+| ------------- | ----------- | ----------- |
+| Control-FREEC | 11.6        | 11.6b       |
+
 ## [3.3.0](https://github.com/nf-core/sarek/releases/tag/3.3.0) - Rapaselet
 
 Rapaselet is a delta formed by the Rapaätno river between the Bielloriehppe massif (formerly written Piellorieppe) and the Skårki massif.

diff --git a/CITATIONS.md b/CITATIONS.md
@@ -1,5 +1,9 @@
 # nf-core/sarek: Citations
 
+## [nf-core/sarek 3](https://www.biorxiv.org/content/10.1101/2023.07.19.549462v2)
+
+> Hanssen F, Garcia MU, Folkersen L, Pedersen AS, Lescai F, Jodoin S, Miller E, Wacker O, Smith N, nf-core community, Gabernet G, Nahnsen S. Scalable and efficient DNA sequencing analysis on different compute infrastructures aiding variant discovery. bioRxiv. 2023 Jul 19:2023-07.
+
 ## [nf-core/sarek](https://pubmed.ncbi.nlm.nih.gov/32269765/)
 
 > Garcia MU, Juhos S, Larsson M, Olason PI, Martin M, Eisfeldt J, DiLorenzo S, Sandgren J, Díaz De Ståhl T, Ewels PA, Wirta V, Nistér M, Käller M, Nystedt B. Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants. F1000Res. 2020 Jan 29;9:63. eCollection 2020. doi: 10.12688/f1000research.16665.2. PubMed PMID: 32269765.
@@ -74,6 +78,8 @@
 
   > McKenna A, Hanna M, Banks E, et al.: The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010 Sep;20(9):1297-303. doi: 10.1101/gr.107524.110. Epub 2010 Jul 19. PubMed PMID: 20644199; PubMed Central PMCID: PMC2928508.
 
+- [GNU sed](http://www.gnu.org/software/sed/)
+
 - [HaplotypeCaller Joint Germline](https://www.biorxiv.org/content/10.1101/201178v3)
 
   > Poplin R. et al, Scaling accurate genetic variant discovery to tens of thousands of samples, bioRxiv 2018. doi: 10.1101/201178
@@ -110,8 +116,6 @@
 
   > Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8. PubMed PMID: 19505943; PubMed Central PMCID: PMC2723002.
 
-- [GNU sed](http://www.gnu.org/software/sed/)
-
 - [snpEff](https://pubmed.ncbi.nlm.nih.gov/22728672/)
 
   > Cingolani P, Platts A, Wang le L, et al.: A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin). Apr-Jun 2012;6(2):80-92. doi: 10.4161/fly.19695. PubMed PMID: 22728672; PubMed Central PMCID: PMC3679285.

diff --git a/conf/test/cache.config b/conf/test/cache.config
@@ -58,11 +58,6 @@ params {
 }
 
 process {
-    withLabel: 'sentieon' {
-        ext.sentieon_auth_mech_base64 = secrets.SENTIEON_AUTH_MECH_BASE64
-        ext.sentieon_auth_data_base64 = secrets.SENTIEON_AUTH_DATA_BASE64
-    }
-
     // This must contain .* in order to properly overwrite the standard config in test cases
     withName:'.*:FREEC_SOMATIC'{
         ext.args = {

diff --git a/docs/usage.md b/docs/usage.md
@@ -1062,7 +1062,7 @@ In particular, Sentieon contains what may be view as speedup version of some sta
 Sentieon supply license in the form of a string-value (a url) or a file. It should be base64-encoded and stored in a nextflow secret named `SENTIEON_LICENSE_BASE64`. If a license string (url) is supplied, then the nextflow secret should be set like this:
 
 ```bash
-nextflow secret set SENTIEON_LICENSE_BASE64 $(echo -n <sentieon_license_string> | base64 -w 0)
+nextflow secrets set SENTIEON_LICENSE_BASE64 $(echo -n <sentieon_license_string> | base64 -w 0)
 ```
 
 If a license file is supplied, then the nextflow secret should be set like this:

diff --git a/modules.json b/modules.json
@@ -77,28 +77,29 @@
                     },
                     "controlfreec/assesssignificance": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "053564d29a20d45323547973c4023914923823df",
                         "installed_by": ["modules"]
                     },
                     "controlfreec/freec": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "053564d29a20d45323547973c4023914923823df",
                         "installed_by": ["modules"]
                     },
                     "controlfreec/freec2bed": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "053564d29a20d45323547973c4023914923823df",
                         "installed_by": ["modules"]
                     },
                     "controlfreec/freec2circos": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "053564d29a20d45323547973c4023914923823df",
                         "installed_by": ["modules"]
                     },
                     "controlfreec/makegraph": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "git_sha": "053564d29a20d45323547973c4023914923823df",
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/controlfreec/makegraph/controlfreec-makegraph.diff"
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
@@ -163,127 +164,127 @@
                     },
                     "gatk4/applybqsr": {
                         "branch": "master",
-                        "git_sha": "240937a2a9c30298110753292be041188891f2cb",
+                        "git_sha": "cf8f9ace77aac01caa5c7cb92af5bbda7adb77bd",
                         "installed_by": ["modules"]
                     },
                     "gatk4/applybqsrspark": {
                         "branch": "master",
-                        "git_sha": "bd8092b67b5103bdd52e300f75889442275c3117",
+                        "git_sha": "cf8f9ace77aac01caa5c7cb92af5bbda7adb77bd",
                         "installed_by": ["modules"]
                     },
                     "gatk4/applyvqsr": {
                         "branch": "master",
-                        "git_sha": "359dcb06bda60c43955752e356e25c91cfd38ae0",
+                        "git_sha": "cf8f9ace77aac01caa5c7cb92af5bbda7adb77bd",
                         "installed_by": ["modules"]
                     },
                     "gatk4/baserecalibrator": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "cf8f9ace77aac01caa5c7cb92af5bbda7adb77bd",
                         "installed_by": ["modules"]
                     },
                     "gatk4/baserecalibratorspark": {
                         "branch": "master",
-                        "git_sha": "4b7d4863a5883b76e6bff13b6e52468fab090c5b",
+                        "git_sha": "cf8f9ace77aac01caa5c7cb92af5bbda7adb77bd",
                         "installed_by": ["modules"]
                     },
                     "gatk4/calculatecontamination": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "cf8f9ace77aac01caa5c7cb92af5bbda7adb77bd",
                         "installed_by": ["modules"]
                     },
                     "gatk4/cnnscorevariants": {
                         "branch": "master",
-                        "git_sha": "8c4542e5d421c4690cf1fa6ec729e9304763fdaf",
+                        "git_sha": "cf8f9ace77aac01caa5c7cb92af5bbda7adb77bd",
                         "installed_by": ["modules"]
                     },
                     "gatk4/createsequencedictionary": {
                         "branch": "master",
-                        "git_sha": "541811d779026c5d395925895fa5ed35e7216cc0",
+                        "git_sha": "cf8f9ace77aac01caa5c7cb92af5bbda7adb77bd",
                         "installed_by": ["modules"]
                     },
                     "gatk4/estimatelibrarycomplexity": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "cf8f9ace77aac01caa5c7cb92af5bbda7adb77bd",
                         "installed_by": ["modules"]
                     },
                     "gatk4/filtermutectcalls": {
                         "branch": "master",
-                        "git_sha": "2df2a11d5b12f2a73bca74f103691bc35d83c5fd",
+                        "git_sha": "cf8f9ace77aac01caa5c7cb92af5bbda7adb77bd",
                         "installed_by": ["modules"]
                     },
                     "gatk4/filtervarianttranches": {
                         "branch": "master",
-                        "git_sha": "541811d779026c5d395925895fa5ed35e7216cc0",
+                        "git_sha": "cf8f9ace77aac01caa5c7cb92af5bbda7adb77bd",
                         "installed_by": ["modules"]
                     },
                     "gatk4/gatherbqsrreports": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "cf8f9ace77aac01caa5c7cb92af5bbda7adb77bd",
                         "installed_by": ["modules"]
                     },
                     "gatk4/gatherpileupsummaries": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "cf8f9ace77aac01caa5c7cb92af5bbda7adb77bd",
                         "installed_by": ["modules"]
                     },
                     "gatk4/genomicsdbimport": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "cf8f9ace77aac01caa5c7cb92af5bbda7adb77bd",
                         "installed_by": ["modules"]
                     },
                     "gatk4/genotypegvcfs": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "cf8f9ace77aac01caa5c7cb92af5bbda7adb77bd",
                         "installed_by": ["modules"]
                     },
                     "gatk4/getpileupsummaries": {
                         "branch": "master",
-                        "git_sha": "2df2a11d5b12f2a73bca74f103691bc35d83c5fd",
+                        "git_sha": "cf8f9ace77aac01caa5c7cb92af5bbda7adb77bd",
                         "installed_by": ["modules"]
                     },
                     "gatk4/haplotypecaller": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "cf8f9ace77aac01caa5c7cb92af5bbda7adb77bd",
                         "installed_by": ["modules"]
                     },
                     "gatk4/intervallisttobed": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "cf8f9ace77aac01caa5c7cb92af5bbda7adb77bd",
                         "installed_by": ["modules"]
                     },
                     "gatk4/learnreadorientationmodel": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "cf8f9ace77aac01caa5c7cb92af5bbda7adb77bd",
                         "installed_by": ["modules"]
                     },
                     "gatk4/markduplicates": {
                         "branch": "master",
-                        "git_sha": "0a261469640941da2488e1a5aa023b64db837c70",
+                        "git_sha": "cf8f9ace77aac01caa5c7cb92af5bbda7adb77bd",
                         "installed_by": ["modules"]
                     },
                     "gatk4/markduplicatesspark": {
                         "branch": "master",
-                        "git_sha": "0a261469640941da2488e1a5aa023b64db837c70",
+                        "git_sha": "cf8f9ace77aac01caa5c7cb92af5bbda7adb77bd",
                         "installed_by": ["modules"]
                     },
                     "gatk4/mergemutectstats": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "cf8f9ace77aac01caa5c7cb92af5bbda7adb77bd",
                         "installed_by": ["modules"]
                     },
                     "gatk4/mergevcfs": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "cf8f9ace77aac01caa5c7cb92af5bbda7adb77bd",
                         "installed_by": ["modules"]
                     },
                     "gatk4/mutect2": {
                         "branch": "master",
-                        "git_sha": "2df2a11d5b12f2a73bca74f103691bc35d83c5fd",
+                        "git_sha": "cf8f9ace77aac01caa5c7cb92af5bbda7adb77bd",
                         "installed_by": ["modules"]
                     },
                     "gatk4/variantrecalibrator": {
                         "branch": "master",
-                        "git_sha": "359dcb06bda60c43955752e356e25c91cfd38ae0",
+                        "git_sha": "cf8f9ace77aac01caa5c7cb92af5bbda7adb77bd",
                         "installed_by": ["modules"]
                     },
                     "manta/germline": {

diff --git a/modules/nf-core/controlfreec/assesssignificance/main.nf b/modules/nf-core/controlfreec/assesssignificance/main.nf
diff --git a/modules/nf-core/controlfreec/freec/main.nf b/modules/nf-core/controlfreec/freec/main.nf
diff --git a/modules/nf-core/controlfreec/freec2bed/main.nf b/modules/nf-core/controlfreec/freec2bed/main.nf
diff --git a/modules/nf-core/controlfreec/freec2circos/main.nf b/modules/nf-core/controlfreec/freec2circos/main.nf
diff --git a/modules/nf-core/controlfreec/makegraph/controlfreec-makegraph.diff b/modules/nf-core/controlfreec/makegraph/controlfreec-makegraph.diff
diff --git a/modules/nf-core/controlfreec/makegraph/main.nf b/modules/nf-core/controlfreec/makegraph/main.nf
diff --git a/modules/nf-core/controlfreec/makegraph/meta.yml b/modules/nf-core/controlfreec/makegraph/meta.yml
diff --git a/modules/nf-core/gatk4/applybqsr/main.nf b/modules/nf-core/gatk4/applybqsr/main.nf