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Fix spelling and language server warnings #689

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Merged
merged 2 commits into from
Mar 20, 2025
Merged

Fix spelling and language server warnings #689

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721a0f2
Update modules to fix spelling and language server warnings
fellen31 Mar 20, 2025
3ebfa80
Merge branch 'dev' into fix-spelling-and-ls
ramprasadn Mar 20, 2025
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11 changes: 7 additions & 4 deletions CHANGELOG.md
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Expand Up @@ -11,8 +11,9 @@ 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)
- Refactored code to address issues highlighted by language server [#688](https://github.com/nf-core/raredisease/pull/688)
- Changed for loop to each in create_pedigree_file [#683](https://github.com/nf-core/raredisease/pull/683)

### `Fixed`

Expand All @@ -26,9 +27,11 @@ 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]

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4 changes: 2 additions & 2 deletions bin/add_most_severe_consequence.py
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Expand Up @@ -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:
Expand Down Expand Up @@ -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:
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2 changes: 1 addition & 1 deletion bin/add_most_severe_pli.py
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Expand Up @@ -84,7 +84,7 @@ def write_pli_annotated_vcf(file_in: TextIO, file_out: TextIO):
if line.startswith("##INFO=<ID=CSQ") and "pLI_gene_value" in line:
pli_ind = parse_vep_csq_schema(line)
file_out.write(
'##INFO=<ID=most_severe_pli,Number=1,Type=Float,Description="Probabililty of a gene being loss-of-function intolerant score.">\n'
'##INFO=<ID=most_severe_pli,Number=1,Type=Float,Description="Probability of a gene being loss-of-function intolerant score.">\n'
)
else:
vcf_record = construct_most_severe_pli_info(line, pli_ind)
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5 changes: 2 additions & 3 deletions modules/local/add_most_severe_consequence/main.nf
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Expand Up @@ -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
"""
Expand All @@ -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
"""
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5 changes: 2 additions & 3 deletions modules/local/add_most_severe_pli/main.nf
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Expand Up @@ -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
"""
Expand All @@ -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
"""
Expand Down