Minor release: 1.1.0 with CNV benchmark subworkflow #164
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typo in README.md
add zenado id
…ols-vcfeval implement rtgtools for somatic small bench
161 cnv benchmark subworkflow
bin/merge_reports.py
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| @@ -191,6 +191,29 @@ def get_happy_resuls(file_paths): | |||
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| return merged_df | |||
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| def get_intersect_resuls(file_paths): | |||
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| def get_intersect_resuls(file_paths): | |
| def get_intersect_results(file_paths): |
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Or is this meant to be called resuls ? I see you have it throughout the script so maybe I am missing something
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this is a sytex mistake :D I realize it but leave it as it is now
| truth_id = "SEQC2" | ||
| truth_vcf = "${params.test_data_base}/testdata/hg38/truth/somatic/cnv_benchmark_calls.vcf" | ||
| regions_bed = "${params.test_data_base}/testdata/hg38/truth/somatic/ngs_benchmark_cnv_gain_loss_loh.bed" | ||
| rename_chr = "${projectDir}/assets/rename_contigs/grch37_grch38.txt" |
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Should this data be in nf-core/testdatasets? could it be useful for other modules?
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It is in test-database, I am linking it through params.test_data_base
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I meant the last row - it is in projectDir not test_data_base, so I was wondering whether there was a reason for that
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For some reason I highlighted everything :D
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test_data_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/variantbenchmarking'
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it is already in test-datasets, that is what I meant :D
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this one too? "${projectDir}/assets/rename_contigs/grch37_grch38.txt"
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this is almost default for the pipeline itself, It is not test purposes.
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| process BEDTOOLS_INTERSECT { | |||
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Is there no way to use https://nf-co.re/modules/bedtools_intersect ?
Or a patch to it? Or is it doing something different?
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The python script I have, is with more functionalities like checking the proper file formats, and summarizing statistics.
workflows/variantbenchmarking.nf
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| }else{ | ||
| log.error "Please specify params.truth_id and params.truth_vcf to perform benchmarking analysis" | ||
| log.error "Please specify params.truth_id and params.truth_vcf or regions_bed to perform benchmarking analysis" |
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Could this not be catched with nf-schema?
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Might be possible, but I couldnt figure out how..
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this is not being validated with nf-schema by the way. This is coming from nextflow_schema.json.
CHANGELOG.md
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| @@ -3,14 +3,37 @@ | |||
| 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). | |||
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| ## v1.0dev - [date] | |||
| ## 1.1.0 - [06.03.2025] | |||
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The date is of yesterday, but I guess it is not a big deal :) In case you decide to do a new PR t could be updated
apply luisas review
fix download_pipeline.yml
PR checklist
nf-core pipelines lint).nextflow run . -profile test,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).