Merge branch 'nf-core:master' into master

This commit is contained in:
James A. Fellows Yates 2022-01-31 13:19:30 +01:00 committed by GitHub
commit 20f9dfde69
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19 changed files with 414 additions and 49 deletions

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@ -0,0 +1,38 @@
process BAMTOOLS_CONVERT {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::bamtools=2.5.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bamtools:2.5.1--h9a82719_9' :
'quay.io/biocontainers/bamtools:2.5.1--h9a82719_9' }"
input:
tuple val(meta), path(bam)
output:
tuple val(meta), path("*.{bed,fasta,fastq,json,pileup,sam,yaml}"), emit: data
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def test = args ==~ /-format (bed|fasta|fastq|json|pileup|sam|yaml)/
if ( test == false ) error "-format option must be provided in args. Possible values: bed fasta fastq json pileup sam yaml"
m = args =~ /-format ([a-z]+)/
ext = m[0][1]
"""
bamtools \\
convert \\
$args \\
-in $bam \\
-out ${prefix}.${ext}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bamtools: \$( bamtools --version | grep -e 'bamtools' | sed 's/^.*bamtools //' )
END_VERSIONS
"""
}

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@ -0,0 +1,52 @@
name: bamtools_convert
description: BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.
keywords:
- bamtools
- bamtools/convert
- bam
- convert
- bed
- fasta
- fastq
- json
- pileup
- sam
- yaml
tools:
- bamtools:
description: C++ API & command-line toolkit for working with BAM data
homepage: http://github.com/pezmaster31/bamtools
documentation: https://github.com/pezmaster31/bamtools/wiki
tool_dev_url: http://github.com/pezmaster31/bamtools
doi: ""
licence: ['MIT']
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: BAM file
pattern: "*.bam"
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"
## TODO nf-core: Delete / customise this example output
- out:
type: file
description: The data in the asked format (bed, fasta, fastq, json, pileup, sam, yaml)
pattern: "*.{bed,fasta,fastq,json,pileup,sam,yaml}"
authors:
- "@sguizard"

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@ -41,7 +41,7 @@ process FREEBAYES {
$args \\
$input > ${prefix}.vcf
gzip --no-name ${prefix}.vcf
bgzip ${prefix}.vcf
cat <<-END_VERSIONS > versions.yml
"${task.process}":
@ -60,7 +60,7 @@ process FREEBAYES {
$args \\
$input > ${prefix}.vcf
gzip --no-name ${prefix}.vcf
bgzip ${prefix}.vcf
cat <<-END_VERSIONS > versions.yml
"${task.process}":

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@ -8,8 +8,7 @@ process GATK4_MERGEBAMALIGNMENT {
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input:
tuple val(meta), path(aligned)
path unmapped
tuple val(meta), path(aligned), path(unmapped)
path fasta
path dict
@ -28,10 +27,10 @@ process GATK4_MERGEBAMALIGNMENT {
}
"""
gatk --java-options "-Xmx${avail_mem}g" MergeBamAlignment \\
ALIGNED=$aligned \\
UNMAPPED=$unmapped \\
R=$fasta \\
O=${prefix}.bam \\
-ALIGNED $aligned \\
-UNMAPPED $unmapped \\
-R $fasta \\
-O ${prefix}.bam \\
$args
cat <<-END_VERSIONS > versions.yml

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@ -2,10 +2,10 @@ process NEXTCLADE_DATASETGET {
tag "$dataset"
label 'process_low'
conda (params.enable_conda ? "bioconda::nextclade=1.9.0" : null)
conda (params.enable_conda ? "bioconda::nextclade=1.10.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/nextclade:1.9.0--h9ee0642_0' :
'quay.io/biocontainers/nextclade:1.9.0--h9ee0642_0' }"
'https://depot.galaxyproject.org/singularity/nextclade:1.10.1--h9ee0642_0' :
'quay.io/biocontainers/nextclade:1.10.1--h9ee0642_0' }"
input:
val dataset

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@ -2,10 +2,10 @@ process NEXTCLADE_RUN {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::nextclade=1.9.0" : null)
conda (params.enable_conda ? "bioconda::nextclade=1.10.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/nextclade:1.9.0--h9ee0642_0' :
'quay.io/biocontainers/nextclade:1.9.0--h9ee0642_0' }"
'https://depot.galaxyproject.org/singularity/nextclade:1.10.1--h9ee0642_0' :
'quay.io/biocontainers/nextclade:1.10.1--h9ee0642_0' }"
input:
tuple val(meta), path(fasta)

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@ -2,10 +2,10 @@ process PRODIGAL {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::prodigal=2.6.3" : null)
conda (params.enable_conda ? "prodigal=2.6.3 pigz=2.6" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/prodigal:2.6.3--h516909a_2' :
'quay.io/biocontainers/prodigal:2.6.3--h516909a_2' }"
'https://depot.galaxyproject.org/singularity/mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0' :
'quay.io/biocontainers/mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0' }"
input:
tuple val(meta), path(genome)
@ -16,13 +16,13 @@ process PRODIGAL {
tuple val(meta), path("${prefix}.fna"), emit: nucleotide_fasta
tuple val(meta), path("${prefix}.faa"), emit: amino_acid_fasta
tuple val(meta), path("${prefix}_all.txt"), emit: all_gene_annotations
path "versions.yml" , emit: versions
path "versions.yml", emit: versions
script:
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
"""
prodigal -i "${genome}" \\
pigz -cdf ${genome} | prodigal \\
$args \\
-f $output_format \\
-d "${prefix}.fna" \\
@ -33,6 +33,7 @@ process PRODIGAL {
cat <<-END_VERSIONS > versions.yml
"${task.process}":
prodigal: \$(prodigal -v 2>&1 | sed -n 's/Prodigal V\\(.*\\):.*/\\1/p')
pigz: \$(pigz -V 2>&1 | sed 's/pigz //g')
END_VERSIONS
"""
}

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@ -5,10 +5,10 @@ keywords:
tools:
- prodigal:
description: Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program
homepage: {}
documentation: {}
homepage: {https://github.com/hyattpd/Prodigal}
documentation: {https://github.com/hyattpd/prodigal/wiki}
tool_dev_url: {}
doi: ""
doi: "10.1186/1471-2105-11-119"
licence: ["GPL v3"]
input:
@ -17,10 +17,12 @@ input:
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
- genome:
type: file
description: BAM/CRAM/SAM file
pattern: "*.{bam,cram,sam}"
description: fasta/fasta.gz file
- output_format:
type: string
description: Output format ("gbk"/"gff"/"sqn"/"sco")
output:
- meta:
@ -32,10 +34,22 @@ output:
type: file
description: File containing software versions
pattern: "versions.yml"
- bam:
- nucleotide_fasta:
type: file
description: Sorted BAM/CRAM/SAM file
pattern: "*.{bam,cram,sam}"
description: nucleotide sequences file
pattern: "*.{fna}"
- amino_acid_fasta:
type: file
description: protein translations file
pattern: "*.{faa}"
- all_gene_annotations:
type: file
description: complete starts file
pattern: "*.{_all.txt}"
- gene_annotations:
type: file
description: gene annotations in output_format given as input
pattern: "*.{output_format}"
authors:
- "@grst"

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@ -46,6 +46,10 @@ bamaligncleaner:
- modules/bamaligncleaner/**
- tests/modules/bamaligncleaner/**
bamtools/convert:
- modules/bamtools/convert/**
- tests/modules/bamtools/convert/**
bamtools/split:
- modules/bamtools/split/**
- tests/modules/bamtools/split/**

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@ -0,0 +1,104 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_EXT_ERROR } from '../../../../modules/bamtools/convert/main.nf'
include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_NOEXT_ERROR } from '../../../../modules/bamtools/convert/main.nf'
include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_BED } from '../../../../modules/bamtools/convert/main.nf'
include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_FASTA } from '../../../../modules/bamtools/convert/main.nf'
include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_FASTQ } from '../../../../modules/bamtools/convert/main.nf'
include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_JSON } from '../../../../modules/bamtools/convert/main.nf'
include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_PILEUP } from '../../../../modules/bamtools/convert/main.nf'
include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_SAM } from '../../../../modules/bamtools/convert/main.nf'
include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_YAML } from '../../../../modules/bamtools/convert/main.nf'
workflow test_bamtools_convert_ext_error {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
]
BAMTOOLS_CONVERT_EXT_ERROR ( input )
}
workflow test_bamtools_convert_noext_error {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
]
BAMTOOLS_CONVERT_NOEXT_ERROR ( input )
}
workflow test_bamtools_convert_bed {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
]
BAMTOOLS_CONVERT_BED ( input )
}
workflow test_bamtools_convert_fasta {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
]
BAMTOOLS_CONVERT_FASTA ( input )
}
workflow test_bamtools_convert_fastq {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
]
BAMTOOLS_CONVERT_FASTQ ( input )
}
workflow test_bamtools_convert_json {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
]
BAMTOOLS_CONVERT_JSON ( input )
}
workflow test_bamtools_convert_pileup {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
]
BAMTOOLS_CONVERT_PILEUP ( input )
}
workflow test_bamtools_convert_sam {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
]
BAMTOOLS_CONVERT_SAM ( input )
}
workflow test_bamtools_convert_yaml {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
]
BAMTOOLS_CONVERT_YAML ( input )
}

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@ -0,0 +1,41 @@
process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName: BAMTOOLS_CONVERT_EXT_ERROR {
ext.args = "-format vcf"
}
withName: BAMTOOLS_CONVERT_NOEXT_ERROR {
ext.args = ""
}
withName: BAMTOOLS_CONVERT_BED {
ext.args = "-format bed"
}
withName: BAMTOOLS_CONVERT_FASTA {
ext.args = "-format fasta"
}
withName: BAMTOOLS_CONVERT_FASTQ {
ext.args = "-format fastq"
}
withName: BAMTOOLS_CONVERT_JSON {
ext.args = "-format json"
}
withName: BAMTOOLS_CONVERT_PILEUP {
ext.args = "-format pileup"
}
withName: BAMTOOLS_CONVERT_SAM {
ext.args = "-format sam"
}
withName: BAMTOOLS_CONVERT_YAML {
ext.args = "-format yaml"
}
}

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@ -0,0 +1,90 @@
- name: bamtools convert test_bamtools_convert_ext_error
command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_ext_error -c tests/config/nextflow.config
tags:
- bamtools
- bamtools/convert
exit_code: 1
- name: bamtools convert test_bamtools_convert_noext_error
command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_noext_error -c tests/config/nextflow.config
tags:
- bamtools
- bamtools/convert
exit_code: 1
- name: bamtools convert test_bamtools_convert_bed
command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_bed -c tests/config/nextflow.config
tags:
- bamtools
- bamtools/convert
files:
- path: output/bamtools/test.bed
md5sum: 4e34cc15bf31e700f5f3a9f8fffb6c81
- path: output/bamtools/versions.yml
md5sum: eb7a144b8a97965d3482f6f96b8a8243
- name: bamtools convert test_bamtools_convert_fasta
command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_fasta -c tests/config/nextflow.config
tags:
- bamtools
- bamtools/convert
files:
- path: output/bamtools/test.fasta
md5sum: 52aeacf78571862b7e97c7d44ac8f827
- path: output/bamtools/versions.yml
md5sum: 42d19a2b2b07f05edb82b34369dfd754
- name: bamtools convert test_bamtools_convert_fastq
command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_fastq -c tests/config/nextflow.config
tags:
- bamtools
- bamtools/convert
files:
- path: output/bamtools/test.fastq
md5sum: e591c48daad2c56638e5d6f21f1f71c5
- path: output/bamtools/versions.yml
md5sum: 13f0bf8a3e1f8f527f96dabaa5c8051e
- name: bamtools convert test_bamtools_convert_json
command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_json -c tests/config/nextflow.config
tags:
- bamtools
- bamtools/convert
files:
- path: output/bamtools/test.json
md5sum: 04afed696f9f14da85a460353645d1f5
- path: output/bamtools/versions.yml
md5sum: 33d633dbd6209cb93c9b071f8c0ed3b3
- name: bamtools convert test_bamtools_convert_pileup
command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_pileup -c tests/config/nextflow.config
tags:
- bamtools
- bamtools/convert
files:
- path: output/bamtools/test.pileup
md5sum: e5a3cb4a3e1bf980a575fafce6a2826f
- path: output/bamtools/versions.yml
md5sum: fd3ad0edd1e085b1a002e0593d1d5814
- name: bamtools convert test_bamtools_convert_sam
command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_sam -c tests/config/nextflow.config
tags:
- bamtools
- bamtools/convert
files:
- path: output/bamtools/test.sam
md5sum: 61ab3d0de16a9da8b651f9c692e19d5e
- path: output/bamtools/versions.yml
md5sum: 4be470ce3cc0143ae5ae415b612a4965
- name: bamtools convert test_bamtools_convert_yaml
command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_yaml -c tests/config/nextflow.config
tags:
- bamtools
- bamtools/convert
files:
- path: output/bamtools/test.yaml
md5sum: 68b56f198da036fef33e150eb773dc3b
- path: output/bamtools/versions.yml
md5sum: 1116abc088c5edf11bee393961c18b3e

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@ -1,34 +1,49 @@
- name: freebayes test_freebayes
command: nextflow run ./tests/modules/freebayes -entry test_freebayes -c ./tests/config/nextflow.config -c ./tests/modules/freebayes/nextflow.config
command: nextflow run tests/modules/freebayes -entry test_freebayes -c tests/config/nextflow.config
tags:
- freebayes
files:
- path: output/freebayes/test.vcf.gz
md5sum: 81d3e6ce7b6343d088b779567c3803eb
- path: output/freebayes/versions.yml
md5sum: 53651eb835af65df829241257584a7d2
- name: freebayes test_freebayes_bed
command: nextflow run ./tests/modules/freebayes -entry test_freebayes_bed -c ./tests/config/nextflow.config -c ./tests/modules/freebayes/nextflow.config
command: nextflow run tests/modules/freebayes -entry test_freebayes_bed -c tests/config/nextflow.config
tags:
- freebayes
files:
- path: output/freebayes/test.vcf.gz
md5sum: 02645d014a63485162a7789007373b2a
- path: output/freebayes/versions.yml
md5sum: becc93c8a0be580c09d55b955d60a5e1
- name: freebayes test_freebayes_cram
command: nextflow run ./tests/modules/freebayes -entry test_freebayes_cram -c ./tests/config/nextflow.config -c ./tests/modules/freebayes/nextflow.config
command: nextflow run tests/modules/freebayes -entry test_freebayes_cram -c tests/config/nextflow.config
tags:
- freebayes
files:
- path: output/freebayes/test.vcf.gz
md5sum: 3d0bfcd2129c62f8863952fa4c1054db
- path: output/freebayes/versions.yml
md5sum: 2e5b266edfc6cab81353cfc72c00f67c
- name: freebayes test_freebayes_somatic
command: nextflow run ./tests/modules/freebayes -entry test_freebayes_somatic -c ./tests/config/nextflow.config -c ./tests/modules/freebayes/nextflow.config
command: nextflow run tests/modules/freebayes -entry test_freebayes_somatic -c tests/config/nextflow.config
tags:
- freebayes
files:
- path: output/freebayes/test.vcf.gz
md5sum: 22fec868210ba3baf685b214bfd8e74b
- path: output/freebayes/versions.yml
md5sum: 8fbdb4c052fb3e42b5508a966125fa05
- name: freebayes test_freebayes_somatic_cram_intervals
command: nextflow run ./tests/modules/freebayes -entry test_freebayes_somatic_cram_intervals -c ./tests/config/nextflow.config -c ./tests/modules/freebayes/nextflow.config
command: nextflow run tests/modules/freebayes -entry test_freebayes_somatic_cram_intervals -c tests/config/nextflow.config
tags:
- freebayes
files:
- path: output/freebayes/test.vcf.gz
md5sum: 527cf2937067bbd4117d95fd472bb928
- path: output/freebayes/versions.yml
md5sum: af97e3dfdc086188739907c3460e49e0

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@ -6,11 +6,11 @@ include { GATK4_MERGEBAMALIGNMENT } from '../../../../modules/gatk4/mergebamalig
workflow test_gatk4_mergebamalignment {
input = [ [ id:'test' ], // meta map
file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_unaligned_bam'], checkIfExists: true)
]
unmapped = file(params.test_data['sarscov2']['illumina']['test_unaligned_bam'], checkIfExists: true)
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
GATK4_MERGEBAMALIGNMENT ( input, unmapped, fasta, dict )
GATK4_MERGEBAMALIGNMENT ( input, fasta, dict )
}

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@ -8,7 +8,8 @@ workflow test_nextclade_datasetget {
dataset = 'sars-cov-2'
reference = 'MN908947'
tag = '2022-01-05T19:54:31Z'
tag = '2022-01-18T12:00:00Z'
NEXTCLADE_DATASETGET ( dataset, reference, tag )
}

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@ -9,12 +9,14 @@
- path: output/nextclade/sars-cov-2/primers.csv
md5sum: 5990c3483bf66ce607aeb90a44e7ef2e
- path: output/nextclade/sars-cov-2/qc.json
md5sum: 018fa0c0b0d2e824954e37e01495d549
md5sum: c512f51fda0212b21ffff05779180963
- path: output/nextclade/sars-cov-2/reference.fasta
md5sum: c7ce05f28e4ec0322c96f24e064ef55c
- path: output/nextclade/sars-cov-2/sequences.fasta
md5sum: 41129d255b99e0e92bdf20e866b99a1b
- path: output/nextclade/sars-cov-2/tag.json
md5sum: 2f6d8e806d9064571ee4188ef1304c9c
md5sum: 402ac2b87e2a6a64a3fbf5ad16497af3
- path: output/nextclade/sars-cov-2/tree.json
md5sum: f8fb33ed62b59142ac20998eb599df6c
md5sum: b8f32f547ff9e2131d6fc66b68fc54b1
- path: output/nextclade/sars-cov-2/virus_properties.json
md5sum: 5f2de3949e07cb633f3d9e4a7654dc81

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@ -9,7 +9,7 @@ workflow test_nextclade_run {
dataset = 'sars-cov-2'
reference = 'MN908947'
tag = '2022-01-05T19:54:31Z'
tag = '2022-01-18T12:00:00Z'
NEXTCLADE_DATASETGET ( dataset, reference, tag )
@ -20,3 +20,4 @@ workflow test_nextclade_run {
NEXTCLADE_RUN ( input, NEXTCLADE_DATASETGET.out.dataset )
}

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@ -6,8 +6,8 @@
files:
- path: output/nextclade/test.json
- path: output/nextclade/test.csv
md5sum: 3b87a4da190ba2e1fdc8418dc3a7ffdb
md5sum: 570c1aa2d5fd25c23d0042c1b06108e1
- path: output/nextclade/test.tsv
md5sum: 449393288e8734a02def139c550a8d9b
md5sum: dd76e1a4c760785489be4e4a860b4d00
- path: output/nextclade/test.tree.json
md5sum: 9c6e33cb7ff860bee6194847bd2c855c
md5sum: 3591b4dc1542995a7ffcffcb1f52b524

View file

@ -16,6 +16,9 @@ def _get_workflow_names():
# test_config = yaml.safe_load(f.read_text())
test_config = yaml.load(f.read_text(), Loader=yaml.BaseLoader)
for workflow in test_config:
# https://github.com/nf-core/modules/pull/1242 - added to cover tests
# that expect an error and therefore will not generate a versions.yml
if 'exit_code' not in workflow:
yield workflow["name"]