Address language server issues #688
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fellen31
reviewed
Mar 20, 2025
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fellen31
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Very nice, missing a changelog though!
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| ch_versions = Channel.empty() | ||
| ch_haplog = Channel.empty() | ||
| ch_haplogrep_in = Channel.empty() |
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Should this be a "Fixed" in the changelog?
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| .map { item -> | ||
| def meta = item[0] | ||
| def model_calls = item[1] | ||
| return [meta.sample, meta, model_calls] | ||
| } |
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I'm not sure I understand why this can't be:
Suggested change
| .map { item -> | |
| def meta = item[0] | |
| def model_calls = item[1] | |
| return [meta.sample, meta, model_calls] | |
| } | |
| .map { meta, model_calls -> | |
| return [meta.sample, meta, model_calls] | |
| } |
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| run_rtgvcfeval: ["rtg_truthvcfs"], | ||
| skip_repeat_calling: ["variant_catalog"], | ||
| skip_repeat_annotation: ["variant_catalog"], | ||
| skip_snv_calling: ["genome"], | ||
| skip_snv_annotation: ["genome", "vcfanno_resources", "vcfanno_toml", "vep_cache", "vep_cache_version", | ||
| "gnomad_af", "score_config_snv", "variant_consequences_snv"], | ||
| skip_sv_annotation: ["genome", "vep_cache", "vep_cache_version", "score_config_sv", "variant_consequences_sv"], | ||
| skip_mt_annotation: ["genome", "mito_name", "vcfanno_resources", "vcfanno_toml", "score_config_mt", | ||
| "vep_cache_version", "vep_cache", "variant_consequences_snv"], | ||
| analysis_type_wes: ["target_bed"], | ||
| variant_caller_sentieon: ["ml_model"], | ||
| skip_germlinecnvcaller: ["ploidy_model", "gcnvcaller_model", "readcount_intervals"], | ||
| skip_me_calling: ["mobile_element_references"], | ||
| skip_me_annotation: ["mobile_element_svdb_annotations", "variant_consequences_snv"], | ||
| skip_gens: ["gens_gnomad_pos", "gens_interval_list", "gens_pon_female", "gens_pon_male"], | ||
| skip_smncopynumbercaller: ["genome"] |
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Could perhaps be aligned.
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Nice! Will have a look to simplify Nallo based on this.
fellen31
approved these changes
Mar 20, 2025
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PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile test_one_sample,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).