All params to entry workflow

.github/workflows/nf-test.yml

@@ -78,7 +78,7 @@ jobs:
           - isMain: false
             profile: "singularity"
         NXF_VER:
-          - "25.04.0"
+          - "25.10.0"
           - "latest-everything"
     env:
       NXF_ANSI_LOG: false

CHANGELOG.md

@@ -35,6 +35,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#262](https://github.com/nf-core/phaseimpute/pull/262) - Change from `master` to `main` branch.
 - [#268](https://github.com/nf-core/phaseimpute/pull/268) - Refactor duplicated QUILT/STITCH posfile preprocessing into a single step.
 - [#273](https://github.com/nf-core/phaseimpute/pull/273) - Update nf-core modules, fix syntax. Remove `SAMTOOLS_REHEADER` patch and pass command through meta map. Update nf-test in Github Action to 0.9.4.
+- [#276](https://github.com/nf-core/phaseimpute/pull/276) - Migrate all `params.value` usage to entry workflow. Use groovy map to store parameters for each step. Use nextflow 25.10 for `getGenomeAttribute()`.
 
 ### `Fixed`
 

README.md

@@ -10,7 +10,7 @@
 [![GitHub Actions Linting Status](https://github.com/nf-core/phaseimpute/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/phaseimpute/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/phaseimpute/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.14329225-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.14329225)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
-[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
 [![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)

conf/steps/initialisation.config

@@ -15,6 +15,15 @@ process {
         publishDir = [ enabled: false ]
     }
 
+    withName: 'PREPARE_GENOME:SAMTOOLS_FAIDX' {
+        publishDir = [
+            path: { "${params.outdir}/initialisation/prepare_genome" },
+            mode: params.publish_dir_mode,
+            enabled: params.publish_all,
+        ]
+        ext.args = "--write-index"
+    }
+
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CUSTOM_GENETICMAPCONVERT'{
         tag = { "${meta.panel_id} ${meta.chr}" }
         ext.prefix = { "${meta.panel_id}_${meta.chr}" }
@@ -24,9 +33,4 @@ process {
             enabled: params.publish_all
         ]
     }
-
-    withName: 'PIPELINE_INITIALISATION:SAMTOOLS_FAIDX' {
-        publishDir = [ enabled: false ]
-        ext.args = "--write-index"
-    }
 }

main.nf

@@ -20,7 +20,18 @@ include { CHRCHECK as CHRCHECK_TRUTH } from './workflows/chrcheck'
 include { CHRCHECK as CHRCHECK_PANEL } from './workflows/chrcheck'
 include { PIPELINE_INITIALISATION    } from './subworkflows/local/utils_nfcore_phaseimpute_pipeline'
 include { PIPELINE_COMPLETION        } from './subworkflows/local/utils_nfcore_phaseimpute_pipeline'
-include { getGenomeAttribute         } from './subworkflows/local/utils_nfcore_phaseimpute_pipeline'
+include { PREPARE_GENOME             } from './subworkflows/local/prepare_genome'
+include { getGenomeAttribute         } from 'plugin/nf-core-utils'
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    GENOME PARAMETER VALUES
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+params.fasta             = getGenomeAttribute('fasta')
+params.fasta_fai         = getGenomeAttribute('fasta_fai')
+params.fasta_gzi         = getGenomeAttribute('fasta_gzi')
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -34,18 +45,27 @@ include { getGenomeAttribute         } from './subworkflows/local/utils_nfcore_p
 workflow NFCORE_PHASEIMPUTE {
 
     take:
-    ch_input       // channel: samplesheet read in from --input
-    ch_input_truth // channel: samplesheet read in from --input-truth
-    ch_fasta       // channel: reference genome FASTA file with index
-    ch_panel       // channel: reference panel variants file
-    ch_regions     // channel: regions to use [[chr, region], region]
-    ch_depth       // channel: depth of coverage file [[depth], depth]
-    ch_map         // channel: map file for imputation
-    ch_posfile     // channel: samplesheet read in from --posfile
-    ch_chunks      // channel: samplesheet read in from --chunks
-    chunk_model    // parameter: chunk model
-    rename_chr     // parameter: rename chromosome prefix
-    max_chr_names  // parameter: max number of chr to show in message
+    steps            // array: List of steps to perform
+    tools            // array: List of tools to use
+    ch_input         // channel: samplesheet read in from --input
+    ch_input_truth   // channel: samplesheet read in from --input-truth
+    ch_fasta         // channel: reference genome FASTA file with index
+    ch_panel         // channel: reference panel variants file
+    ch_regions       // channel: regions to use [[chr, region], region]
+    ch_depth         // channel: depth of coverage file [[depth], depth]
+    ch_map           // channel: map file for imputation
+    ch_posfile       // channel: samplesheet read in from --posfile
+    ch_chunks        // channel: samplesheet read in from --chunks
+    sheets_given     // map: input sheets given
+    rename_chr       // parameter: rename chromosome prefix
+    max_chr_names    // parameter: max number of chr to show in message
+    params_simulate  // map: parameters use for simulation step [depth: float, genotype: path]
+    params_panelprep // map: parameters use for panelprep step  [normalize: boolean, remove_samples: string, compute_freq: boolean, phase: boolean, chunk_model: string ]
+    params_impute    // map: parameters use for imputation step [batch_size: integer, k_val: integer, n_gen: integer, buffer: integer]
+    params_validate  // map: parameters use for validation step [bins: string, min_val_gl: float, min_val_dp: integer]
+    params_multiqc   // map: parameters use for multiqc report  [config: path, logo: path, methods_description: string]
+    seed             // integer
+    outdir           // path
 
     main:
 
@@ -56,7 +76,6 @@ workflow NFCORE_PHASEIMPUTE {
     ch_input_impute         = channel.empty()
     ch_input_simulate       = channel.empty()
     ch_input_validate       = channel.empty()
-    def steps               = params.steps.split(',') as List
 
     //  Check input files for contigs names consistency
     lst_chr = ch_regions.map {meta, _region -> meta.chr }
@@ -88,6 +107,8 @@ workflow NFCORE_PHASEIMPUTE {
     // WORKFLOW: Run pipeline
     //
     PHASEIMPUTE (
+        steps,
+        tools,
         ch_input_impute,
         ch_input_simulate,
         ch_input_validate,
@@ -99,12 +120,16 @@ workflow NFCORE_PHASEIMPUTE {
         ch_map,
         ch_posfile,
         ch_chunks,
-        chunk_model,
-        params.multiqc_config,
-        params.multiqc_logo,
-        params.multiqc_methods_description,
-        params.outdir
+        sheets_given,
+        params_simulate,
+        params_panelprep,
+        params_impute,
+        params_validate,
+        params_multiqc,
+        seed,
+        outdir
     )
+
     emit:
     multiqc_report = PHASEIMPUTE.out.multiqc_report // channel: /path/to/multiqc_report.html
 }
@@ -118,6 +143,58 @@ workflow NFCORE_PHASEIMPUTE {
 workflow {
 
     main:
+    def steps = params.steps.split(',') as List
+    def tools = params.tools ? params.tools.split(',') as List : []
+
+    def sheets_given = [
+        input_target : params.input,
+        input_truth  : params.input_truth,
+        input_region : params.input_region,
+        input_panel  : params.panel,
+        input_posfile: params.posfile,
+        input_chunks : params.chunks,
+        input_map    : params.map,
+    ]
+
+    def params_simulate = [
+        depth   : params.depth,
+        genotype: params.genotype
+    ]
+
+    def params_panelprep = [
+        normalize     : params.normalize,
+        remove_samples: params.remove_samples,
+        compute_freq  : params.compute_freq,
+        phase         : params.phase,
+        chunk_model   : params.chunk_model
+    ]
+
+    def params_impute = [
+        batch_size: params.batch_size,
+        k_val     : params.k_val,
+        n_gen     :params.n_gen,
+        buffer    :params.buffer,
+    ]
+
+    def params_validate = [
+        bins      : params.bins,
+        min_val_gl: params.min_val_gl,
+        min_val_dp: params.min_val_dp
+    ]
+
+    def params_multiqc = [
+        config             : params.multiqc_config,
+        logo               : params.multiqc_logo,
+        methods_description: params.multiqc_methods_description
+    ]
+
+    PREPARE_GENOME(
+        params.genome ?: file(params.fasta, checkIfExists:true).getBaseName(),
+        params.fasta,
+        params.fasta_fai,
+        params.fasta_gzi
+    )
+
     //
     // SUBWORKFLOW: Run initialisation tasks
     //
@@ -127,28 +204,44 @@ workflow {
         params.monochrome_logs,
         args,
         params.outdir,
-        params.input,
         params.help,
         params.help_full,
-        params.show_hidden
+        params.show_hidden,
+        PREPARE_GENOME.out.ch_fasta_fai_gzi,
+        sheets_given,
+        steps,
+        tools,
+        params.max_chr_names,
+        params_simulate,
+        params_panelprep,
+        params_impute
     )
 
     //
     // WORKFLOW: Run main workflow
     //
     NFCORE_PHASEIMPUTE (
-        PIPELINE_INITIALISATION.out.input,
-        PIPELINE_INITIALISATION.out.input_truth,
-        PIPELINE_INITIALISATION.out.fasta,
-        PIPELINE_INITIALISATION.out.panel,
-        PIPELINE_INITIALISATION.out.regions,
-        PIPELINE_INITIALISATION.out.depth,
-        PIPELINE_INITIALISATION.out.gmap,
-        PIPELINE_INITIALISATION.out.posfile,
-        PIPELINE_INITIALISATION.out.chunks,
-        PIPELINE_INITIALISATION.out.chunk_model,
+        steps,
+        tools,
+        PIPELINE_INITIALISATION.out.ch_input_target,
+        PIPELINE_INITIALISATION.out.ch_input_truth,
+        PIPELINE_INITIALISATION.out.ch_fasta_index,
+        PIPELINE_INITIALISATION.out.ch_panel,
+        PIPELINE_INITIALISATION.out.ch_regions,
+        PIPELINE_INITIALISATION.out.ch_depth,
+        PIPELINE_INITIALISATION.out.ch_map,
+        PIPELINE_INITIALISATION.out.ch_posfile,
+        PIPELINE_INITIALISATION.out.ch_chunks,
+        sheets_given,
         params.rename_chr,
-        params.max_chr_names
+        params.max_chr_names,
+        params_simulate,
+        params_panelprep,
+        params_impute,
+        params_validate,
+        params_multiqc,
+        params.seed,
+        params.outdir,
     )
     //
     // SUBWORKFLOW: Run completion tasks

nextflow.config

@@ -61,7 +61,7 @@ params {
     batch_size                 = 100
 
     // QUILT
-    ngen                       = 100
+    n_gen                      = 100
     buffer                     = 10000
 
     // STITCH
@@ -348,7 +348,7 @@ manifest {
     description     = """Phasing and imputation pipeline"""
     mainScript      = 'main.nf'
     defaultBranch   = 'main'
-    nextflowVersion = '!>=25.04.0'
+    nextflowVersion = '!>=25.10.0'
     version         = '1.2.0dev'
     doi             = 'https://doi.org/10.5281/zenodo.14329225'
 }
@@ -357,6 +357,7 @@ manifest {
 plugins {
     id 'nf-schema@2.5.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
     id 'nf-co2footprint@1.0.0-beta' // Calculate the carbon footprint of a Nextflow pipeline
+    id 'nf-core-utils@0.4.0'
 }
 
 // CO2 footprint calculation

nextflow_schema.json

@@ -468,7 +468,7 @@
                     "default": 10000,
                     "description": "Buffer of region to perform imputation over. So imputation is run form regionStart-buffer to regionEnd+buffer, and reported for regionStart to regionEnd, including the bases of regionStart and regionEnd."
                 },
-                "ngen": {
+                "n_gen": {
                     "type": "integer",
                     "default": 100,
                     "description": "Number of generations since founding of the population to use for imputation."

ro-crate-metadata.json

@@ -171,7 +171,7 @@
             "url": {
                 "@id": "https://www.nextflow.io/"
             },
-            "version": "!>=25.04.0"
+            "version": "!>=25.10.0"
         },
         {
             "@id": "#6b9b8e0a-2e44-4e58-a934-5726c0a3604e",

subworkflows/local/prepare_genome/main.nf

@@ -0,0 +1,50 @@
+//
+// Prepare reference genome files
+//
+
+include { SAMTOOLS_FAIDX } from '../../../modules/nf-core/samtools/faidx'
+
+workflow PREPARE_GENOME {
+    take:
+    genome         // genome name
+    fasta_path     // path to fasta
+    fasta_fai_path // path to fasta_fai
+    fasta_gzi_path // path to fasta_gzi
+
+    main:
+
+    def is_compressed = fasta_path.toString().endsWith('.gz') || fasta_path.toString().endsWith('.bgz')
+    ch_fasta  = channel.of([
+        [genome: genome],
+        file(fasta_path, checkIfExists:true),
+        []
+    ])
+
+    if (fasta_fai_path) {
+        ch_fai = channel.of(file(fasta_fai_path, checkIfExists:true))
+    } else {
+        SAMTOOLS_FAIDX(ch_fasta, false)
+        ch_fai = SAMTOOLS_FAIDX.out.fai.map{ _meta, fasta_fai -> fasta_fai }
+    }
+    if (is_compressed) {
+        if (fasta_gzi_path) {
+            ch_gzi = channel.of(file(fasta_gzi_path, checkIfExists:true))
+        } else if (!fasta_fai_path) {
+            ch_gzi = SAMTOOLS_FAIDX.out.gzi.map{ _meta, gzi -> gzi }
+        } else {
+            SAMTOOLS_FAIDX(ch_fasta, false)
+            ch_gzi = SAMTOOLS_FAIDX.out.gzi.map{ _meta, gzi -> gzi }
+        }
+    } else {
+        ch_gzi = channel.of([])
+    }
+
+    ch_fasta_fai_gzi = ch_fasta
+        .map{ meta, fasta, _fai -> [meta, fasta] }
+        .combine(ch_fai)
+        .combine(ch_gzi)
+        .collect()
+
+    emit:
+    ch_fasta_fai_gzi
+}