Merge pull request #271 from nf-core/final-release-adjustments

scwatts · web-flow · commit de7699976ed1 · 2025-12-09T11:23:06.000+11:00
Final release adjustments
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project mostly adheres to
 [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [[2.3.0](https://github.com/nf-core/oncoanalyser/releases/tag/2.3.0)] Spotted Nightjar
+## [[2.3.0](https://github.com/nf-core/oncoanalyser/releases/tag/2.3.0)] Spotted Nightjar - 2025-12-09
 
 - [268](https://github.com/nf-core/oncoanalyser/pull/268) - Apply minor fixes and updates
   - Samplesheet / version collection fixes, misc adjustments
diff --git a/docs/usage.md b/docs/usage.md
@@ -142,7 +142,7 @@ row as the first line with the below columns:
 | `sample_id`     | Sample identifier                                                                                                                                                   |
 | `sample_type`   | Sample type: `tumor`, `normal`                                                                                                                                      |
 | `sequence_type` | Sequence type: `dna`, `rna`                                                                                                                                         |
-| `filetype`      | File type: e.g. `fastq`, `bam`, `bai`; a full list of valid values can be found [here](https://github.com/nf-core/oncoanalyser/blob/2.3.0/lib/Constants.groovy#L82) |
+| `filetype`      | File type: e.g. `fastq`, `bam`, `bai`; a full list of valid values can be found [here](https://github.com/nf-core/oncoanalyser/blob/2.3.0/lib/Constants.groovy#L80) |
 | `info`          | Additional sample information such as sequencing library and lane for [FASTQ](#fastq) files, this column is only required when running an analysis from FASTQ       |
 | `filepath`      | Absolute filepath to input file, which can be a local filepath or supported protocol (http, https, ftp, s3, az, gz)                                                 |
 
@@ -743,7 +743,7 @@ Please see: [Staging reference data: Automatic staging](#automatic-staging)
 ## Process selection
 
 It is possible to exclude or manually select specific processes when running `oncoanalyser`. The full list of processes that can
-be selected is available [here](https://github.com/nf-core/oncoanalyser/blob/2.3.0/lib/Constants.groovy#L55).
+be selected is available [here](https://github.com/nf-core/oncoanalyser/blob/2.3.0/lib/Constants.groovy#L53).
 
 :::warning
 
diff --git a/modules/local/amber/environment.yml b/modules/local/amber/environment.yml
@@ -2,6 +2,5 @@ name: amber
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::hmftools-amber=4.2
diff --git a/modules/local/bamtools/environment.yml b/modules/local/bamtools/environment.yml
@@ -2,6 +2,5 @@ name: bamtools
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::hmftools-bam-tools=1.5
diff --git a/modules/local/bwa-mem2/mem/environment.yml b/modules/local/bwa-mem2/mem/environment.yml
@@ -2,7 +2,6 @@ name: bwa-mem2_mem
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::bwa-mem2=2.3
   - bioconda::samtools=1.21
diff --git a/modules/local/chord/environment.yml b/modules/local/chord/environment.yml
@@ -2,6 +2,5 @@ name: chord
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::hmftools-chord=2.1.2
diff --git a/modules/local/cider/environment.yml b/modules/local/cider/environment.yml
@@ -2,6 +2,5 @@ name: cider
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::hmftools-cider=1.1
diff --git a/modules/local/cobalt/panel_normalisation/environment.yml b/modules/local/cobalt/panel_normalisation/environment.yml
@@ -2,6 +2,5 @@ name: cobalt_panel_normalisation
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::hmftools-cobalt=2.2
diff --git a/modules/local/cobalt/run/environment.yml b/modules/local/cobalt/run/environment.yml
@@ -2,6 +2,5 @@ name: cobalt_run
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::hmftools-cobalt=2.2
diff --git a/modules/local/cuppa/environment.yml b/modules/local/cuppa/environment.yml
@@ -2,7 +2,6 @@ name: cuppa
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::hmftools-cuppa=2.3.2
   - conda-forge::r-stringr>=1.5
diff --git a/modules/local/custom/extract_tarball/environment.yml b/modules/local/custom/extract_tarball/environment.yml
@@ -0,0 +1,6 @@
+name: custom_extracttarball
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - conda-forge::tar=1.34
diff --git a/modules/local/custom/extract_tarball/main.nf b/modules/local/custom/extract_tarball/main.nf
@@ -1,7 +1,7 @@
 process CUSTOM_EXTRACTTARBALL {
     label 'process_single'
 
-    conda "conda-forge::tar=1.34"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
         'quay.io/nf-core/ubuntu:20.04' }"
diff --git a/modules/local/esvee/environment.yml b/modules/local/esvee/environment.yml
@@ -2,6 +2,5 @@ name: esvee
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::hmftools-esvee=1.2
diff --git a/modules/local/fastp/environment.yml b/modules/local/fastp/environment.yml
@@ -2,6 +2,5 @@ name: fastp
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::fastp=0.23.4
diff --git a/modules/local/gatk4/bwaindeximage/environment.yml b/modules/local/gatk4/bwaindeximage/environment.yml
@@ -0,0 +1,6 @@
+name: gatk4_bwa_index_image
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::gatk4=4.6.1.0
diff --git a/modules/local/gatk4/bwaindeximage/main.nf b/modules/local/gatk4/bwaindeximage/main.nf
@@ -2,7 +2,7 @@ process GATK4_BWA_INDEX_IMAGE {
     tag "${genome_fasta.name}"
     label 'process_medium'
 
-    conda "bioconda::gatk4=4.6.1.0"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0' :
         'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }"
diff --git a/modules/local/gridss/index/environment.yml b/modules/local/gridss/index/environment.yml
@@ -2,6 +2,5 @@ name: gridss_index
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::gridss=2.13.2=h50ea8bc_3
diff --git a/modules/local/isofox/panel_normalisation/environment.yml b/modules/local/isofox/panel_normalisation/environment.yml
@@ -2,6 +2,5 @@ name: isofox_panel_normalisation
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::hmftools-isofox=1.7.2
diff --git a/modules/local/isofox/run/environment.yml b/modules/local/isofox/run/environment.yml
@@ -2,6 +2,5 @@ name: isofox_run
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::hmftools-isofox=1.7.2
diff --git a/modules/local/lilac/environment.yml b/modules/local/lilac/environment.yml
@@ -2,6 +2,5 @@ name: lilac
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::hmftools-lilac=1.7.3
diff --git a/modules/local/linx/germline/environment.yml b/modules/local/linx/germline/environment.yml
@@ -2,6 +2,5 @@ name: linx_germline
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::hmftools-linx=2.2
diff --git a/modules/local/linx/somatic/environment.yml b/modules/local/linx/somatic/environment.yml
@@ -2,6 +2,5 @@ name: linx_somatic
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::hmftools-linx=2.2
diff --git a/modules/local/linx/visualiser/environment.yml b/modules/local/linx/visualiser/environment.yml
@@ -2,6 +2,5 @@ name: linx_visualiser
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::hmftools-linx=2.2
diff --git a/modules/local/linxreport/environment.yml b/modules/local/linxreport/environment.yml
@@ -2,6 +2,5 @@ name: linxreport
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::r-linxreport=1.1.0
diff --git a/modules/local/neo/annotate_fusions/environment.yml b/modules/local/neo/annotate_fusions/environment.yml
@@ -2,6 +2,5 @@ name: neo_annotate_fusions
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::hmftools-isofox=1.7.2
diff --git a/modules/local/neo/finder/environment.yml b/modules/local/neo/finder/environment.yml
@@ -2,6 +2,5 @@ name: neo_finder
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::hmftools-neo=1.2.1
diff --git a/modules/local/neo/scorer/environment.yml b/modules/local/neo/scorer/environment.yml
@@ -2,6 +2,5 @@ name: neo_scorer
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::hmftools-neo=1.2.1
diff --git a/modules/local/orange/environment.yml b/modules/local/orange/environment.yml
@@ -2,6 +2,5 @@ name: orange
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::hmftools-orange=4.1.2
diff --git a/modules/local/pave/germline/environment.yml b/modules/local/pave/germline/environment.yml
@@ -2,6 +2,5 @@ name: pave_germline
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::hmftools-pave=1.8
diff --git a/modules/local/pave/pon_creation/environment.yml b/modules/local/pave/pon_creation/environment.yml
@@ -2,6 +2,5 @@ name: pave_pon_creation
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::hmftools-pave=1.8
diff --git a/modules/local/pave/somatic/environment.yml b/modules/local/pave/somatic/environment.yml
@@ -2,6 +2,5 @@ name: pave_somatic
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::hmftools-pave=1.8
diff --git a/modules/local/peach/environment.yml b/modules/local/peach/environment.yml
@@ -2,6 +2,5 @@ name: peach
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::hmftools-peach=2.0.0
diff --git a/modules/local/purple/environment.yml b/modules/local/purple/environment.yml
@@ -2,6 +2,5 @@ name: purple
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::hmftools-purple=4.3
diff --git a/modules/local/redux/environment.yml b/modules/local/redux/environment.yml
@@ -2,6 +2,5 @@ name: redux
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::hmftools-redux=1.2.2
diff --git a/modules/local/sage/append/environment.yml b/modules/local/sage/append/environment.yml
@@ -2,6 +2,5 @@ name: sage_append
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::hmftools-sage=4.1
diff --git a/modules/local/sage/germline/environment.yml b/modules/local/sage/germline/environment.yml
@@ -2,6 +2,5 @@ name: sage_germline
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::hmftools-sage=4.1
diff --git a/modules/local/sage/somatic/environment.yml b/modules/local/sage/somatic/environment.yml
@@ -2,6 +2,5 @@ name: sage_somatic
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::hmftools-sage=4.1
diff --git a/modules/local/sambamba/merge/environment.yml b/modules/local/sambamba/merge/environment.yml
@@ -2,6 +2,5 @@ name: sambamba_merge
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::sambamba=1.0.1
diff --git a/modules/local/sigs/environment.yml b/modules/local/sigs/environment.yml
@@ -2,6 +2,5 @@ name: sigs
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::hmftools-sigs=1.2.1
diff --git a/modules/local/star/align/environment.yml b/modules/local/star/align/environment.yml
@@ -2,6 +2,5 @@ name: star_align
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::star=2.7.3a
diff --git a/modules/local/teal/pipeline/environment.yml b/modules/local/teal/pipeline/environment.yml
@@ -2,6 +2,5 @@ name: teal_pipeline
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::hmftools-teal=1.3.6
diff --git a/modules/local/teal/prep/environment.yml b/modules/local/teal/prep/environment.yml
@@ -2,6 +2,5 @@ name: teal_prep
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::hmftools-teal=1.3.6
diff --git a/modules/local/virusbreakend/environment.yml b/modules/local/virusbreakend/environment.yml
@@ -2,7 +2,6 @@ name: virusbreakend
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::gridss=2.13.2=h50ea8bc_3
   - repeatmasker=4.1.5
diff --git a/modules/local/virusinterpreter/environment.yml b/modules/local/virusinterpreter/environment.yml
@@ -2,6 +2,5 @@ name: virusinterpreter
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::hmftools-virus-interpreter=1.7.2
diff --git a/modules/local/wisp/environment.yml b/modules/local/wisp/environment.yml
@@ -2,6 +2,5 @@ name: wisp
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::hmftools-wisp=1.2
diff --git a/modules/nf-core/bwamem2/index/bwamem2-index.diff b/modules/nf-core/bwamem2/index/bwamem2-index.diff
diff --git a/modules/nf-core/bwamem2/index/environment.yml b/modules/nf-core/bwamem2/index/environment.yml
diff --git a/modules/nf-core/gatk4/markduplicates/environment.yml b/modules/nf-core/gatk4/markduplicates/environment.yml
diff --git a/modules/nf-core/gatk4/markduplicates/gatk4-markduplicates.diff b/modules/nf-core/gatk4/markduplicates/gatk4-markduplicates.diff
diff --git a/modules/nf-core/gatk4/markduplicates/main.nf b/modules/nf-core/gatk4/markduplicates/main.nf
diff --git a/modules/nf-core/star/genomegenerate/environment.yml b/modules/nf-core/star/genomegenerate/environment.yml
diff --git a/modules/nf-core/star/genomegenerate/star-genomegenerate.diff b/modules/nf-core/star/genomegenerate/star-genomegenerate.diff
