fix: parameters not resolving properly when igenomes are used #530

ramprasadn · 2024-03-11T08:43:08Z

PR checklist

Addresses https://nfcore.slack.com/archives/C04QR0T3G3H/p1709811356971549

Pretext: To illustrate the problem and the solution, I did a couple of test runs using the test config after setting ignore_igenomes to false. I also removed the bwa parameter from the nextflow.config, so we can see if it gets set to the value in igenomes.config.

Below is the list of resolved parameters as it enters the workflow in the current dev branch (notice the lack of bwa parameter in the list as it is not set anywhere).

        input:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/samplesheet_trio.csv
        genome:GRCh37
        igenomes_base:s3://ngi-igenomes/igenomes/
        igenomes_ignore:false
        local_genomes:null
        save_reference:false
        mito_name:MT
        analysis_type:wgs
        bait_padding:100
        run_rtgvcfeval:false
        save_mapped_as_cram:false
        skip_eklipse:false
        skip_fastp:true
        skip_fastqc:false
        skip_gens:true
        skip_germlinecnvcaller:true
        skip_haplocheck:false
        skip_peddy:true
        skip_me_annotation:false
        skip_mt_annotation:false
        skip_qualimap:false
        skip_snv_annotation:false
        skip_sv_annotation:false
        skip_mt_subsample:false
        skip_vcf2cytosure:false
        skip_vep_filter:false
        cadd_resources:null
        platform:illumina
        ngsbits_samplegender_method:xy
        fasta:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta
        fai:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta.fai
        bwamem2:null
        call_interval:null
        gcnvcaller_model:null
        gens_interval_list:null
        gens_pon_female:null
        gens_pon_male:null
        gens_gnomad_pos:null
        gnomad_af:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz
        gnomad_af_idx:null
        intervals_wgs:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target_wgs.interval_list
        intervals_y:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/targetY.interval_list
        known_dbsnp:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz
        known_dbsnp_tbi:null
        mobile_element_references:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mobile_element_references.tsv
        mobile_element_svdb_annotations:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv
        ml_model:https://s3.amazonaws.com/sentieon-release/other/SentieonDNAscopeModel1.0.model
        mt_fasta:null
        ploidy_model:null
        reduced_penetrance:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reduced_penetrance.tsv
        readcount_intervals:null
        rtg_truthvcfs:null
        sample_id_map:null
        sequence_dictionary:null
        score_config_mt:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini
        score_config_snv:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini
        score_config_sv:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_sv.ini
        sdf:null
        svdb_query_bedpedbs:null
        svdb_query_dbs:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv
        target_bed:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target.bed
        variant_catalog:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_catalog.json
        variant_consequences_snv:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt
        variant_consequences_sv:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt
        vep_filters:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/hgnc.txt
        vep_filters_scout_fmt:null
        vcf2cytosure_blacklist:null
        vcfanno_resources:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_resources.txt
        vcfanno_toml:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_config.toml
        vcfanno_lua:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_functions.lua
        vep_cache:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz
        vep_plugin_files:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_files.csv
        aligner:bwa
        min_trimmed_length:40
        mt_subsample_rd:150
        mt_subsample_seed:30
        rmdup:false
        cnvnator_binsize:1000
        variant_caller:deepvariant
        vep_cache_version:107
        sentieon_dnascope_pcr_indel_model:CONSERVATIVE
        variant_type:snp,indel
        multiqc_config:null
        multiqc_title:null
        multiqc_logo:null
        max_multiqc_email_size:25.MB
        multiqc_methods_description:null
        outdir:results
        publish_dir_mode:copy
        email:null
        email_on_fail:null
        plaintext_email:false
        monochrome_logs:false
        hook_url:null
        help:false
        version:false
        config_profile_name:Test profile
        config_profile_description:Minimal test dataset to check pipeline function
        custom_config_version:master
        custom_config_base:https://raw.githubusercontent.com/nf-core/configs/master
        config_profile_contact:null
        config_profile_url:null
        max_memory:6.GB
        max_cpus:2
        max_time:2.h
        validationFailUnrecognisedParams:false
        validation-fail-unrecognised-params:false
        validationLenientMode:false
        validation-lenient-mode:false
        validationSchemaIgnoreParams:genomes,igenomes_base
        validation-schema-ignore-params:genomes,igenomes_base
        validationShowHiddenParams:false
        validation-show-hidden-params:false
        validate_params:true

Resolved parameters as it enters the workflow after the fix (notice the presence of bwa parameter in the list, and it has resolved to the right version on igenomes).

        input:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/samplesheet_trio.csv
        genome:GRCh37
        igenomes_base:s3://ngi-igenomes/igenomes/
        igenomes_ignore:false
        local_genomes:null
        save_reference:false
        mito_name:MT
        analysis_type:wgs
        bait_padding:100
        run_rtgvcfeval:false
        save_mapped_as_cram:false
        skip_eklipse:false
        skip_fastp:true
        skip_fastqc:false
        skip_gens:true
        skip_germlinecnvcaller:true
        skip_haplocheck:false
        skip_peddy:true
        skip_me_annotation:false
        skip_mt_annotation:false
        skip_qualimap:false
        skip_snv_annotation:false
        skip_sv_annotation:false
        skip_mt_subsample:false
        skip_vcf2cytosure:false
        skip_vep_filter:false
        cadd_resources:null
        platform:illumina
        ngsbits_samplegender_method:xy
        aligner:bwa
        min_trimmed_length:40
        mt_subsample_rd:150
        mt_subsample_seed:30
        rmdup:false
        cnvnator_binsize:1000
        variant_caller:deepvariant
        vep_cache_version:107
        ml_model:https://s3.amazonaws.com/sentieon-release/other/SentieonDNAscopeModel1.0.model
        sentieon_dnascope_pcr_indel_model:CONSERVATIVE
        variant_type:snp,indel
        multiqc_config:null
        multiqc_title:null
        multiqc_logo:null
        max_multiqc_email_size:25.MB
        multiqc_methods_description:null
        outdir:results
        publish_dir_mode:copy
        email:null
        email_on_fail:null
        plaintext_email:false
        monochrome_logs:false
        hook_url:null
        help:false
        version:false
        config_profile_name:Test profile
        config_profile_description:Minimal test dataset to check pipeline function
        custom_config_version:master
        custom_config_base:https://raw.githubusercontent.com/nf-core/configs/master
        config_profile_contact:null
        config_profile_url:null
        max_memory:6.GB
        max_cpus:2
        max_time:2.h
        validationFailUnrecognisedParams:false
        validation-fail-unrecognised-params:false
        validationLenientMode:false
        validation-lenient-mode:false
        validationSchemaIgnoreParams:genomes,igenomes_base
        validation-schema-ignore-params:genomes,igenomes_base
        validationShowHiddenParams:false
        validation-show-hidden-params:false
        validate_params:true
        fai:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta.fai
        gnomad_af:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz
        intervals_wgs:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target_wgs.interval_list
        intervals_y:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/targetY.interval_list
        known_dbsnp:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz
        mobile_element_references:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mobile_element_references.tsv
        mobile_element_svdb_annotations:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv
        reduced_penetrance:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reduced_penetrance.tsv
        score_config_mt:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini
        score_config_snv:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini
        score_config_sv:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_sv.ini
        svdb_query_dbs:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv
        target_bed:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target.bed
        variant_catalog:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_catalog.json
        vcfanno_lua:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_functions.lua
        vcfanno_resources:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_resources.txt
        vcfanno_toml:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_config.toml
        variant_consequences_snv:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt
        variant_consequences_sv:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt
        vep_cache:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz
        vep_filters:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/hgnc.txt
        vep_plugin_files:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_files.csv
        fasta:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta
        bwa:s3://ngi-igenomes/igenomes//Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/version0.6.0/
        bwamem2:null
        call_interval:null
        gcnvcaller_model:null
        gens_interval_list:null
        gens_pon_female:null
        gens_pon_male:null
        gens_gnomad_pos:null
        gnomad_af_idx:null
        known_dbsnp_tbi:null
        mt_fasta:null
        ploidy_model:null
        readcount_intervals:null
        rtg_truthvcfs:null
        sample_id_map:null
        sequence_dictionary:null
        sdf:null
        svdb_query_bedpedbs:null
        vep_filters_scout_fmt:null
        vcf2cytosure_blacklist:null]

github-actions · 2024-03-11T08:45:37Z

`nf-core lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit c1d7666

+| ✅ 179 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 2.0.0
pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

files_exist - File is ignored: conf/modules.config
files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: assets/nf-core-raredisease_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_dark.png

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .editorconfig
files_exist - File found: .prettierignore
files_exist - File found: .prettierrc.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
files_exist - File found: nextflow.config
files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/CONTRIBUTING.md
files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/branch.yml
files_exist - File found: .github/workflows/ci.yml
files_exist - File found: .github/workflows/linting_comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: assets/nf-core-raredisease_logo_light.png
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-raredisease_logo_light.png
files_exist - File found: docs/images/nf-core-raredisease_logo_dark.png
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
files_exist - File found: docs/README.md
files_exist - File found: docs/usage.md
files_exist - File found: main.nf
files_exist - File found: assets/multiqc_config.yml
files_exist - File found: conf/base.config
files_exist - File found: conf/igenomes.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: modules.json
files_exist - File found: pyproject.toml
files_exist - File not found check: Singularity
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: docs/images/nf-core-raredisease_logo.png
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/WorkflowRaredisease.groovy
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
nextflow_config - Config variable found: manifest.name
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: manifest.homePage
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: params.validationShowHiddenParams
nextflow_config - Config variable found: params.validationSchemaIgnoreParams
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
nextflow_config - Config variable (correctly) not found: params.enable_conda
nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
nextflow_config - Config manifest.name began with nf-core/
nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config params.custom_config_version is set to master
nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.outdir= results
nextflow_config - Config default value correct: params.bait_padding= 100
nextflow_config - Config default value correct: params.genome= GRCh38
nextflow_config - Config default value correct: params.mito_name= chrM
nextflow_config - Config default value correct: params.analysis_type= wgs
nextflow_config - Config default value correct: params.platform= illumina
nextflow_config - Config default value correct: params.ngsbits_samplegender_method= xy
nextflow_config - Config default value correct: params.skip_vcf2cytosure= true
nextflow_config - Config default value correct: params.aligner= bwamem2
nextflow_config - Config default value correct: params.min_trimmed_length= 40
nextflow_config - Config default value correct: params.mt_subsample_rd= 150
nextflow_config - Config default value correct: params.mt_subsample_seed= 30
nextflow_config - Config default value correct: params.cnvnator_binsize= 1000
nextflow_config - Config default value correct: params.sentieon_dnascope_pcr_indel_model= CONSERVATIVE
nextflow_config - Config default value correct: params.variant_caller= deepvariant
nextflow_config - Config default value correct: params.variant_type= snp,indel
nextflow_config - Config default value correct: params.vep_cache_version= 110
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Config default value correct: params.max_cpus= 16
nextflow_config - Config default value correct: params.max_memory= 128.GB
nextflow_config - Config default value correct: params.max_time= 240.h
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.validate_params= true
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - CODE_OF_CONDUCT.md matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/workflows/branch.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - .github/workflows/linting.yml matches the template
files_unchanged - assets/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
files_unchanged - pyproject.toml matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - '.github/workflows/ci.yml' checks minimum NF version
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
readme - README Nextflow minimum version badge matched config. Badge: 23.04.0, Config: 23.04.0
readme - README Zenodo placeholder was replaced with DOI.
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (641 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: awstest.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
multiqc_config - 'assets/multiqc_config.yml' contains report_section_order
multiqc_config - 'assets/multiqc_config.yml' contains export_plots
multiqc_config - 'assets/multiqc_config.yml' contains report_comment
multiqc_config - 'assets/multiqc_config.yml' follows the ordering scheme of the minimally required plugins.
multiqc_config - 'assets/multiqc_config.yml' contains a matching 'report_comment'.
multiqc_config - 'assets/multiqc_config.yml' contains 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

nf-core/tools version 2.13.1
Run at 2024-03-11 11:53:19

ramprasadn · 2024-03-11T09:40:23Z

@maxulysse @nvnieuwk what do you guys think?

nvnieuwk · 2024-03-11T09:42:20Z

This does work if you work with and without igenomes? what if you supply a fasta from the cli or a params file?

ramprasadn · 2024-03-11T09:58:09Z

Yupe, works without igenomes as well.

input:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/samplesheet_trio.csv
genome:GRCh37
igenomes_base:s3://ngi-igenomes/igenomes/
igenomes_ignore:true
local_genomes:null
save_reference:false
mito_name:MT
analysis_type:wgs
bait_padding:100
run_rtgvcfeval:false
save_mapped_as_cram:false
skip_eklipse:false
skip_fastp:true
skip_fastqc:false
skip_gens:true
skip_germlinecnvcaller:true
skip_haplocheck:false
skip_peddy:true
skip_me_annotation:false
skip_mt_annotation:false
skip_qualimap:false
skip_snv_annotation:false
skip_sv_annotation:false
skip_mt_subsample:false
skip_vcf2cytosure:false
skip_vep_filter:false
cadd_resources:null
platform:illumina
ngsbits_samplegender_method:xy
aligner:bwa
min_trimmed_length:40
mt_subsample_rd:150
mt_subsample_seed:30
rmdup:false
cnvnator_binsize:1000
variant_caller:deepvariant
vep_cache_version:107
ml_model:https://s3.amazonaws.com/sentieon-release/other/SentieonDNAscopeModel1.0.model
sentieon_dnascope_pcr_indel_model:CONSERVATIVE
variant_type:snp,indel
multiqc_config:null
multiqc_title:null
multiqc_logo:null
max_multiqc_email_size:25.MB
multiqc_methods_description:null
outdir:results
publish_dir_mode:copy
email:null
email_on_fail:null
plaintext_email:false
monochrome_logs:false
hook_url:null
help:false
version:false
config_profile_name:Test profile
config_profile_description:Minimal test dataset to check pipeline function
custom_config_version:master
custom_config_base:https://raw.githubusercontent.com/nf-core/configs/master
config_profile_contact:null
config_profile_url:null
max_memory:6.GB
max_cpus:2
max_time:2.h
validationFailUnrecognisedParams:false
validation-fail-unrecognised-params:false
validationLenientMode:false
validation-lenient-mode:false
validationSchemaIgnoreParams:genomes,igenomes_base
validation-schema-ignore-params:genomes,igenomes_base
validationShowHiddenParams:false
validation-show-hidden-params:false
validate_params:true
fasta:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta
fai:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta.fai
gnomad_af:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz
intervals_wgs:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target_wgs.interval_list
intervals_y:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/targetY.interval_list
known_dbsnp:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz
mobile_element_references:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mobile_element_references.tsv
mobile_element_svdb_annotations:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv
reduced_penetrance:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reduced_penetrance.tsv
score_config_mt:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini
score_config_snv:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini
score_config_sv:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_sv.ini
svdb_query_dbs:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv
target_bed:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target.bed
variant_catalog:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_catalog.json
vcfanno_lua:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_functions.lua
vcfanno_resources:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_resources.txt
vcfanno_toml:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_config.toml
variant_consequences_snv:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt
variant_consequences_sv:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt
vep_cache:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz
vep_filters:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/hgnc.txt
vep_plugin_files:https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_files.csv
genomes:[:]
bwa:null
bwamem2:null
call_interval:null
gcnvcaller_model:null
gens_interval_list:null
gens_pon_female:null
gens_pon_male:null
gens_gnomad_pos:null
gnomad_af_idx:null
known_dbsnp_tbi:null
mt_fasta:null
ploidy_model:null
readcount_intervals:null
rtg_truthvcfs:null
sample_id_map:null
sequence_dictionary:null
sdf:null
svdb_query_bedpedbs:null
vep_filters_scout_fmt:null
vcf2cytosure_blacklist:null

nvnieuwk · 2024-03-11T10:02:26Z

Awesome! seems like a good solution then!

ramprasadn · 2024-03-11T10:04:24Z

I haven't tested using a params file, but parameters resolve fine when you supply a parameter via cli. So I don't see a reason why it wouldn't work with a params file 😄

fix?

1353e06

ramprasadn marked this pull request as ready for review March 11, 2024 08:51

fix lint

c1d7666

ramprasadn mentioned this pull request Mar 11, 2024

Release 2.0.0 #528

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jemten approved these changes Mar 12, 2024

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ramprasadn merged commit bc8c70b into nf-core:dev Mar 12, 2024
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ramprasadn deleted the parameter-resolution branch March 12, 2024 07:54

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fix: parameters not resolving properly when igenomes are used #530

fix: parameters not resolving properly when igenomes are used #530

ramprasadn commented Mar 11, 2024 •

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ramprasadn commented Mar 11, 2024

nvnieuwk commented Mar 11, 2024

ramprasadn commented Mar 11, 2024

nvnieuwk commented Mar 11, 2024

ramprasadn commented Mar 11, 2024

fix: parameters not resolving properly when igenomes are used #530

fix: parameters not resolving properly when igenomes are used #530

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ramprasadn commented Mar 11, 2024 • edited Loading

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nf-core lint overall result: Passed ✅ ⚠️

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nvnieuwk commented Mar 11, 2024

ramprasadn commented Mar 11, 2024

nvnieuwk commented Mar 11, 2024

ramprasadn commented Mar 11, 2024

ramprasadn commented Mar 11, 2024 •

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`nf-core lint` overall result: Passed ✅ ⚠️