mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
Merge branch 'master' into bowtie2-test-fix
This commit is contained in:
commit
9f6a1ae4a4
16 changed files with 277 additions and 91 deletions
40
modules/genomescope2/main.nf
Normal file
40
modules/genomescope2/main.nf
Normal file
|
@ -0,0 +1,40 @@
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|||
process GENOMESCOPE2 {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::genomescope2=2.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/genomescope2:2.0--py310r41hdfd78af_5':
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'quay.io/biocontainers/genomescope2:2.0--py310r41hdfd78af_5' }"
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input:
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tuple val(meta), path(histogram)
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output:
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tuple val(meta), path("*_linear_plot.png") , emit: linear_plot_png
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tuple val(meta), path("*_transformed_linear_plot.png"), emit: transformed_linear_plot_png
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tuple val(meta), path("*_log_plot.png") , emit: log_plot_png
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tuple val(meta), path("*_transformed_log_plot.png") , emit: transformed_log_plot_png
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tuple val(meta), path("*_model.txt") , emit: model
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tuple val(meta), path("*_summary.txt") , emit: summary
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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||||
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script:
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def args = task.ext.args ?: ''
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prefix = task.ext.prefix ?: "${meta.id}"
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"""
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genomescope2 \\
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--input $histogram \\
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$args \\
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--output . \\
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--name_prefix $prefix
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cat <<-END_VERSIONS > versions.yml
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'${task.process}':
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genomescope2: \$( genomescope2 -v | sed 's/GenomeScope //' )
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END_VERSIONS
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||||
"""
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||||
}
|
67
modules/genomescope2/meta.yml
Normal file
67
modules/genomescope2/meta.yml
Normal file
|
@ -0,0 +1,67 @@
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|||
name: "genomescope2"
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description: Estimate genome heterozygosity, repeat content, and size from sequencing reads using a kmer-based statistical approach
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keywords:
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- "genome size"
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- "genome heterozygosity"
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- "repeat content"
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tools:
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- "genomescope2":
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description: "Reference-free profiling of polyploid genomes"
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homepage: "http://qb.cshl.edu/genomescope/genomescope2.0/"
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documentation: "https://github.com/tbenavi1/genomescope2.0/blob/master/README.md"
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tool_dev_url: "https://github.com/tbenavi1/genomescope2.0"
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doi: "https://doi.org/10.1038/s41467-020-14998-3"
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||||
licence: "['Apache License, Version 2.0 (Apache-2.0)']"
|
||||
|
||||
input:
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||||
- meta:
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||||
type: map
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description: |
|
||||
Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- histogram:
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type: file
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||||
description: A K-mer histogram file
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pattern: "*.hist"
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||||
|
||||
output:
|
||||
- meta:
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type: map
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||||
description: |
|
||||
Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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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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- linear_plot_png:
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type: file
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description: A genomescope2 linear plot in PNG format
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pattern: "*_linear_plot.png"
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- linear_plot_png:
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type: file
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||||
description: A genomescope2 linear plot in PNG format
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pattern: "*_linear_plot.png"
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- transformed_linear_plot_png:
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type: file
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||||
description: A genomescope2 transformed linear plot in PNG format
|
||||
pattern: "*_transformed_linear_plot.png"
|
||||
- log_plot_png:
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||||
type: file
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||||
description: A genomescope2 log plot in PNG format
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pattern: "*_log_plot.png"
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- transformed_log_plot_png:
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type: file
|
||||
description: A genomescope2 transformed log plot in PNG format
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pattern: "*_transformed_log_plot.png"
|
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- model:
|
||||
type: file
|
||||
description: Genomescope2 model fit summary
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pattern: "*_model.txt"
|
||||
- summary:
|
||||
type: file
|
||||
description: Genomescope2 histogram summary
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pattern: "*_summary.txt"
|
||||
|
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authors:
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- "@mahesh-panchal"
|
|
@ -35,12 +35,13 @@ process RTGTOOLS_VCFEVAL {
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|||
def eval_regions = evaluation_regions ? "--evaluation-regions=$evaluation_regions" : ""
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def truth_index = truth_vcf_tbi ? "" : "rtg index $truth_vcf"
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def query_index = query_vcf_tbi ? "" : "rtg index $query_vcf"
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def avail_mem = task.memory.toGiga() + "G"
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"""
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$truth_index
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$query_index
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rtg vcfeval \\
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rtg RTG_MEM=$avail_mem vcfeval \\
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$args \\
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--baseline=$truth_vcf \\
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$bed_regions \\
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|
|
|
@ -1,34 +0,0 @@
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//
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// Download FASTQ sequencing reads from the NCBI's Sequence Read Archive (SRA).
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//
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params.prefetch_options = [:]
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params.fasterqdump_options = [:]
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|
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include { SRATOOLS_PREFETCH } from '../../../modules/sratools/prefetch/main' addParams( options: params.prefetch_options )
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include { SRATOOLS_FASTERQDUMP } from '../../../modules/sratools/fasterqdump/main' addParams( options: params.fasterqdump_options )
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workflow SRA_FASTQ {
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take:
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sra_ids // channel: [ val(meta), val(id) ]
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|
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main:
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ch_versions = Channel.empty()
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|
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//
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// Prefetch sequencing reads in SRA format.
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//
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SRATOOLS_PREFETCH ( sra_ids )
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ch_versions = ch_versions.mix( SRATOOLS_PREFETCH.out.versions.first() )
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|
||||
//
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||||
// Convert the SRA format into one or more compressed FASTQ files.
|
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//
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SRATOOLS_FASTERQDUMP ( SRATOOLS_PREFETCH.out.sra )
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ch_versions = ch_versions.mix( SRATOOLS_FASTERQDUMP.out.versions.first() )
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|
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emit:
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reads = SRATOOLS_FASTERQDUMP.out.reads // channel: [ val(meta), [ reads ] ]
|
||||
versions = ch_versions // channel: [ versions.yml ]
|
||||
}
|
38
subworkflows/nf-core/srafastq/main.nf
Normal file
38
subworkflows/nf-core/srafastq/main.nf
Normal file
|
@ -0,0 +1,38 @@
|
|||
include { CUSTOM_SRATOOLSNCBISETTINGS } from '../../../modules/custom/sratoolsncbisettings/main'
|
||||
include { SRATOOLS_PREFETCH } from '../../../modules/sratools/prefetch/main'
|
||||
include { SRATOOLS_FASTERQDUMP } from '../../../modules/sratools/fasterqdump/main'
|
||||
|
||||
/**
|
||||
* Download FASTQ sequencing reads from the NCBI's Sequence Read Archive (SRA).
|
||||
*/
|
||||
workflow SRAFASTQ {
|
||||
take:
|
||||
sra_ids // channel: [ val(meta), val(id) ]
|
||||
|
||||
main:
|
||||
|
||||
ch_versions = Channel.empty()
|
||||
|
||||
//
|
||||
// Detect existing NCBI user settings or create new ones.
|
||||
//
|
||||
CUSTOM_SRATOOLSNCBISETTINGS()
|
||||
def settings = CUSTOM_SRATOOLSNCBISETTINGS.out.ncbi_settings
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||||
ch_versions = ch_versions.mix( CUSTOM_SRATOOLSNCBISETTINGS.out.versions )
|
||||
|
||||
//
|
||||
// Prefetch sequencing reads in SRA format.
|
||||
//
|
||||
SRATOOLS_PREFETCH ( sra_ids, settings )
|
||||
ch_versions = ch_versions.mix( SRATOOLS_PREFETCH.out.versions.first() )
|
||||
|
||||
//
|
||||
// Convert the SRA format into one or more compressed FASTQ files.
|
||||
//
|
||||
SRATOOLS_FASTERQDUMP ( SRATOOLS_PREFETCH.out.sra, settings )
|
||||
ch_versions = ch_versions.mix( SRATOOLS_FASTERQDUMP.out.versions.first() )
|
||||
|
||||
emit:
|
||||
reads = SRATOOLS_FASTERQDUMP.out.reads // channel: [ val(meta), [ reads ] ]
|
||||
versions = ch_versions // channel: [ versions.yml ]
|
||||
}
|
|
@ -1,11 +1,14 @@
|
|||
name: sra_fastq
|
||||
description: Download FASTQ sequencing reads from the NCBI's Sequence Read Archive (SRA).
|
||||
keywords:
|
||||
- SRA
|
||||
- NCBI
|
||||
- sequencing
|
||||
- FASTQ
|
||||
- prefetch
|
||||
- dump
|
||||
- fasterq-dump
|
||||
modules:
|
||||
- custom/sratoolsncbisettings
|
||||
- sratools/prefetch
|
||||
- sratools/fasterqdump
|
||||
input:
|
||||
|
@ -17,7 +20,7 @@ input:
|
|||
- id:
|
||||
type: string
|
||||
description: >
|
||||
SRA identifier.
|
||||
SRA run identifier.
|
||||
# TODO Update when we decide on a standard for subworkflow docs
|
||||
output:
|
||||
- meta:
|
|
@ -839,6 +839,10 @@ genmap/mappability:
|
|||
- modules/genmap/mappability/**
|
||||
- tests/modules/genmap/mappability/**
|
||||
|
||||
genomescope2:
|
||||
- modules/genomescope2/**
|
||||
- tests/modules/genomescope2/**
|
||||
|
||||
genrich:
|
||||
- modules/genrich/**
|
||||
- tests/modules/genrich/**
|
||||
|
@ -1647,14 +1651,14 @@ samtools/bam2fq:
|
|||
- modules/samtools/bam2fq/**
|
||||
- tests/modules/samtools/bam2fq/**
|
||||
|
||||
samtools/convert:
|
||||
- modules/samtools/convert/**
|
||||
- tests/modules/samtools/convert/**
|
||||
|
||||
samtools/collatefastq:
|
||||
- modules/samtools/collatefastq/**
|
||||
- tests/modules/samtools/collatefastq/**
|
||||
|
||||
samtools/convert:
|
||||
- modules/samtools/convert/**
|
||||
- tests/modules/samtools/convert/**
|
||||
|
||||
samtools/depth:
|
||||
- modules/samtools/depth/**
|
||||
- tests/modules/samtools/depth/**
|
||||
|
|
19
tests/modules/genomescope2/main.nf
Normal file
19
tests/modules/genomescope2/main.nf
Normal file
|
@ -0,0 +1,19 @@
|
|||
#!/usr/bin/env nextflow
|
||||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { MERYL_COUNT } from '../../../modules/meryl/count/main.nf'
|
||||
include { MERYL_HISTOGRAM } from '../../../modules/meryl/histogram/main.nf'
|
||||
include { GENOMESCOPE2 } from '../../../modules/genomescope2/main.nf'
|
||||
|
||||
workflow test_genomescope2 {
|
||||
|
||||
input = [
|
||||
[ id:'test', single_end:false ], // meta map
|
||||
file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true)
|
||||
]
|
||||
|
||||
MERYL_COUNT ( input )
|
||||
MERYL_HISTOGRAM ( MERYL_COUNT.out.meryl_db )
|
||||
GENOMESCOPE2 ( MERYL_HISTOGRAM.out.hist )
|
||||
}
|
13
tests/modules/genomescope2/nextflow.config
Normal file
13
tests/modules/genomescope2/nextflow.config
Normal file
|
@ -0,0 +1,13 @@
|
|||
process {
|
||||
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
|
||||
withName: 'MERYL.*' {
|
||||
ext.args = 'k=21'
|
||||
}
|
||||
|
||||
withName: 'GENOMESCOPE2' {
|
||||
ext.args = '-k 21 -p 1'
|
||||
}
|
||||
|
||||
}
|
22
tests/modules/genomescope2/test.yml
Normal file
22
tests/modules/genomescope2/test.yml
Normal file
|
@ -0,0 +1,22 @@
|
|||
- name: genomescope2 test_genomescope2
|
||||
command: nextflow run tests/modules/genomescope2 -entry test_genomescope2 -c tests/config/nextflow.config
|
||||
tags:
|
||||
- genomescope2
|
||||
files:
|
||||
- path: output/genomescope2/test_linear_plot.png
|
||||
md5sum: 94c165c5028156299a1d4d05766cac51
|
||||
- path: output/genomescope2/test_log_plot.png
|
||||
md5sum: 9d25ca463d92a0c73a893da7fd3979ba
|
||||
- path: output/genomescope2/test_model.txt
|
||||
md5sum: 3caf62f715f64a2f2b8fdff5d079cb84
|
||||
- path: output/genomescope2/test_summary.txt
|
||||
md5sum: 7452860e2cea99b85f3ff60daeac77f5
|
||||
- path: output/genomescope2/test_transformed_linear_plot.png
|
||||
md5sum: 99a64c1c18d8670f64cb863d4334abbb
|
||||
- path: output/genomescope2/test_transformed_log_plot.png
|
||||
md5sum: b4e029c9fb9987ca33b17392a691c1b4
|
||||
- path: output/genomescope2/versions.yml
|
||||
md5sum: 18afeb26f62a47f680b2bb3e27da9cbc
|
||||
- path: output/meryl/test.hist
|
||||
md5sum: f75362ab9cd70d96621b3690e952085f
|
||||
- path: output/meryl/versions.yml
|
|
@ -1,23 +0,0 @@
|
|||
#!/usr/bin/env nextflow
|
||||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { SRA_FASTQ } from '../../../../subworkflows/nf-core/sra_fastq/main.nf' addParams( [:] )
|
||||
|
||||
workflow test_sra_fastq_single_end {
|
||||
input = [
|
||||
[ id:'test_single_end', single_end:true ], // meta map
|
||||
'SRR13255544'
|
||||
]
|
||||
|
||||
SRA_FASTQ ( input )
|
||||
}
|
||||
|
||||
workflow test_sra_fastq_paired_end {
|
||||
input = [
|
||||
[ id:'test_paired_end', single_end:false ], // meta map
|
||||
'SRR11140744'
|
||||
]
|
||||
|
||||
SRA_FASTQ ( input )
|
||||
}
|
|
@ -1,27 +0,0 @@
|
|||
- name: sra fastq single-end
|
||||
command: nextflow run ./tests/subworkflows/nf-core/sra_fastq -entry test_sra_fastq_single_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- subworkflows
|
||||
# - subworkflows/sra_fastq
|
||||
# Modules
|
||||
# - sratools
|
||||
# - sratools/prefetch
|
||||
# - sratools/fasterqdump
|
||||
files:
|
||||
- path: output/sratools/SRR13255544.fastq.gz
|
||||
md5sum: 1054c7b71884acdb5eed8a378f18be82
|
||||
|
||||
- name: sra fastq paired-end
|
||||
command: nextflow run ./tests/subworkflows/nf-core/sra_fastq -entry test_sra_fastq_paired_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- subworkflows
|
||||
# - subworkflows/sra_fastq
|
||||
# Modules
|
||||
# - sratools
|
||||
# - sratools/prefetch
|
||||
# - sratools/fasterqdump
|
||||
files:
|
||||
- path: output/sratools/SRR11140744_1.fastq.gz
|
||||
md5sum: 193809c784a4ea132ab2a253fa4f55b6
|
||||
- path: output/sratools/SRR11140744_2.fastq.gz
|
||||
md5sum: 3e3b3af3413f50a1685fd7b3f1456d4e
|
29
tests/subworkflows/nf-core/srafastq/main.nf
Normal file
29
tests/subworkflows/nf-core/srafastq/main.nf
Normal file
|
@ -0,0 +1,29 @@
|
|||
#!/usr/bin/env nextflow
|
||||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { SRAFASTQ } from '../../../../subworkflows/nf-core/srafastq/main.nf'
|
||||
|
||||
workflow test_srafastq_single_end {
|
||||
input = Channel.of(
|
||||
[
|
||||
[ id:'test_single_end1', single_end:true ], // meta map
|
||||
'DRR000774'
|
||||
],
|
||||
[
|
||||
[ id:'test_single_end2', single_end:true ], // meta map
|
||||
'DRR000775'
|
||||
]
|
||||
)
|
||||
|
||||
SRAFASTQ ( input )
|
||||
}
|
||||
|
||||
workflow test_srafastq_paired_end {
|
||||
input = [
|
||||
[ id:'test_paired_end', single_end:false ], // meta map
|
||||
'SRR11140744'
|
||||
]
|
||||
|
||||
SRAFASTQ ( input )
|
||||
}
|
5
tests/subworkflows/nf-core/srafastq/nextflow.config
Normal file
5
tests/subworkflows/nf-core/srafastq/nextflow.config
Normal file
|
@ -0,0 +1,5 @@
|
|||
process {
|
||||
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
|
||||
}
|
29
tests/subworkflows/nf-core/srafastq/test.yml
Normal file
29
tests/subworkflows/nf-core/srafastq/test.yml
Normal file
|
@ -0,0 +1,29 @@
|
|||
- name: srafastq single-end
|
||||
command: nextflow run ./tests/subworkflows/nf-core/srafastq -entry test_srafastq_single_end -c tests/config/nextflow.config -c tests/subworkflows/nf-core/srafastq/nextflow.config
|
||||
tags:
|
||||
- subworkflows
|
||||
# - subworkflows/srafastq
|
||||
# Modules
|
||||
# - sratools
|
||||
# - sratools/prefetch
|
||||
# - sratools/fasterqdump
|
||||
files:
|
||||
- path: output/sratools/DRR000774.fastq.gz
|
||||
md5sum: 19029a1132115b55277a0d79ee089b49
|
||||
- path: output/sratools/DRR000775.fastq.gz
|
||||
md5sum: 59ff24c86ecb260752668c059c2a1eaf
|
||||
|
||||
- name: srafastq paired-end
|
||||
command: nextflow run ./tests/subworkflows/nf-core/srafastq -entry test_srafastq_paired_end -c tests/config/nextflow.config -c tests/subworkflows/nf-core/srafastq/nextflow.config
|
||||
tags:
|
||||
- subworkflows
|
||||
# - subworkflows/srafastq
|
||||
# Modules
|
||||
# - sratools
|
||||
# - sratools/prefetch
|
||||
# - sratools/fasterqdump
|
||||
files:
|
||||
- path: output/sratools/SRR11140744_1.fastq.gz
|
||||
md5sum: 193809c784a4ea132ab2a253fa4f55b6
|
||||
- path: output/sratools/SRR11140744_2.fastq.gz
|
||||
md5sum: 3e3b3af3413f50a1685fd7b3f1456d4e
|
Loading…
Reference in a new issue