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atrigilaatrigila
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Merge pull request #40 from atrigila/add_tool_stitch
Add tool stitch
2 parents 411233e + 7a6c61d commit d8b1980

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-388
lines changed

34 files changed

+1173
-388
lines changed

‎.github/workflows/ci.yml

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@@ -31,6 +31,7 @@ jobs:
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- "test"
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- "test_sim"
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- "test_quilt"
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- "test_stitch"
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steps:
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- name: Check out pipeline code
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uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4

‎.nf-core.yml

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@@ -1 +1,3 @@
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repository_type: pipeline
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lint:
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subworkflow_changes: false

‎assets/schema_posfile.json

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{
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"$schema": "http://json-schema.org/draft-07/schema",
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"$id": "https://raw.githubusercontent.com/nf-core/phaseimpute/master/assets/schema_posfile.json",
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"title": "nf-core/phaseimpute pipeline - params.posfile schema",
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"description": "Schema for the file provided with params.posfile",
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"type": "array",
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"items": {
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"type": "object",
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"properties": {
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"chr": {
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"type": "string",
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"pattern": "^\\S+$",
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"errorMessage": "Chromosome name must be provided as a string and cannot contain spaces",
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"meta": ["chr"]
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},
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"file": {
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"type": "string",
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"pattern": "^\\S+\\.txt$",
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"errorMessage": "Posfile per chromosome must be provided. Must have .txt extension"
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}
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},
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"required": ["chr", "file"]
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}
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}

‎conf/steps/imputation_glimpse1.config

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@@ -81,4 +81,26 @@ process {
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path: { "${params.outdir}/imputation/glimpse1" }
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]
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}
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withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_GLIMPSE1:.*' {
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publishDir = [
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[
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path: { "${params.outdir}/imputation/glimpse1/concat" },
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mode: params.publish_dir_mode,
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],
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]
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}
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withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_GLIMPSE1:BCFTOOLS_CONCAT' {
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ext.args = {[
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"--ligate",
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"--output-type z",
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].join(" ").trim()}
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ext.prefix = { "${meta.id}_glimpse1" }
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}
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withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_GLIMPSE1:BCFTOOLS_INDEX' {
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ext.args = "--tbi"
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ext.prefix = { "${meta.id}_glimpse1" }
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}
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}

‎conf/steps/imputation_quilt.config

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@@ -39,50 +39,6 @@ process {
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ext.prefix = { "${meta.id}_${meta.chr}" }
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}
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withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:MAKE_CHUNKS:BCFTOOLS_INDEX' {
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cpus = 2
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memory = 400.MB
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maxRetries = 2
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}
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withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:MAKE_CHUNKS:BCFTOOLS_INDEX_2' {
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ext.args = '--tbi'
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cpus = 2
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memory = 400.MB
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maxRetries = 2
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}
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withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:MAKE_CHUNKS:BCFTOOLS_INDEX_3' {
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ext.args = '--tbi'
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cpus = 2
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memory = 400.MB
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maxRetries = 2
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}
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withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:MAKE_CHUNKS:BCFTOOLS_VIEW' {
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ext.args = '-v snps -Oz'
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ext.prefix = { "${meta.id}_${meta.chr}_biallelic" }
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cpus = 2
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memory = 400.MB
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maxRetries = 2
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}
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withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:MAKE_CHUNKS:BCFTOOLS_NORM' {
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ext.args = '-m +any --output-type z'
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ext.prefix = { "${meta.id}_${meta.chr}_multiallelic" }
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cpus = 2
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memory = 400.MB
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maxRetries = 2
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}
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withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:MAKE_CHUNKS:BCFTOOLS_CONVERT' {
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ext.args = '--haplegendsample test'
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ext.prefix = { "${meta.id}_${meta.chr}_convert" }
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cpus = 2
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memory = 400.MB
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maxRetries = 2
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}
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withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:IMPUTE_QUILT:.*' {
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publishDir = [
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[
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publishDir = [enabled: false]
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}
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withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:IMPUTE_QUILT:INDEX1' {
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withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:IMPUTE_QUILT:BCFTOOLS_INDEX_1' {
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ext.args = "--tbi"
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publishDir = [enabled: false]
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}
@@ -107,8 +63,30 @@ process {
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ext.prefix = { "${meta.id}_R${meta.region.replace(':','_')}.impute.annotate" }
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}
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withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:IMPUTE_QUILT:INDEX2' {
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withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:IMPUTE_QUILT:BCFTOOLS_INDEX_2' {
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ext.args = "--tbi"
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}
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withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_QUILT:.*' {
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publishDir = [
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[
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path: { "${params.outdir}/imputation/quilt/concat" },
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mode: params.publish_dir_mode,
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],
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]
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}
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withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_QUILT:BCFTOOLS_CONCAT' {
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ext.args = {[
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"--ligate",
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"--output-type z",
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].join(" ").trim()}
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ext.prefix = { "${meta.id}_quilt" }
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}
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withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_QUILT:BCFTOOLS_INDEX' {
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ext.args = "--tbi"
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ext.prefix = { "${meta.id}_quilt" }
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}
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}

‎conf/steps/imputation_stitch.config

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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Config file for defining DSL2 per module options and publishing paths
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Available keys to override module options:
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ext.args = Additional arguments appended to command in module.
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ext.args2 = Second set of arguments appended to command in module (multi-tool modules).
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ext.args3 = Third set of arguments appended to command in module (multi-tool modules).
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ext.prefix = File name prefix for output files.
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----------------------------------------------------------------------------------------
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*/
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process {
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withName: CUSTOM_DUMPSOFTWAREVERSIONS {
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publishDir = [
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path: { "${params.outdir}/pipeline_info" },
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mode: params.publish_dir_mode,
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pattern: '*_versions.yml'
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]
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}
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withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:PREPARE_POSFILE_TSV:.*' {
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publishDir = [
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path: { "${params.outdir}/prep_panel/posfile/" },
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mode: params.publish_dir_mode,
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enabled: true
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]
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}
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withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:PREPARE_POSFILE_TSV:GAWK' {
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ext.args = "'{ key = \$1 FS \$2 } !seen[key]++'"
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ext.prefix = { "${meta.id}_${meta.chr}_posfile_stitch" }
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ext.suffix = ".txt"
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}
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withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:PREPARE_INPUT_STITCH:BCFTOOLS_NORM' {
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ext.args = '-m +any --output-type z'
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ext.prefix = { "${meta.id}_${meta.chr}_multiallelic" }
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maxRetries = 2
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publishDir = [enabled: false]
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}
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withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:PREPARE_INPUT_STITCH:BCFTOOLS_VIEW' {
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ext.args = '-v snps -Oz'
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ext.prefix = { "${meta.id}_${meta.chr}_biallelic" }
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maxRetries = 2
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publishDir = [enabled: false]
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}
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withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:PREPARE_INPUT_STITCH:BCFTOOLS_INDEX' {
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maxRetries = 2
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publishDir = [enabled: false]
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}
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withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:PREPARE_INPUT_STITCH:BCFTOOLS_INDEX_2' {
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ext.args = '--tbi'
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maxRetries = 2
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publishDir = [enabled: false]
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}
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withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:PREPARE_POSFILE_TSV:BCFTOOLS_QUERY' {
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ext.args = [
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"-f'%CHROM\t%POS\t%REF\t%ALT\\n'",
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].join(' ')
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ext.prefix = { "${meta.id}_${meta.chr}_posfile_stitch" }
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publishDir = [enabled: false]
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}
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withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_IMPUTE_STITCH:.*' {
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publishDir = [
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path: { "${params.outdir}/imputation/stitch/" },
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mode: params.publish_dir_mode,
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enabled: true
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]
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}
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withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_IMPUTE_STITCH:BCFTOOLS_INDEX' {
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ext.args = '--tbi'
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maxRetries = 2
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publishDir = [enabled: false]
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}
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withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_STITCH:.*' {
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publishDir = [
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[
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path: { "${params.outdir}/imputation/stitch/concat" },
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mode: params.publish_dir_mode,
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],
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]
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}
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withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_STITCH:BCFTOOLS_CONCAT' {
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ext.args = {[
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"--ligate",
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"--output-type z",
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].join(" ").trim()}
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ext.prefix = { "${meta.id}_stitch" }
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}
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withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_STITCH:BCFTOOLS_INDEX' {
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ext.args = "--tbi"
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ext.prefix = { "${meta.id}_stitch" }
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}
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}

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