diff --git a/CHANGELOG.md b/CHANGELOG.md index 999c2383..86a67bc2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,23 @@ 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). +## v1.1.5 - [2024-03-20] + +### `Added` + +### `Fixed` + +- [#346](https://github.com/nf-core/funcscan/pull/346) Pinned version of nf-validation to 1.1.3 + +### `Dependencies` + +| Plugin | Previous | New version | +| ------------- | -------- | ----------- | +| Bakta | 1.8.2 | 1.9.3 | +| nf-validation | Latest | 1.1.3 | + +### `Deprecated` + ## v1.1.4 - [2023-11-07] ### `Added` @@ -20,7 +37,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | ------------- | ---------------- | ----------- | | AMRFinderPlus | 3.10.42 | 3.11.18 | | Bakta | 1.7.0 | 1.8.2 | -| MultiQC | 1.14 | 1.15 | +| MultiQC | 1.14 | 1.15 | ### `Deprecated` diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 8357c829..042e6c78 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/funcscan + This report has been generated by the nf-core/funcscan analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-funcscan-methods-description": order: -1000 diff --git a/modules.json b/modules.json index 5e5f7456..d4f3ca49 100644 --- a/modules.json +++ b/modules.json @@ -47,12 +47,12 @@ }, "bakta/bakta": { "branch": "master", - "git_sha": "f05fa7c6753f92be861d606378860dcd5c828880", + "git_sha": "9d0f89b445e1f5b2fb30476f4be9a8b519c07846", "installed_by": ["modules"] }, "bakta/baktadbdownload": { "branch": "master", - "git_sha": "f05fa7c6753f92be861d606378860dcd5c828880", + "git_sha": "7c06e6820fa3918bc28a040e794f8a2b39fabadb", "installed_by": ["modules"] }, "bioawk": { diff --git a/modules/nf-core/bakta/bakta/environment.yml b/modules/nf-core/bakta/bakta/environment.yml new file mode 100644 index 00000000..efb92265 --- /dev/null +++ b/modules/nf-core/bakta/bakta/environment.yml @@ -0,0 +1,7 @@ +name: bakta_bakta +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::bakta=1.9.3 diff --git a/modules/nf-core/bakta/bakta/main.nf b/modules/nf-core/bakta/bakta/main.nf index fd0b76f2..9a32c3da 100644 --- a/modules/nf-core/bakta/bakta/main.nf +++ b/modules/nf-core/bakta/bakta/main.nf @@ -2,10 +2,10 @@ process BAKTA_BAKTA { tag "$meta.id" label 'process_medium' - conda "bioconda::bakta=1.8.2" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bakta:1.8.2--pyhdfd78af_0' : - 'biocontainers/bakta:1.8.2--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/bakta:1.9.3--pyhdfd78af_0' : + 'biocontainers/bakta:1.9.3--pyhdfd78af_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/bakta/bakta/meta.yml b/modules/nf-core/bakta/bakta/meta.yml index 0dfa07e2..c0e53e2a 100644 --- a/modules/nf-core/bakta/bakta/meta.yml +++ b/modules/nf-core/bakta/bakta/meta.yml @@ -12,7 +12,6 @@ tools: tool_dev_url: https://github.com/oschwengers/bakta doi: "10.1099/mgen.0.000685" licence: ["GPL v3"] - input: - meta: type: map @@ -33,7 +32,6 @@ input: - prodigal_tf: type: file description: Training file to use for Prodigal (optional) - output: - meta: type: map @@ -84,8 +82,11 @@ output: type: file description: hypothetical protein CDS amino acid sequences as FASTA pattern: "*.hypotheticals.faa" - authors: - "@rpetit3" - "@oschwengers" - "@jfy133" +maintainers: + - "@rpetit3" + - "@oschwengers" + - "@jfy133" diff --git a/modules/nf-core/bakta/baktadbdownload/environment.yml b/modules/nf-core/bakta/baktadbdownload/environment.yml new file mode 100644 index 00000000..f6a53ff7 --- /dev/null +++ b/modules/nf-core/bakta/baktadbdownload/environment.yml @@ -0,0 +1,7 @@ +name: bakta_baktadbdownload +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::bakta=1.9.3 diff --git a/modules/nf-core/bakta/baktadbdownload/main.nf b/modules/nf-core/bakta/baktadbdownload/main.nf index de7e2199..e512d77d 100644 --- a/modules/nf-core/bakta/baktadbdownload/main.nf +++ b/modules/nf-core/bakta/baktadbdownload/main.nf @@ -1,10 +1,10 @@ process BAKTA_BAKTADBDOWNLOAD { label 'process_single' - conda "bioconda::bakta=1.8.2" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bakta:1.8.2--pyhdfd78af_0' : - 'biocontainers/bakta:1.8.2--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/bakta:1.9.3--pyhdfd78af_0' : + 'biocontainers/bakta:1.9.3--pyhdfd78af_0' }" output: path "db*" , emit: db diff --git a/modules/nf-core/bakta/baktadbdownload/meta.yml b/modules/nf-core/bakta/baktadbdownload/meta.yml index 996f5b0c..21acacda 100644 --- a/modules/nf-core/bakta/baktadbdownload/meta.yml +++ b/modules/nf-core/bakta/baktadbdownload/meta.yml @@ -15,7 +15,6 @@ tools: tool_dev_url: https://github.com/oschwengers/bakta doi: "10.1099/mgen.0.000685" licence: ["GPL v3"] - output: - versions: type: file @@ -25,7 +24,9 @@ output: type: directory description: BAKTA database directory pattern: "db*/" - authors: - "@jfy133" - "@jasmezz" +maintainers: + - "@jfy133" + - "@jasmezz" diff --git a/nextflow.config b/nextflow.config index 77dd905a..fe5ded07 100644 --- a/nextflow.config +++ b/nextflow.config @@ -342,7 +342,7 @@ singularity.registry = 'quay.io' // Nextflow plugins plugins { - id 'nf-validation' // Validation of pipeline parameters and creation of an input channel from a sample sheet + id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet } // Load igenomes.config if required @@ -391,7 +391,7 @@ manifest { description = """Pipeline for screening for functional components of assembled contigs""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '1.1.4' + version = '1.1.5' doi = '10.5281/zenodo.7643099' } diff --git a/nextflow_schema.json b/nextflow_schema.json index eb6d7e9c..60f5e16f 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -311,7 +311,7 @@ }, "annotation_prokka_retaincontigheaders": { "type": "boolean", - "fa_icon":"fas fa-remove-format", + "fa_icon": "fas fa-remove-format", "help_text": "This parameter allows prokka to retain the original contig names by activating `PROKKA`'s `--force` flag. If this parameter is set to `false` it activates `PROKKA`'s flags `--locus-tag PROKKA --centre CENTER` so the locus tags (contig names) will be PROKKA_# and the center tag will be CENTER. By default `PROKKA` changes contig headers to avoid errors that might rise due to long contig headers, so this must be turned on if the user has short contig names that should be retained by `PROKKA`. \n\n> Modifies tool parameter(s):\n> - Prokka: `--locus-tag PROKKA --centre CENTER`\n> - Prokka: `--force`", "description": "Retains contig names." }