From 721a0f2a21e565e03f8de38b23fbcb38353f1224 Mon Sep 17 00:00:00 2001 From: fellen31 Date: Thu, 20 Mar 2025 15:05:04 +0100 Subject: [PATCH] Update modules to fix spelling and language server warnings --- CHANGELOG.md | 9 ++++++--- bin/add_most_severe_consequence.py | 4 ++-- bin/add_most_severe_pli.py | 2 +- modules/local/add_most_severe_consequence/main.nf | 5 ++--- modules/local/add_most_severe_pli/main.nf | 5 ++--- 5 files changed, 13 insertions(+), 12 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1c4cf06f2..2d80c383e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` - Changed for loop to each in create_pedigree_file [#683](https://github.com/nf-core/raredisease/pull/683) +- Updated `add_most_severe_consequence` and `add_most_severe_pli` to fix spelling and language server warnings [#689](https://github.com/nf-core/raredisease/pull/689) ### `Fixed` @@ -23,9 +24,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Tool updates -| Tool | Old version | New version | -| ----------- | ----------- | ----------- | -| DeepVariant | 1.6.1 | 1.8.0 | +| Tool | Old version | New version | +| --------------------------- | ----------- | ----------- | +| DeepVariant | 1.6.1 | 1.8.0 | +| add_most_severe_consequence | 1.0 | 1.1 | +| add_most_severe_pli | 1.0 | 1.1 | ## 2.4.0 - Vitalstatistix [2025-02-24] diff --git a/bin/add_most_severe_consequence.py b/bin/add_most_severe_consequence.py index cb1538c7f..78dcfb947 100755 --- a/bin/add_most_severe_consequence.py +++ b/bin/add_most_severe_consequence.py @@ -14,7 +14,7 @@ def parse_vep_csq_transcripts( transcripts: list, allele_ind: int, csq_ind: int, hgnc_ind: int, var_csq: list ) -> Tuple[list, list, list, list]: """ - Parse conseqences for each transcript and return HGNC IDs, alleles, and their severity rank + Parse consequences for each transcript and return HGNC IDs, alleles, and their severity rank based on the term's ranking in the ensembl consequences list. Args: @@ -51,7 +51,7 @@ def construct_most_severe_consequence_info( line: str, allele_ind: int, csq_ind: int, hgnc_ind: int, var_csq: list ) -> list: """ - Parse conseqences for each transcript and return HGNC IDs, alleles, and their severity rank + Parse consequences for each transcript and return HGNC IDs, alleles, and their severity rank based on the term's ranking in the ensembl consequences list. Args: diff --git a/bin/add_most_severe_pli.py b/bin/add_most_severe_pli.py index b578fe286..abb1f5b7b 100755 --- a/bin/add_most_severe_pli.py +++ b/bin/add_most_severe_pli.py @@ -84,7 +84,7 @@ def write_pli_annotated_vcf(file_in: TextIO, file_out: TextIO): if line.startswith("##INFO=\n' + '##INFO=\n' ) else: vcf_record = construct_most_severe_pli_info(line, pli_ind) diff --git a/modules/local/add_most_severe_consequence/main.nf b/modules/local/add_most_severe_consequence/main.nf index 0c5728115..dd9975219 100644 --- a/modules/local/add_most_severe_consequence/main.nf +++ b/modules/local/add_most_severe_consequence/main.nf @@ -19,14 +19,13 @@ process ADD_MOST_SEVERE_CSQ { task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ add_most_severe_consequence.py --file_in ${vcf} --file_out ${prefix}.vcf --variant_csq ${variant_consequences} cat <<-END_VERSIONS > versions.yml "${task.process}": - add_most_severe_consequence: v1.0 + add_most_severe_consequence: v1.1 python: \$(python --version | sed 's/Python //g') END_VERSIONS """ @@ -38,7 +37,7 @@ process ADD_MOST_SEVERE_CSQ { cat <<-END_VERSIONS > versions.yml "${task.process}": - add_most_severe_consequence: v1.0 + add_most_severe_consequence: v1.1 python: \$(python --version | sed 's/Python //g') END_VERSIONS """ diff --git a/modules/local/add_most_severe_pli/main.nf b/modules/local/add_most_severe_pli/main.nf index f2975a220..e1bfe67db 100644 --- a/modules/local/add_most_severe_pli/main.nf +++ b/modules/local/add_most_severe_pli/main.nf @@ -18,14 +18,13 @@ process ADD_MOST_SEVERE_PLI { task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ add_most_severe_pli.py --file_in ${vcf} --file_out ${prefix}.vcf cat <<-END_VERSIONS > versions.yml "${task.process}": - add_most_severe_pli: v1.0 + add_most_severe_pli: v1.1 python: \$(python --version | sed 's/Python //g') END_VERSIONS """ @@ -37,7 +36,7 @@ process ADD_MOST_SEVERE_PLI { cat <<-END_VERSIONS > versions.yml "${task.process}": - add_most_severe_pli: v1.0 + add_most_severe_pli: v1.1 python: \$(python --version | sed 's/Python //g') END_VERSIONS """