Merge branch 'tag' into 'dev'

Tag v1.1.1

See merge request epi2melabs/workflows/wf-transcriptomes!163

.pre-commit-config.yaml

@@ -8,7 +8,7 @@ repos:
         always_run: true
         pass_filenames: false
         additional_dependencies:
-          - epi2melabs>=0.0.52
+          - epi2melabs>=0.0.51
       - id: build_models
         name: build_models
         entry: datamodel-codegen --strict-nullable --base-class workflow_glue.results_schema_helpers.BaseModel --use-schema-description --disable-timestamp --input results_schema.yml --input-file-type openapi --output bin/workflow_glue/results_schema.py

CHANGELOG.md

@@ -4,7 +4,7 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [unreleased]
+## [v1.1.1]
 ### Changed
 - Improved handling of different annotation file types (eg. `.gtf/.gff/.gff3`) in `de_analysis` mode.
 - Improved handling of annotation files that do not contain version numbers in transcript_id (such as gtf's from Ensembl).

README.md

@@ -122,13 +122,6 @@ input_reads.fastq   ─── input_directory  ─── input_directory
 | analyse_unclassified | boolean | Analyse unclassified reads from input directory. By default the workflow will not process reads in the unclassified directory. | If selected and if the input is a multiplex directory the workflow will also process the unclassified directory. | False |
 
 
-### Output Options
-
-| Nextflow parameter name  | Type | Description | Help | Default |
-|--------------------------|------|-------------|------|---------|
-| out_dir | string | Directory for output of all user-facing files. |  | output |
-
-
 ### Sample Options
 
 | Nextflow parameter name  | Type | Description | Help | Default |

docs/06_input_parameters.md

@@ -11,13 +11,6 @@
 | analyse_unclassified | boolean | Analyse unclassified reads from input directory. By default the workflow will not process reads in the unclassified directory. | If selected and if the input is a multiplex directory the workflow will also process the unclassified directory. | False |
 
 
-### Output Options
-
-| Nextflow parameter name  | Type | Description | Help | Default |
-|--------------------------|------|-------------|------|---------|
-| out_dir | string | Directory for output of all user-facing files. |  | output |
-
-
 ### Sample Options
 
 | Nextflow parameter name  | Type | Description | Help | Default |

nextflow.config

@@ -116,7 +116,7 @@ manifest {
     description     = 'Transcriptome analysis including gene fusions, differential expression as well as assembly and annotation of cDNA and direct RNA sequencing data.'
     mainScript      = 'main.nf'
     nextflowVersion = '>=23.04.2'
-    version         = 'v1.1.0'
+    version         = 'v1.1.1'
 }
 
 epi2melabs {