mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-20 23:32:05 +00:00
Update umitools/dedup module to make --output-stats optional
This commit is contained in:
Harshil Patel
parent
91f9a0711d
commit
84f02a08a5
5 changed files with 135 additions and 69 deletions
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@ -9,12 +9,13 @@ process UMITOOLS_DEDUP {
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input:
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tuple val(meta), path(bam), path(bai)
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val get_output_stats
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output:
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tuple val(meta), path("*.bam") , emit: bam
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tuple val(meta), path("*edit_distance.tsv"), emit: tsv_edit_distance
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tuple val(meta), path("*per_umi.tsv") , emit: tsv_per_umi
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tuple val(meta), path("*per_position.tsv") , emit: tsv_umi_per_position
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tuple val(meta), path("*edit_distance.tsv"), optional:true, emit: tsv_edit_distance
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tuple val(meta), path("*per_umi.tsv") , optional:true, emit: tsv_per_umi
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tuple val(meta), path("*per_position.tsv") , optional:true, emit: tsv_umi_per_position
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path "versions.yml" , emit: versions
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when:
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@ -24,12 +25,13 @@ process UMITOOLS_DEDUP {
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def paired = meta.single_end ? "" : "--paired"
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def stats = get_output_stats ? "--output-stats $prefix" : ""
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"""
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umi_tools \\
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dedup \\
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-I $bam \\
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-S ${prefix}.bam \\
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--output-stats $prefix \\
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$stats \\
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$paired \\
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$args
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@ -26,6 +26,10 @@ input:
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description: |
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BAM index files corresponding to the input BAM file.
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pattern: "*.{bai}"
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- get_output_stats:
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type: boolean
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description: |
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Whether or not to generate output stats.
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output:
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- meta:
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type: map
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@ -12,45 +12,72 @@ include { UMITOOLS_DEDUP } from '../../../../modules/umitools/dedup/main.nf'
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// Test with no UMI
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//
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workflow test_umitools_dedup_no_umi {
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input = [ [ id:'test'], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ],
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[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ]
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input = [
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[ id:'test'], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
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]
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get_output_stats = false
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UMITOOLS_DEDUP ( input )
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UMITOOLS_DEDUP ( input, get_output_stats )
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}
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//
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// Test with single-end data
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// Test with single-end data without --output-stats
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//
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workflow test_umitools_dedup_single_end {
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input = [ [ id:'test', single_end:true ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
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workflow test_umitools_dedup_single_end_no_stats {
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input = [
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[ id:'test', single_end:true ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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get_output_stats = false
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UMITOOLS_EXTRACT ( input )
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BWA_INDEX ( fasta )
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BWA_MEM ( UMITOOLS_EXTRACT.out.reads, BWA_INDEX.out.index, true )
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SAMTOOLS_INDEX ( BWA_MEM.out.bam )
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UMITOOLS_DEDUP(BWA_MEM.out.bam.join(SAMTOOLS_INDEX.out.bai, by: [0]))
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UMITOOLS_DEDUP ( BWA_MEM.out.bam.join(SAMTOOLS_INDEX.out.bai, by: [0]), get_output_stats )
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}
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//
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// Test with paired-end data
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// Test with paired-end data without --output-stats
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//
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workflow test_umitools_dedup_paired_end {
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input = [ [ id:'test', single_end:false ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
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workflow test_umitools_dedup_paired_end_no_stats {
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input = [
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[ id:'test', single_end:false ], // meta map
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[
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file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
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]
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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get_output_stats = false
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UMITOOLS_EXTRACT ( input )
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BWA_INDEX ( fasta )
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BWA_MEM ( UMITOOLS_EXTRACT.out.reads, BWA_INDEX.out.index, true )
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SAMTOOLS_INDEX ( BWA_MEM.out.bam )
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UMITOOLS_DEDUP(BWA_MEM.out.bam.join(SAMTOOLS_INDEX.out.bai, by: [0]))
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UMITOOLS_DEDUP ( BWA_MEM.out.bam.join(SAMTOOLS_INDEX.out.bai, by: [0]), get_output_stats )
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}
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//
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// Test with paired-end data with --output-stats
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//
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workflow test_umitools_dedup_paired_end_stats {
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input = [
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[ id:'test', single_end:false ], // meta map
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[
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file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
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]
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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get_output_stats = true
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UMITOOLS_EXTRACT ( input )
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BWA_INDEX ( fasta )
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BWA_MEM ( UMITOOLS_EXTRACT.out.reads, BWA_INDEX.out.index, true )
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SAMTOOLS_INDEX ( BWA_MEM.out.bam )
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UMITOOLS_DEDUP ( BWA_MEM.out.bam.join(SAMTOOLS_INDEX.out.bai, by: [0]), get_output_stats )
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}
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@ -7,11 +7,7 @@ process {
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}
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withName: UMITOOLS_DEDUP {
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ext.args = ''
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ext.prefix = 'dedup'
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ext.prefix = { "${meta.id}.dedup" }
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}
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withName: BWA_MEM {
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ext.args2 = ''
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}
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}
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@ -1,54 +1,91 @@
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- name: umitools dedup test_umitools_dedup_no_umi
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command: nextflow run tests/modules/umitools/dedup -entry test_umitools_dedup_no_umi -c tests/config/nextflow.config
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command: nextflow run ./tests/modules/umitools/dedup -entry test_umitools_dedup_no_umi -c ./tests/config/nextflow.config -c ./tests/modules/umitools/dedup/nextflow.config
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tags:
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- umitools/dedup
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- umitools
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files:
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- path: output/umitools/dedup.bam
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- path: output/umitools/test.dedup.bam
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md5sum: 53b4edc399db81b87d2343e78af73cf0
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- path: output/umitools/dedup_edit_distance.tsv
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md5sum: 65186b0964e2f8d970cc04d736d8b119
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- path: output/umitools/dedup_per_umi.tsv
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md5sum: 8e6783a4a79437b095f095f2aefe7c01
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- path: output/umitools/dedup_per_umi_per_position.tsv
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md5sum: 9386db4a104b8e4e32f3ca4a84efa4ac
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- path: output/umitools/versions.yml
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md5sum: 4aaaa33565bcd9a984255139933d6446
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- name: umitools dedup test_umitools_dedup_single_end
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command: nextflow run tests/modules/umitools/dedup -entry test_umitools_dedup_single_end -c tests/config/nextflow.config
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- name: umitools dedup test_umitools_dedup_single_end_no_stats
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command: nextflow run ./tests/modules/umitools/dedup -entry test_umitools_dedup_single_end_no_stats -c ./tests/config/nextflow.config -c ./tests/modules/umitools/dedup/nextflow.config
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tags:
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- umitools
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- umitools/dedup
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- umitools
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files:
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- path: output/bwa/bwa/genome.amb
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md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
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- path: output/bwa/bwa/genome.ann
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md5sum: c32e11f6c859f166c7525a9c1d583567
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- path: output/bwa/bwa/genome.bwt
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md5sum: 0469c30a1e239dd08f68afe66fde99da
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- path: output/bwa/bwa/genome.pac
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md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
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- path: output/bwa/bwa/genome.sa
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md5sum: ab3952cabf026b48cd3eb5bccbb636d1
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- path: output/bwa/test.bam
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md5sum: ea41a3cdca1856b22845e1067fd31f37
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- path: output/bwa/versions.yml
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md5sum: ce4d987f2c53f4c01b31d210c357b24a
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md5sum: 3ecbe569cadb9b6c881917ce60779f75
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- path: output/samtools/test.bam.bai
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md5sum: 095af0ad3921212597ffd7c342ecd5a0
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- path: output/samtools/versions.yml
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md5sum: 69b7cde627c9b4e8403dfc125db71cc7
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- path: output/umitools/dedup.bam
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md5sum: d95df177063432748ff33f473910cb1e
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- path: output/umitools/versions.yml
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md5sum: 730e768dd199d2f5bfb6fd0850446344
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- path: output/umitools/test.dedup.bam
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md5sum: 8f7c519e110d6515d858eda6b16727ac
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- path: output/umitools/test.umi_extract.fastq.gz
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- path: output/umitools/test.umi_extract.log
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- name: umitools dedup test_umitools_dedup_paired_end
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command: nextflow run tests/modules/umitools/dedup -entry test_umitools_dedup_paired_end -c tests/config/nextflow.config
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- name: umitools dedup test_umitools_dedup_paired_end_no_stats
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command: nextflow run ./tests/modules/umitools/dedup -entry test_umitools_dedup_paired_end_no_stats -c ./tests/config/nextflow.config -c ./tests/modules/umitools/dedup/nextflow.config
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tags:
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- umitools
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- umitools/dedup
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- umitools
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files:
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- path: output/bwa/bwa/genome.amb
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md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
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- path: output/bwa/bwa/genome.ann
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md5sum: c32e11f6c859f166c7525a9c1d583567
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- path: output/bwa/bwa/genome.bwt
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md5sum: 0469c30a1e239dd08f68afe66fde99da
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- path: output/bwa/bwa/genome.pac
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md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
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- path: output/bwa/bwa/genome.sa
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md5sum: ab3952cabf026b48cd3eb5bccbb636d1
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- path: output/bwa/test.bam
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md5sum: 1ad786cae0ff2254c655e3a206929617
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- path: output/bwa/versions.yml
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md5sum: b524c5ddf61c20f4a0a93ae8fc78b851
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md5sum: e7dcbac1825bf210409b762dbb4fec8f
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- path: output/samtools/test.bam.bai
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md5sum: 7496f4056a8e86327ca93e350f282fc2
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- path: output/samtools/versions.yml
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md5sum: 72fc2ab934fd4bca0f7f14a705530d34
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- path: output/umitools/dedup.bam
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md5sum: e8d1eae2aacef76254948c5568e94555
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- path: output/umitools/versions.yml
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md5sum: fd39e05042d354b3d8de49b617d3183d
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md5sum: f75780d1de7860329b7fb4afeadc4bed
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- path: output/umitools/test.dedup.bam
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md5sum: d75284de88b05569a66667e5b9936be9
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- path: output/umitools/test.umi_extract.log
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- path: output/umitools/test.umi_extract_1.fastq.gz
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- path: output/umitools/test.umi_extract_2.fastq.gz
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- name: umitools dedup test_umitools_dedup_paired_end_stats
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command: nextflow run ./tests/modules/umitools/dedup -entry test_umitools_dedup_paired_end_stats -c ./tests/config/nextflow.config -c ./tests/modules/umitools/dedup/nextflow.config
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tags:
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- umitools/dedup
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- umitools
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files:
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- path: output/bwa/bwa/genome.amb
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md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
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- path: output/bwa/bwa/genome.ann
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md5sum: c32e11f6c859f166c7525a9c1d583567
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- path: output/bwa/bwa/genome.bwt
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md5sum: 0469c30a1e239dd08f68afe66fde99da
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- path: output/bwa/bwa/genome.pac
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md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
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- path: output/bwa/bwa/genome.sa
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md5sum: ab3952cabf026b48cd3eb5bccbb636d1
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- path: output/bwa/test.bam
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md5sum: e7dcbac1825bf210409b762dbb4fec8f
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- path: output/samtools/test.bam.bai
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md5sum: f75780d1de7860329b7fb4afeadc4bed
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- path: output/umitools/test.dedup.bam
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md5sum: d75284de88b05569a66667e5b9936be9
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- path: output/umitools/test.dedup_edit_distance.tsv
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md5sum: c247a49b58768e6e2e86a6c08483e612
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- path: output/umitools/test.dedup_per_umi.tsv
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md5sum: 10e35ca37f2bfb521ac6dd7314951a68
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- path: output/umitools/test.dedup_per_umi_per_position.tsv
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md5sum: 2e1a12e6f720510880068deddeefe063
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- path: output/umitools/test.umi_extract.log
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- path: output/umitools/test.umi_extract_1.fastq.gz
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- path: output/umitools/test.umi_extract_2.fastq.gz
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