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add subworkflow bam_qc_picard
This commit is contained in:
Matthias De Smet
parent
d07d270743
commit
d85f9c7011
4 changed files with 161 additions and 0 deletions
43
subworkflows/nf-core/bam_qc_picard/main.nf
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43
subworkflows/nf-core/bam_qc_picard/main.nf
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//
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// Run QC steps on BAM/CRAM files using Picard
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//
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params.options = [:]
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include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../modules/picardcollectmultiplemetrics/main' addParams( options: params.options )
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include { PICARD_COLLECTWGSMETRICS } from '../../../modules/picardcollectwgsmetrics/main' addParams( options: params.options )
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include { PICARD_COLLECTHSMETRICS } from '../../../modules/picardcollecthsmetrics/main' addParams( options: params.options )
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workflow BAM_QC_PICARD {
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take:
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ch_bam_bai // channel: [ val(meta), [ bam ], [bai/csi] ]
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ch_fasta // channel: [ fasta ]
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ch_bait_interval // channel: [ bait_interval ]
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ch_target_interval // channel: [ target_interval ]
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main:
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ch_versions = Channel.empty()
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PICARD_COLLECTMULTIPLEMETRICS( ch_bam_bai, ch_fasta] )
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ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions.first())
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if (!ch_bait_interval.isEmpty() || !ch_target_interval.isEmpty()) {
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if (ch_bait_interval.isEmpty()) {
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throw new Error("Bait interval channel is empty")
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}
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if (ch_target_interval.isEmpty()) {
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throw new Error("Target interval channel is empty")
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}
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PICARD_COLLECTHSMETRICS( ch_bam_bai, ch_fasta, ch_bait_interval, ch_target_interval )
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ch_versions = ch_versions.mix(PICARD_COLLECTHSMETRICS.out.versions.first())
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} else {
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PICARD_COLLECTWGSMETRICS( ch_bam_bai, ch_fasta )
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ch_versions = ch_versions.mix(PICARD_COLLECTWGSMETRICS.out.versions.first())
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}
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emit:
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hs_metrics = PICARD_COLLECTHSMETRICS.out.hs_metrics // channel: [ val(meta), [ hs_metrics ] ]
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wgs_metrics = PICARD_COLLECTWGSMETRICS.out.metrics // channel: [ val(meta), [ wgs_metrics ] ]
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multiple_metrics = PICARD_COLLECTMULTIPLEMETRICS.out.metrics // channel: [ val(meta), [ multiple_metrics ] ]
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versions = ch_versions // channel: [ versions.yml ]
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}
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64
subworkflows/nf-core/bam_qc_picard/meta.yml
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64
subworkflows/nf-core/bam_qc_picard/meta.yml
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name: bam_qc
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description: Produces comprehensive statistics from BAM file
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keywords:
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- statistics
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- counts
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- hs_metrics
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- wgs_metrics
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- bam
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- sam
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- cram
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modules:
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- picard/collectmultiplemetrics
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- picard/collectwgsmetrics
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- picard/collecthsmetrics
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- bam:
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type: file
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description: BAM/CRAM/SAM file
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pattern: "*.{bam,cram,sam}"
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- bai:
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type: file
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description: Index for BAM/CRAM/SAM file
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pattern: "*.{bai,crai,sai}"
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- fasta:
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type: optional file
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description: Reference file the CRAM was created with
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pattern: "*.{fasta,fa}"
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- bait_intervals:
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type: optional file
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description: An interval list file that contains the locations of the baits used.
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pattern: "baits.interval_list"
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- target_intervals:
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type: optional file
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description: An interval list file that contains the locations of the targets.
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pattern: "targets.interval_list"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- hs_metrics:
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type: file
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description: Alignment metrics files generated by picard CollectHsMetrics
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pattern: "*_collecthsmetrics.txt"
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- wgs_metrics:
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type: file
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description: Alignment metrics files generated by picard CollectWgsMetrics
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pattern: "*_{metrics}"
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- multiple_metrics:
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type: file
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description: Alignment metrics files generated by picard CollectMultipleMetrics
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pattern: "*_{metrics}"
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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authors:
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- "@matthdsm"
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21
tests/subworkflows/nf-core/bam_qc_picard/main.nf
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tests/subworkflows/nf-core/bam_qc_picard/main.nf
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { BAM_QC_PICARD } from '../../../../subworkflows/nf-core/bam_qc_picard/main' addParams([:])
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workflow test_bam_qc_picard_wgs {
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input = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
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]
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BAM_QC_PICARD ( input, [], [], [] )
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}
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workflow test_bam_qc_picard_targetted {
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input = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
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]
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BAM_QC_PICARD ( input, [], file(params.test_data['sarscov2']['genome']['baits_interval_list'], checkIfExists: true), file(params.test_data['sarscov2']['genome']['targets_interval_list'], checkIfExists: true) )
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}
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33
tests/subworkflows/nf-core/bam_qc_picard/test.yml
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tests/subworkflows/nf-core/bam_qc_picard/test.yml
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- name: bam qc picard wgs
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command: nextflow run ./tests/subworkflows/nf-core/bam_qc_picard -entry test_bam_qc_picard_wgs -c tests/config/nextflow.config
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tags:
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- subworkflows
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# - subworkflows/bam_qc_picard
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# Modules
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# - picard
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# - picard/collectmultiplemetrics
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# - picard/collectwgsmetrics
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files:
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- path: ./output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
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- path: ./output/picard/test.CollectMultipleMetrics.insert_size_metrics
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- path: ./output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
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- path: ./output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
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- path: ./output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
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- path: ./output/picard/test.CollectWgsMetrics.coverage_metrics
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- name: bam qc picard targetted
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command: nextflow run ./tests/subworkflows/nf-core/bam_qc_picard -entry test_bam_qc_picard_targetted -c tests/config/nextflow.config
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tags:
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- subworkflows
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# - subworkflows/bam_qc_picard
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# Modules
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# - picard
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# - picard/collectmultiplemetrics
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# - picard/collecthsmetrics
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files:
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- path: ./output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
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- path: ./output/picard/test.CollectMultipleMetrics.insert_size_metrics
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- path: ./output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
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- path: ./output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
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- path: ./output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
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- path: ./output/picard/test_collecthsmetrics.txt
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