Merge pull request #1398 from maxulysse/3.17.0dev

maxulysse · web-flow · commit 224655a5511a · 2024-10-08T15:25:21.000+02:00
Back to dev
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,18 @@
 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
+
+### Credits
+
+### Enhancements & fixes
+
+- [PR #1398](https://github.com/nf-core/rnaseq/pull/1398) - Bump pipeline version to 3.17.0dev
+
+### Parameters
+
+### Software dependencies
+
 ## [[3.16.0](https://github.com/nf-core/rnaseq/releases/tag/3.16.0)] - 2024-10-02
 
 ### Credits
@@ -37,7 +49,9 @@ Special thanks to the following for their contributions to the release:
 |               | `--bracken_precision`       |
 
 > **NB:** Parameter has been **updated** if both old and new parameter information is present.
+>
 > **NB:** Parameter has been **added** if just the new parameter information is present.
+>
 > **NB:** Parameter has been **removed** if new parameter information isn't present.
 
 ### Software dependencies
diff --git a/nextflow.config b/nextflow.config
@@ -345,7 +345,7 @@ manifest {
     description     = """RNA sequencing analysis pipeline for gene/isoform quantification and extensive quality control."""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '3.16.0'
+    version         = '3.17.0dev'
     doi             = 'https://doi.org/10.5281/zenodo.1400710'
 }
 
diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
@@ -43,7 +43,7 @@
                     "untar": 1.34
                 },
                 "Workflow": {
-                    "nf-core/rnaseq": "v3.16.0"
+                    "nf-core/rnaseq": "v3.17.0dev"
                 }
             },
             [
@@ -227,7 +227,7 @@
                     "untar": 1.34
                 },
                 "Workflow": {
-                    "nf-core/rnaseq": "v3.16.0"
+                    "nf-core/rnaseq": "v3.17.0dev"
                 }
             },
             [
diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap
@@ -43,7 +43,7 @@
                     "untar": 1.34
                 },
                 "Workflow": {
-                    "nf-core/rnaseq": "v3.16.0"
+                    "nf-core/rnaseq": "v3.17.0dev"
                 }
             },
             [
@@ -221,7 +221,7 @@
                     "untar": 1.34
                 },
                 "Workflow": {
-                    "nf-core/rnaseq": "v3.16.0"
+                    "nf-core/rnaseq": "v3.17.0dev"
                 }
             },
             [
diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap
@@ -44,7 +44,7 @@
                     "untar": 1.34
                 },
                 "Workflow": {
-                    "nf-core/rnaseq": "v3.16.0"
+                    "nf-core/rnaseq": "v3.17.0dev"
                 }
             },
             [
@@ -224,7 +224,7 @@
                     "untar": 1.34
                 },
                 "Workflow": {
-                    "nf-core/rnaseq": "v3.16.0"
+                    "nf-core/rnaseq": "v3.17.0dev"
                 }
             },
             [
diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap
@@ -56,7 +56,7 @@
                     "untar": 1.34
                 },
                 "Workflow": {
-                    "nf-core/rnaseq": "v3.16.0"
+                    "nf-core/rnaseq": "v3.17.0dev"
                 }
             },
             [
@@ -305,7 +305,7 @@
                     "untar": 1.34
                 },
                 "Workflow": {
-                    "nf-core/rnaseq": "v3.16.0"
+                    "nf-core/rnaseq": "v3.17.0dev"
                 }
             },
             [
diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap
@@ -134,7 +134,7 @@
                     "untar": 1.34
                 },
                 "Workflow": {
-                    "nf-core/rnaseq": "v3.16.0"
+                    "nf-core/rnaseq": "v3.17.0dev"
                 }
             },
             [
@@ -1321,7 +1321,7 @@
                     "untar": 1.34
                 },
                 "Workflow": {
-                    "nf-core/rnaseq": "v3.16.0"
+                    "nf-core/rnaseq": "v3.17.0dev"
                 }
             },
             [
diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap
@@ -140,7 +140,7 @@
                     "untar": 1.34
                 },
                 "Workflow": {
-                    "nf-core/rnaseq": "v3.16.0"
+                    "nf-core/rnaseq": "v3.17.0dev"
                 }
             },
             [
@@ -1571,7 +1571,7 @@
                     "untar": 1.34
                 },
                 "Workflow": {
-                    "nf-core/rnaseq": "v3.16.0"
+                    "nf-core/rnaseq": "v3.17.0dev"
                 }
             },
             [
diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap
@@ -50,7 +50,7 @@
                     "untar": 1.34
                 },
                 "Workflow": {
-                    "nf-core/rnaseq": "v3.16.0"
+                    "nf-core/rnaseq": "v3.17.0dev"
                 }
             },
             [
@@ -378,7 +378,7 @@
                     "untar": 1.34
                 },
                 "Workflow": {
-                    "nf-core/rnaseq": "v3.16.0"
+                    "nf-core/rnaseq": "v3.17.0dev"
                 }
             },
             [
diff --git a/tests/skip_qc.nf.test.snap b/tests/skip_qc.nf.test.snap
@@ -40,7 +40,7 @@
                     "untar": 1.34
                 },
                 "Workflow": {
-                    "nf-core/rnaseq": "v3.16.0"
+                    "nf-core/rnaseq": "v3.17.0dev"
                 }
             },
             [
@@ -169,7 +169,7 @@
                     "untar": 1.34
                 },
                 "Workflow": {
-                    "nf-core/rnaseq": "v3.16.0"
+                    "nf-core/rnaseq": "v3.17.0dev"
                 }
             },
             [
diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap
@@ -130,7 +130,7 @@
                     "untar": 1.34
                 },
                 "Workflow": {
-                    "nf-core/rnaseq": "v3.16.0"
+                    "nf-core/rnaseq": "v3.17.0dev"
                 }
             },
             [
diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap
@@ -134,7 +134,7 @@
                     "untar": 1.34
                 },
                 "Workflow": {
-                    "nf-core/rnaseq": "v3.16.0"
+                    "nf-core/rnaseq": "v3.17.0dev"
                 }
             },
             [
@@ -1450,7 +1450,7 @@
                     "untar": 1.34
                 },
                 "Workflow": {
-                    "nf-core/rnaseq": "v3.16.0"
+                    "nf-core/rnaseq": "v3.17.0dev"
                 }
             },
             [
diff --git a/workflows/rnaseq/assets/multiqc/multiqc_config.yml b/workflows/rnaseq/assets/multiqc/multiqc_config.yml
@@ -1,5 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/rnaseq/releases/tag/3.16.0" target="_blank">nf-core/rnaseq</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/rnaseq/3.16.0/docs/output" target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/rnaseq/tree/dev" target="_blank">nf-core/rnaseq</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/rnaseq/dev/docs/output" target="_blank">documentation</a>.
 report_section_order:
   # Important checks and failures
   sample-status:

Original file line number	Diff line number	Diff line change
`@@ -345,7 +345,7 @@ manifest {`
`345`	`345`	`description = """RNA sequencing analysis pipeline for gene/isoform quantification and extensive quality control."""`
`346`	`346`	`mainScript = 'main.nf'`
`347`	`347`	`nextflowVersion = '!>=23.04.0'`
`348`		`- version = '3.16.0'`
	`348`	`+ version = '3.17.0dev'`
`349`	`349`	`doi = 'https://doi.org/10.5281/zenodo.1400710'`
`350`	`350`	`}`
`351`	`351`
Original file line number	Diff line number	Diff line change
`@@ -43,7 +43,7 @@`
`43`	`43`	`"untar": 1.34`
`44`	`44`	`},`
`45`	`45`	`"Workflow": {`
`46`		`- "nf-core/rnaseq": "v3.16.0"`
	`46`	`+ "nf-core/rnaseq": "v3.17.0dev"`
`47`	`47`	`}`
`48`	`48`	`},`
`49`	`49`	`[`
`@@ -227,7 +227,7 @@`
`227`	`227`	`"untar": 1.34`
`228`	`228`	`},`
`229`	`229`	`"Workflow": {`
`230`		`- "nf-core/rnaseq": "v3.16.0"`
	`230`	`+ "nf-core/rnaseq": "v3.17.0dev"`
`231`	`231`	`}`
`232`	`232`	`},`
`233`	`233`	`[`
Original file line number	Diff line number	Diff line change
`@@ -44,7 +44,7 @@`
`44`	`44`	`"untar": 1.34`
`45`	`45`	`},`
`46`	`46`	`"Workflow": {`
`47`		`- "nf-core/rnaseq": "v3.16.0"`
	`47`	`+ "nf-core/rnaseq": "v3.17.0dev"`
`48`	`48`	`}`
`49`	`49`	`},`
`50`	`50`	`[`
`@@ -224,7 +224,7 @@`
`224`	`224`	`"untar": 1.34`
`225`	`225`	`},`
`226`	`226`	`"Workflow": {`
`227`		`- "nf-core/rnaseq": "v3.16.0"`
	`227`	`+ "nf-core/rnaseq": "v3.17.0dev"`
`228`	`228`	`}`
`229`	`229`	`},`
`230`	`230`	`[`
Original file line number	Diff line number	Diff line change
`@@ -56,7 +56,7 @@`
`56`	`56`	`"untar": 1.34`
`57`	`57`	`},`
`58`	`58`	`"Workflow": {`
`59`		`- "nf-core/rnaseq": "v3.16.0"`
	`59`	`+ "nf-core/rnaseq": "v3.17.0dev"`
`60`	`60`	`}`
`61`	`61`	`},`
`62`	`62`	`[`
`@@ -305,7 +305,7 @@`
`305`	`305`	`"untar": 1.34`
`306`	`306`	`},`
`307`	`307`	`"Workflow": {`
`308`		`- "nf-core/rnaseq": "v3.16.0"`
	`308`	`+ "nf-core/rnaseq": "v3.17.0dev"`
`309`	`309`	`}`
`310`	`310`	`},`
`311`	`311`	`[`
Original file line number	Diff line number	Diff line change
`@@ -134,7 +134,7 @@`
`134`	`134`	`"untar": 1.34`
`135`	`135`	`},`
`136`	`136`	`"Workflow": {`
`137`		`- "nf-core/rnaseq": "v3.16.0"`
	`137`	`+ "nf-core/rnaseq": "v3.17.0dev"`
`138`	`138`	`}`
`139`	`139`	`},`
`140`	`140`	`[`
`@@ -1321,7 +1321,7 @@`
`1321`	`1321`	`"untar": 1.34`
`1322`	`1322`	`},`
`1323`	`1323`	`"Workflow": {`
`1324`		`- "nf-core/rnaseq": "v3.16.0"`
	`1324`	`+ "nf-core/rnaseq": "v3.17.0dev"`
`1325`	`1325`	`}`
`1326`	`1326`	`},`
`1327`	`1327`	`[`
Original file line number	Diff line number	Diff line change
`@@ -140,7 +140,7 @@`
`140`	`140`	`"untar": 1.34`
`141`	`141`	`},`
`142`	`142`	`"Workflow": {`
`143`		`- "nf-core/rnaseq": "v3.16.0"`
	`143`	`+ "nf-core/rnaseq": "v3.17.0dev"`
`144`	`144`	`}`
`145`	`145`	`},`
`146`	`146`	`[`
`@@ -1571,7 +1571,7 @@`
`1571`	`1571`	`"untar": 1.34`
`1572`	`1572`	`},`
`1573`	`1573`	`"Workflow": {`
`1574`		`- "nf-core/rnaseq": "v3.16.0"`
	`1574`	`+ "nf-core/rnaseq": "v3.17.0dev"`
`1575`	`1575`	`}`
`1576`	`1576`	`},`
`1577`	`1577`	`[`
Original file line number	Diff line number	Diff line change
`@@ -50,7 +50,7 @@`
`50`	`50`	`"untar": 1.34`
`51`	`51`	`},`
`52`	`52`	`"Workflow": {`
`53`		`- "nf-core/rnaseq": "v3.16.0"`
	`53`	`+ "nf-core/rnaseq": "v3.17.0dev"`
`54`	`54`	`}`
`55`	`55`	`},`
`56`	`56`	`[`
`@@ -378,7 +378,7 @@`
`378`	`378`	`"untar": 1.34`
`379`	`379`	`},`
`380`	`380`	`"Workflow": {`
`381`		`- "nf-core/rnaseq": "v3.16.0"`
	`381`	`+ "nf-core/rnaseq": "v3.17.0dev"`
`382`	`382`	`}`
`383`	`383`	`},`
`384`	`384`	`[`
Original file line number	Diff line number	Diff line change
`@@ -40,7 +40,7 @@`
`40`	`40`	`"untar": 1.34`
`41`	`41`	`},`
`42`	`42`	`"Workflow": {`
`43`		`- "nf-core/rnaseq": "v3.16.0"`
	`43`	`+ "nf-core/rnaseq": "v3.17.0dev"`
`44`	`44`	`}`
`45`	`45`	`},`
`46`	`46`	`[`
`@@ -169,7 +169,7 @@`
`169`	`169`	`"untar": 1.34`
`170`	`170`	`},`
`171`	`171`	`"Workflow": {`
`172`		`- "nf-core/rnaseq": "v3.16.0"`
	`172`	`+ "nf-core/rnaseq": "v3.17.0dev"`
`173`	`173`	`}`
`174`	`174`	`},`
`175`	`175`	`[`