Merge branch 'master' into update-panaroo/run

* master:
  new module: indeppairwise (nf-core#3150)

modules/nf-core/plink/indeppairwise/main.nf

@@ -0,0 +1,43 @@
+
+process PLINK_INDEPPAIRWISE {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "bioconda::plink=1.90b6.21"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/plink:1.90b6.21--h779adbc_1':
+        'quay.io/biocontainers/plink:1.90b6.21--h779adbc_1' }"
+
+    input:
+    tuple val(meta), path(bed),  path(bim), path(fam)
+    val(window_size)
+    val(variant_count)
+    val(r2_threshold)
+
+    output:
+    tuple val(meta), path("*.prune.in")                    , emit: prunein
+    tuple val(meta), path("*.prune.out")    , optional:true, emit: pruneout
+    path "versions.yml"                                    , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    plink \\
+        --bed ${bed}  \\
+        --bim ${bim}  \\
+        --fam ${fam}  \\
+        --threads $task.cpus \\
+        --indep-pairwise ${window_size} ${variant_count} ${r2_threshold} \\
+        $args \\
+        --out $prefix
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        plink: \$(echo \$(plink --version) | sed 's/^PLINK v//;s/64.*//')
+    END_VERSIONS
+    """
+}

modules/nf-core/plink/indeppairwise/meta.yml

@@ -0,0 +1,68 @@
+name: plink_indeppairwise
+description: Produce a pruned subset of markers that are in approximate linkage equilibrium with each other. Pairs of variants in the current window with squared correlation greater than the threshold are noted and variants are greedily pruned from the window until no such pairs remain.
+keywords:
+  - plink
+  - indep pairwise
+  - variant pruning
+  - bim
+  - fam
+tools:
+  - "plink":
+      description: "Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner."
+      homepage: "https://www.cog-genomics.org/plink"
+      documentation: "https://www.cog-genomics.org/plink/1.9/data"
+      tool_dev_url: "https://www.cog-genomics.org/plink/1.9/dev"
+      licence: ["GPL"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bed:
+      type: file
+      description: PLINK binary biallelic genotype table file
+      pattern: "*.{bed}"
+  - bim:
+      type: file
+      description: PLINK extended MAP file
+      pattern: "*.{bim}"
+  - fam:
+      type: file
+      description: PLINK sample information file
+      pattern: "*.{fam}"
+  - window_size:
+      type: number
+      description: Window size in variant count or kilobase (if the 'kb' modifier is present) units, a variant count to shift the window at the end of each step, and a variance inflation factor (VIF) threshold.
+      pattern: "*.{}"
+  - variant_count:
+      type: number
+      description: Variant count to shift the window at the end of each step.
+      pattern: "*.{}"
+  - r2_threshold:
+      type: number
+      description: Pairwise r2 threshold. At each step, pairs of variants in the current window with squared correlation greater than the threshold are noted, and variants are greedily pruned from the window until no such pairs remain
+      pattern: "*.{}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - prunein:
+      type: file
+      description: File with IDs of pruned subset of markers that are in approximate linkage equilibrium with each other
+      pattern: "*.{prune.in}"
+  - pruneout:
+      type: file
+      description: File with IDs of excluded variants
+      pattern: "*.{prune.out}"
+
+authors:
+  - "@atrigila"

tests/config/pytest_modules.yml

@@ -2531,6 +2531,10 @@ plink/indep:
   - modules/nf-core/plink/indep/**
   - tests/modules/nf-core/plink/indep/**
 
+plink/indeppairwise:
+  - modules/nf-core/plink/indeppairwise/**
+  - tests/modules/nf-core/plink/indeppairwise/**
+
 plink/recode:
   - modules/nf-core/plink/recode/**
   - tests/modules/nf-core/plink/recode/**

tests/modules/nf-core/plink/indeppairwise/main.nf

@@ -0,0 +1,28 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PLINK_INDEPPAIRWISE } from '../../../../../modules/nf-core/plink/indeppairwise/main.nf'
+include { PLINK_VCF           } from '../../../../../modules/nf-core/plink/vcf/main.nf'
+
+workflow test_plink_indeppairwise {
+
+    input = [
+            [ id:'test', single_end:false ], // meta map
+            file("https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz", checkIfExists: true)
+            ]
+
+    PLINK_VCF ( input )
+
+    bed_ch = PLINK_VCF.out.bed
+    bim_ch = PLINK_VCF.out.bim
+    fam_ch = PLINK_VCF.out.fam
+
+    ch_bed_bim_fam = bed_ch.join(bim_ch).join(fam_ch)
+
+    ch_window_size = Channel.value(50)
+    ch_variant_count = Channel.value(5)
+    ch_r2_threshold = Channel.value(0.2)
+
+    PLINK_INDEPPAIRWISE ( ch_bed_bim_fam, ch_window_size, ch_variant_count, ch_r2_threshold )
+}

tests/modules/nf-core/plink/indeppairwise/nextflow.config

@@ -0,0 +1,8 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: PLINK_VCF {
+        ext.args = ' --make-bed --biallelic-only strict --vcf-half-call missing --allow-extra-chr'
+    }
+}

tests/modules/nf-core/plink/indeppairwise/test.yml

@@ -0,0 +1,17 @@
+- name: plink indeppairwise test_plink_indeppairwise
+  command: nextflow run ./tests/modules/nf-core/plink/indeppairwise -entry test_plink_indeppairwise -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/plink/indeppairwise/nextflow.config
+  tags:
+    - plink
+    - plink/indeppairwise
+  files:
+    - path: output/plink/test.bed
+      md5sum: 0cbb7bb2e4c9e23c75da1f338f9268bf
+    - path: output/plink/test.bim
+      md5sum: fe302f9edc5a217e55f1b6b17f187d2e
+    - path: output/plink/test.fam
+      md5sum: 619946963dc461d0e2ae4359da08eeb2
+    - path: output/plink/test.prune.in
+      md5sum: 50c7ab703f7b5c01d7c7ddc7517aea37
+    - path: output/plink/test.prune.out
+      md5sum: 6104a59d98bda81014870ecd059573fb
+    - path: output/plink/versions.yml