Merge branch 'master' into new-module-rtg/vcfeval

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nvnieuwk 2022-05-09 16:18:00 +02:00 committed by GitHub
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13 changed files with 200 additions and 48 deletions

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@ -0,0 +1,34 @@
process MERYL_HISTOGRAM {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::meryl=1.3" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/meryl:1.3--h87f3376_1':
'quay.io/biocontainers/meryl:1.3--h87f3376_1' }"
input:
tuple val(meta), path(meryl_db)
output:
tuple val(meta), path("*.hist"), emit: hist
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
meryl histogram \\
threads=$task.cpus \\
$args \\
$meryl_db > ${prefix}.hist
cat <<-END_VERSIONS > versions.yml
"${task.process}":
meryl: \$( meryl --version |& sed 's/meryl //' )
END_VERSIONS
"""
}

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@ -0,0 +1,41 @@
name: "meryl_histogram"
description: A genomic k-mer counter (and sequence utility) with nice features.
keywords:
- k-mer
- histogram
tools:
- "meryl":
description: "A genomic k-mer counter (and sequence utility) with nice features. "
homepage: "https://github.com/marbl/meryl"
documentation: "https://meryl.readthedocs.io/en/latest/quick-start.html"
tool_dev_url: "https://github.com/marbl/meryl"
doi: ""
licence: "['GPL']"
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- meryl_dbs:
type: directory
description: Meryl k-mer database
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"
- hist:
type: file
description: Histogram of k-mers
pattern: "*.hist"
authors:
- "@mahesh-panchal"

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@ -1,5 +1,4 @@
//There is a -L option to only output alignments in interval, might be an option for exons/panel data?
process SAMTOOLS_BAMTOCRAM {
process SAMTOOLS_CONVERT {
tag "$meta.id"
label 'process_medium'
@ -14,8 +13,8 @@ process SAMTOOLS_BAMTOCRAM {
path fai
output:
tuple val(meta), path("*.cram"), path("*.crai"), emit: cram_crai
path "versions.yml" , emit: versions
tuple val(meta), path("*.{cram,bam}"), path("*.{crai,bai}") , emit: alignment_index
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
@ -23,9 +22,17 @@ process SAMTOOLS_BAMTOCRAM {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def output_extension = input.getExtension() == "bam" ? "cram" : "bam"
"""
samtools view --threads ${task.cpus} --reference ${fasta} -C $args $input > ${prefix}.cram
samtools index -@${task.cpus} ${prefix}.cram
samtools view \\
--threads ${task.cpus} \\
--reference ${fasta} \\
$args \\
$input \\
-o ${prefix}.${output_extension}
samtools index -@${task.cpus} ${prefix}.${output_extension}
cat <<-END_VERSIONS > versions.yml
"${task.process}":

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@ -1,5 +1,5 @@
name: samtools_bamtocram
description: filter/convert and then index CRAM file
name: samtools_convert
description: convert and then index CRAM -> BAM or BAM -> CRAM file
keywords:
- view
- index
@ -23,12 +23,12 @@ input:
e.g. [ id:'test', single_end:false ]
- input:
type: file
description: BAM/SAM file
pattern: "*.{bam,sam}"
description: BAM/CRAM file
pattern: "*.{bam,cram}"
- index:
type: file
description: BAM/SAM index file
pattern: "*.{bai,sai}"
description: BAM/CRAM index file
pattern: "*.{bai,crai}"
- fasta:
type: file
description: Reference file to create the CRAM file
@ -39,10 +39,10 @@ output:
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- cram_crai:
- alignment_index:
type: file
description: filtered/converted CRAM file + index
pattern: "*{.cram,.crai}"
description: filtered/converted BAM/CRAM file + index
pattern: "*{.bam/cram,.bai/crai}"
- version:
type: file
description: File containing software version

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@ -1218,6 +1218,10 @@ meryl/count:
- modules/meryl/count/**
- tests/modules/meryl/count/**
meryl/histogram:
- modules/meryl/histogram/**
- tests/modules/meryl/histogram/**
metabat2/jgisummarizebamcontigdepths:
- modules/metabat2/jgisummarizebamcontigdepths/**
- tests/modules/metabat2/jgisummarizebamcontigdepths/**
@ -1635,9 +1639,9 @@ samtools/bam2fq:
- modules/samtools/bam2fq/**
- tests/modules/samtools/bam2fq/**
samtools/bamtocram:
- modules/samtools/bamtocram/**
- tests/modules/samtools/bamtocram/**
samtools/convert:
- modules/samtools/convert/**
- tests/modules/samtools/convert/**
samtools/collatefastq:
- modules/samtools/collatefastq/**
@ -1771,14 +1775,14 @@ slimfastq:
- modules/slimfastq/**
- tests/modules/slimfastq/**
snapaligner/index:
- modules/snapaligner/index/**
- tests/modules/snapaligner/index/**
snapaligner/align:
- modules/snapaligner/align/**
- tests/modules/snapaligner/align/**
snapaligner/index:
- modules/snapaligner/index/**
- tests/modules/snapaligner/index/**
snpdists:
- modules/snpdists/**
- tests/modules/snpdists/**

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@ -0,0 +1,17 @@
#!/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'
workflow test_meryl_histogram {
input = [
[ id:'test' ], // meta map
file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
]
MERYL_COUNT ( input )
MERYL_HISTOGRAM ( MERYL_COUNT.out.meryl_db )
}

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@ -1,5 +1,6 @@
process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
ext.args = 'k=21'
}

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@ -0,0 +1,10 @@
- name: meryl histogram test_meryl_histogram
command: nextflow run tests/modules/meryl/histogram -entry test_meryl_histogram -c tests/config/nextflow.config
tags:
- meryl/histogram
- meryl
files:
- path: output/meryl/test.hist
md5sum: 4bfdc8b287ee0cfd9922bbfa8cd64650
- path: output/meryl/versions.yml
md5sum: 050038f1b1df79977a393cce1b4b2ddb

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@ -1,17 +0,0 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { SAMTOOLS_BAMTOCRAM } from '../../../../modules/samtools/bamtocram/main.nf'
workflow test_samtools_bamtocram {
input = [ [ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
SAMTOOLS_BAMTOCRAM ( input, fasta, fai )
}

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@ -1,9 +0,0 @@
- name: samtools bamtocram test_samtools_bamtocram
command: nextflow run ./tests/modules/samtools/bamtocram -entry test_samtools_bamtocram -c ./tests/config/nextflow.config -c ./tests/modules/samtools/bamtocram/nextflow.config
tags:
- samtools/bamtocram
- samtools
files:
- path: output/samtools/test.cram
- path: output/samtools/test.cram.crai
- path: output/samtools/versions.yml

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@ -0,0 +1,31 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { SAMTOOLS_CONVERT as SAMTOOLS_BAMTOCRAM } from '../../../../modules/samtools/convert/main.nf'
include { SAMTOOLS_CONVERT as SAMTOOLS_CRAMTOBAM } from '../../../../modules/samtools/convert/main.nf'
workflow test_samtools_convert_bamtocram {
input = [ [ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
SAMTOOLS_BAMTOCRAM ( input, fasta, fai )
}
workflow test_samtools_convert_cramtobam {
input = [ [ id:'test', single_end:false ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true)
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
SAMTOOLS_CRAMTOBAM ( input, fasta, fai )
}

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@ -0,0 +1,12 @@
process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName:SAMTOOLS_BAMTOCRAM{
ext.args = "-C"
}
withName:SAMTOOLS_CRAMTOBAM{
ext.args = "-b"
}
}

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@ -0,0 +1,21 @@
- name: samtools convert test_samtools_convert_bamtocram
command: nextflow run tests/modules/samtools/convert -entry test_samtools_convert_bamtocram -c tests/config/nextflow.config
tags:
- samtools
- samtools/convert
files:
- path: output/samtools/test.cram
- path: output/samtools/test.cram.crai
- path: output/samtools/versions.yml
- name: samtools convert test_samtools_convert_cramtobam
command: nextflow run tests/modules/samtools/convert -entry test_samtools_convert_cramtobam -c tests/config/nextflow.config
tags:
- samtools
- samtools/convert
files:
- path: output/samtools/test.bam
md5sum: c262b6dc15f9b480bdb47d6d018b4b56
- path: output/samtools/test.bam.bai
md5sum: 6e8f5034f728401bfa841c8e70c62463
- path: output/samtools/versions.yml