Prerelease changes v1.0.0

CHANGELOG.md

@@ -3,7 +3,9 @@
 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).
 
-## v1.0dev - [date]
+## v1.0.0 - 2024-04-12
+
+Initial release of nf-core/riboseq, created with the [nf-core](https://nf-co.re/) template.
 
 - [[#3](https://github.com/nf-core/riboseq/pull/3)] - Re-initialise base template ([@maxulysse](https://github.com/maxulysse), review by [@pinin4fjords](https://github.com/pinin4fjords))
 - [[#4](https://github.com/nf-core/riboseq/pull/4)] - Initialise testing an base template functionality ([@pinin4fjords](https://github.com/pinin4fjords), review by [@maxulysse](https://github.com/maxulysse))
@@ -21,9 +23,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#42](https://github.com/nf-core/riboseq/pull/42) - Add alignment based quantification with Salmon ([@pinin4fjords](https://github.com/pinin4fjords), review by [@maxulysse](https://github.com/maxulysse))
 - [#43](https://github.com/nf-core/riboseq/pull/43) - Add translational efficiency analysis with anota2seq ([@pinin4fjords](https://github.com/pinin4fjords), review by )
 - [#44](https://github.com/nf-core/riboseq/pull/44) - Fix lack of fastqc in multiqc report ([@pinin4fjords](https://github.com/pinin4fjords), review by [@mashehu](https://github.com/mashehu))
-- [#45](https://github.com/nf-core/riboseq/pull/45) - Update CI from rnaseq, strip unused rnaseq components ([@pinin4fjords](https://github.com/pinin4fjords), review by)
-
-Initial release of nf-core/riboseq, created with the [nf-core](https://nf-co.re/) template.
+- [#45](https://github.com/nf-core/riboseq/pull/45) - Update CI from rnaseq, strip unused rnaseq components ([@pinin4fjords](https://github.com/pinin4fjords), review by [@jfy133](https://github.com/jfy133))
+- [#46](https://github.com/nf-core/riboseq/pull/46) - Prerelease changes v1.0.0 ([@pinin4fjords](https://github.com/pinin4fjords), review by )
 
 ### `Added`
 

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
 
-  This report has been generated by the <a href="https://github.com/nf-core/riboseq/tree/dev" target="_blank">nf-core/riboseq</a> analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/riboseq/dev/docs/output" target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/riboseq/releases/tag/1.0.0" target="_blank">nf-core/riboseq</a> analysis pipeline. For information about how to interpret these results, please see the
+  <a href="https://nf-co.re/riboseq/1.0.0/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-riboseq-methods-description":
     order: -1000

modules.json

@@ -42,12 +42,12 @@
                     },
                     "fastp": {
                         "branch": "master",
-                        "git_sha": "003920c7f9a8ae19b69a97171922880220bedf56",
+                        "git_sha": "95cf5fe0194c7bf5cb0e3027a2eb7e7c89385080",
                         "installed_by": ["fastq_fastqc_umitools_fastp"]
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "f4ae1d942bd50c5c0b9bd2de1393ce38315ba57c",
+                        "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
                         "installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore"]
                     },
                     "fq/subsample": {
@@ -162,7 +162,7 @@
                     },
                     "trimgalore": {
                         "branch": "master",
-                        "git_sha": "d2c5e76f291379f3dd403e48e46ed7e6ba5da744",
+                        "git_sha": "a98418419ae6c9df3cf6cf108d1e1aba71037d5a",
                         "installed_by": ["fastq_fastqc_umitools_trimgalore"]
                     },
                     "tximeta/tximport": {
@@ -216,7 +216,7 @@
                     },
                     "fastq_fastqc_umitools_fastp": {
                         "branch": "master",
-                        "git_sha": "003920c7f9a8ae19b69a97171922880220bedf56",
+                        "git_sha": "cabcc0dadf8366aa7a9930066a7b3dd90d9825d5",
                         "installed_by": ["preprocess_rnaseq"]
                     },
                     "fastq_fastqc_umitools_trimgalore": {

nextflow.config

@@ -302,7 +302,7 @@ manifest {
     description     = """Analysis of ribosome profiling, or Ribo-Seq (also named ribosome footprinting)"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '1.0dev'
+    version         = '1.0.0'
     doi             = ''
 }
 

nextflow_schema.json

@@ -524,7 +524,9 @@
                     "fa_icon": "fas fa-fast-forward"
                 },
                 "skip_ribotricer": {
-                    "type": "boolean"
+                    "type": "boolean",
+                    "description": "Skip Riboricer.",
+                    "fa_icon": "fas fa-fast-forward"
                 }
             }
         },