Update DASTool to 1.1.4 (#1471)

* fix: remove left-over unnecessary code

* Update DASTool

* Fix tests

* Fix test.ymls

* Fix container build version

* Make tests less strict to account for variability

* Apply suggestions from code review

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>

* Add missing description

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
This commit is contained in:
James A. Fellows Yates 2022-04-01 11:33:07 +02:00 committed by GitHub
parent 5e7daa7b96
commit 8ce6810787
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10 changed files with 216 additions and 44 deletions

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@ -2,27 +2,28 @@ process DASTOOL_DASTOOL {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::das_tool=1.1.3" : null) conda (params.enable_conda ? "bioconda::das_tool=1.1.4" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/das_tool:1.1.3--r41hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/das_tool:1.1.4--r41hdfd78af_1' :
'quay.io/biocontainers/das_tool:1.1.3--r41hdfd78af_0' }" 'quay.io/biocontainers/das_tool:1.1.4--r41hdfd78af_1' }"
input: input:
tuple val(meta), path(contigs), path(bins) tuple val(meta), path(contigs), path(bins)
path(proteins) path(proteins)
path(db_directory) path(db_directory)
val(search_engine)
output: output:
tuple val(meta), path("*.log") , emit: log tuple val(meta), path("*.log") , emit: log
tuple val(meta), path("*_summary.txt") , emit: summary tuple val(meta), path("*_summary.tsv") , emit: summary
tuple val(meta), path("*_DASTool_scaffolds2bin.txt") , emit: scaffolds2bin tuple val(meta), path("*_DASTool_contig2bin.tsv") , emit: contig2bin
tuple val(meta), path("*.eval") , optional: true, emit: eval tuple val(meta), path("*.eval") , optional: true, emit: eval
tuple val(meta), path("*_DASTool_bins/*.fa") , optional: true, emit: bins tuple val(meta), path("*_DASTool_bins/*.fa") , optional: true, emit: bins
tuple val(meta), path("*.pdf") , optional: true, emit: pdfs tuple val(meta), path("*.pdf") , optional: true, emit: pdfs
tuple val(meta), path("*.proteins.faa") , optional: true, emit: fasta_proteins tuple val(meta), path("*.candidates.faa") , optional: true, emit: fasta_proteins
tuple val(meta), path("*.faa") , optional: true, emit: candidates_faa
tuple val(meta), path("*.archaea.scg") , optional: true, emit: fasta_archaea_scg tuple val(meta), path("*.archaea.scg") , optional: true, emit: fasta_archaea_scg
tuple val(meta), path("*.bacteria.scg") , optional: true, emit: fasta_bacteria_scg tuple val(meta), path("*.bacteria.scg") , optional: true, emit: fasta_bacteria_scg
tuple val(meta), path("*.b6") , optional: true, emit: b6
tuple val(meta), path("*.seqlength") , optional: true, emit: seqlength tuple val(meta), path("*.seqlength") , optional: true, emit: seqlength
path "versions.yml" , emit: versions path "versions.yml" , emit: versions
@ -33,17 +34,12 @@ process DASTOOL_DASTOOL {
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
def bin_list = bins instanceof List ? bins.join(",") : "$bins" def bin_list = bins instanceof List ? bins.join(",") : "$bins"
def engine = search_engine ? "--search_engine $search_engine" : "--search_engine diamond"
def db_dir = db_directory ? "--db_directory $db_directory" : "" def db_dir = db_directory ? "--db_directory $db_directory" : ""
def clean_contigs = contigs.toString() - ".gz" def clean_contigs = contigs.toString() - ".gz"
def decompress_contigs = contigs.toString() == clean_contigs ? "" : "gunzip -q -f $contigs" def decompress_contigs = contigs.toString() == clean_contigs ? "" : "gunzip -q -f $contigs"
def decompress_proteins = proteins ? "gunzip -f $proteins" : ""
def clean_proteins = proteins ? proteins.toString() - ".gz" : "" def clean_proteins = proteins ? proteins.toString() - ".gz" : ""
def proteins_pred = proteins ? "--proteins $clean_proteins" : "" def decompress_proteins = proteins ? "gunzip -f $proteins" : ""
def proteins_pred = proteins ? "-p $clean_proteins" : ""
if (! search_engine) {
log.info('[DAS_Tool] Default search engine (USEARCH) is proprietary software and not available in bioconda. Using DIAMOND as alternative.')
}
""" """
$decompress_proteins $decompress_proteins
@ -53,15 +49,14 @@ process DASTOOL_DASTOOL {
$args \\ $args \\
$proteins_pred \\ $proteins_pred \\
$db_dir \\ $db_dir \\
$engine \\
-t $task.cpus \\ -t $task.cpus \\
--bins $bin_list \\ -i $bin_list \\
-c $clean_contigs \\ -c $clean_contigs \\
-o $prefix -o $prefix
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":
dastool: \$( DAS_Tool --version 2>&1 | grep "DAS Tool" | sed 's/DAS Tool version //' ) dastool: \$( DAS_Tool --version 2>&1 | grep "DAS Tool" | sed 's/DAS Tool //' )
END_VERSIONS END_VERSIONS
""" """
} }

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@ -34,8 +34,8 @@ input:
pattern: "*.{fa.gz,fas.gz,fasta.gz}" pattern: "*.{fa.gz,fas.gz,fasta.gz}"
- bins: - bins:
type: file type: file
description: "Scaffolds2bin tabular file generated with dastool/scaffolds2bin" description: "FastaToContig2Bin tabular file generated with dastool/fastatocontig2bin"
pattern: "*.scaffolds2bin.tsv" pattern: "*.tsv"
- proteins: - proteins:
type: file type: file
description: Predicted proteins in prodigal fasta format (>scaffoldID_geneNo) description: Predicted proteins in prodigal fasta format (>scaffoldID_geneNo)
@ -43,9 +43,6 @@ input:
- db_directory: - db_directory:
type: file type: file
description: (optional) Directory of single copy gene database. description: (optional) Directory of single copy gene database.
- search_engine:
type: val
description: Engine used for single copy gene identification. USEARCH is not supported due to it being proprietary [blast/diamond]
output: output:
- meta: - meta:
@ -65,14 +62,17 @@ output:
type: file type: file
description: Summary of output bins including quality and completeness estimates description: Summary of output bins including quality and completeness estimates
pattern: "*summary.txt" pattern: "*summary.txt"
- scaffolds2bin: - contig2bin:
type: file type: file
description: Scaffolds to bin file of output bins description: Scaffolds to bin file of output bins
pattern: "*.scaffolds2bin.txt" pattern: "*.contig2bin.txt"
- eval: - eval:
type: file type: file
description: Quality and completeness estimates of input bin sets description: Quality and completeness estimates of input bin sets
pattern: "*.eval" pattern: "*.eval"
- bins:
description: Final refined bins in fasta format
pattern: "*.fa"
- pdfs: - pdfs:
type: file type: file
description: Plots showing the amount of high quality bins and score distribution of bins per method description: Plots showing the amount of high quality bins and score distribution of bins per method
@ -89,6 +89,10 @@ output:
type: file type: file
description: Results of bacterial single-copy-gene prediction description: Results of bacterial single-copy-gene prediction
pattern: "*.bacteria.scg" pattern: "*.bacteria.scg"
- b6:
type: file
description: Results in b6 format
pattern: "*.b6"
- seqlength: - seqlength:
type: file type: file
description: Summary of contig lengths description: Summary of contig lengths

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@ -0,0 +1,41 @@
process DASTOOL_FASTATOCONTIG2BIN {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::das_tool=1.1.4" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/das_tool:1.1.4--r41hdfd78af_1' :
'quay.io/biocontainers/das_tool:1.1.4--r41hdfd78af_1' }"
input:
tuple val(meta), path(fasta)
val(extension)
output:
tuple val(meta), path("*.tsv"), emit: fastatocontig2bin
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}"
def file_extension = extension ? extension : "fasta"
def clean_fasta = fasta.toString() - ".gz"
def decompress_fasta = fasta.toString() == clean_fasta ? "" : "gunzip -q -f $fasta"
"""
$decompress_fasta
Fasta_to_Contig2Bin.sh \\
$args \\
-i . \\
-e $file_extension \\
> ${prefix}.tsv
cat <<-END_VERSIONS > versions.yml
"${task.process}":
dastool: \$( DAS_Tool --version 2>&1 | grep "DAS Tool" | sed 's/DAS Tool //' )
END_VERSIONS
"""
}

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@ -0,0 +1,56 @@
name: dastool_fastatocontig2bin
description: Helper script to convert a set of bins in fasta format to tabular scaffolds2bin format
keywords:
- binning
- das tool
- table
- de novo
- bins
- contigs
- assembly
- das_tool
tools:
- dastool:
description: |
DAS Tool is an automated method that integrates the results
of a flexible number of binning algorithms to calculate an optimized, non-redundant
set of bins from a single assembly.
homepage: https://github.com/cmks/DAS_Tool
documentation: https://github.com/cmks/DAS_Tool
tool_dev_url: https://github.com/cmks/DAS_Tool
doi: "10.1038/s41564-018-0171-1"
licence: ["BSD"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- fasta:
type: file
description: Fasta of list of fasta files recommended to be gathered via with .collect() of bins
pattern: "*.{fa,fa.gz,fas,fas.gz,fna,fna.gz,fasta,fasta.gz}"
- extension:
type: val
description: Fasta file extension (fa | fas | fasta | ...), without .gz suffix, if gzipped input.
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"
- fastatocontig2bin:
type: file
description: tabular contig2bin file for DAS tool input
pattern: "*.tsv"
authors:
- "@maxibor"
- "@jfy133"

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@ -487,6 +487,10 @@ dastool/dastool:
- modules/dastool/dastool/** - modules/dastool/dastool/**
- tests/modules/dastool/dastool/** - tests/modules/dastool/dastool/**
dastool/fastatocontig2bin:
- modules/dastool/fastatocontig2bin/**
- tests/modules/dastool/fastatocontig2bin/**
dastool/scaffolds2bin: dastool/scaffolds2bin:
- modules/dastool/scaffolds2bin/** - modules/dastool/scaffolds2bin/**
- tests/modules/dastool/scaffolds2bin/** - tests/modules/dastool/scaffolds2bin/**

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@ -3,7 +3,7 @@ nextflow.enable.dsl = 2
include { METABAT2_METABAT2 } from '../../../../modules/metabat2/metabat2/main.nf' include { METABAT2_METABAT2 } from '../../../../modules/metabat2/metabat2/main.nf'
include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../modules/metabat2/jgisummarizebamcontigdepths/main.nf' include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../modules/metabat2/jgisummarizebamcontigdepths/main.nf'
include { DASTOOL_SCAFFOLDS2BIN } from '../../../../modules/dastool/scaffolds2bin/main.nf' include { DASTOOL_FASTATOCONTIG2BIN } from '../../../../modules/dastool/fastatocontig2bin/main.nf'
include { DASTOOL_DASTOOL } from '../../../../modules/dastool/dastool/main.nf' include { DASTOOL_DASTOOL } from '../../../../modules/dastool/dastool/main.nf'
workflow test_dastool_dastool { workflow test_dastool_dastool {
@ -21,13 +21,13 @@ workflow test_dastool_dastool {
METABAT2_METABAT2 ( input_metabat2 ) METABAT2_METABAT2 ( input_metabat2 )
DASTOOL_SCAFFOLDS2BIN ( METABAT2_METABAT2.out.fasta.collect(), "fa") DASTOOL_FASTATOCONTIG2BIN ( METABAT2_METABAT2.out.fasta.collect(), "fa")
Channel.of([ [ id:'test', single_end:false ], // meta map Channel.of([ [ id:'test', single_end:false ], // meta map
file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)]) file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)])
.join(DASTOOL_SCAFFOLDS2BIN.out.scaffolds2bin) .join( DASTOOL_FASTATOCONTIG2BIN.out.fastatocontig2bin )
.set {input_dastool} .set {input_dastool}
DASTOOL_DASTOOL ( input_dastool, [], [], [] )
DASTOOL_DASTOOL ( input_dastool, [], [] )
} }

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@ -1,29 +1,28 @@
- name: dastool dastool test_dastool_dastool - name: dastool dastool test_dastool_dastool
command: nextflow run ./tests/modules/dastool/dastool -entry test_dastool_dastool -c ./tests/config/nextflow.config -c ./tests/modules/dastool/dastool/nextflow.config command: nextflow run tests/modules/dastool/dastool -entry test_dastool_dastool -c tests/config/nextflow.config
tags: tags:
- dastool
- dastool/dastool - dastool/dastool
- dastool
files: files:
- path: output/dastool/test.seqlength - path: output/dastool/test.seqlength
md5sum: b815a5811008c36808a59b1d0dcfab24 md5sum: b815a5811008c36808a59b1d0dcfab24
- path: output/dastool/test.tsv - path: output/dastool/test.tsv
md5sum: 6e46c0be14dded7cb13af38f54feea47 md5sum: 6e46c0be14dded7cb13af38f54feea47
- path: output/dastool/test_DASTool.log - path: output/dastool/test_DASTool.log
contains: - path: output/dastool/test_DASTool_contig2bin.tsv
- "DAS Tool run on"
- path: output/dastool/test_DASTool_scaffolds2bin.txt
md5sum: 6e46c0be14dded7cb13af38f54feea47 md5sum: 6e46c0be14dded7cb13af38f54feea47
- path: output/dastool/test_DASTool_summary.txt - path: output/dastool/test_DASTool_summary.tsv
md5sum: a3efa8717b30dfada78dc5ae9a3dc396 md5sum: ab9dd3709a59a69bc66030b9e0ff3d5b
- path: output/dastool/test_proteins.faa
- path: output/dastool/test_proteins.faa.all.b6
md5sum: 39c11237ef22ac73109aaac267e185d0
- path: output/dastool/test_proteins.faa.archaea.scg - path: output/dastool/test_proteins.faa.archaea.scg
md5sum: e79d82eecee25821d1658ea4f082601d md5sum: e79d82eecee25821d1658ea4f082601d
- path: output/dastool/test_proteins.faa.bacteria.scg - path: output/dastool/test_proteins.faa.bacteria.scg
md5sum: 8132cfb17cf398d41c036ead55c96ffe md5sum: 8132cfb17cf398d41c036ead55c96ffe
- path: output/dastool/test_test.tsv.eval - path: output/dastool/test_proteins.faa.findSCG.b6
md5sum: a3efa8717b30dfada78dc5ae9a3dc396 md5sum: 48e90e12cd6c88d00608777dbc48a82a
- path: output/metabat2/bins/test.1.fa.gz - path: output/dastool/test_proteins.faa.scg.candidates.faa
md5sum: 2b297bf557cc3831b800348859331268 md5sum: d94b7bed0f8aa9cf2824d72c548c537c
- path: output/metabat2/test.tsv.gz - path: output/dastool/versions.yml
md5sum: 619338fa5019e361d5545ce385a6961f md5sum: 004e04c6a38652df2e0c59c44e29c9de
- path: output/metabat2/test.txt.gz
md5sum: 745a0446af6ef68b930975e9ce5a95d6

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@ -0,0 +1,48 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { GUNZIP } from '../../../../modules/gunzip/main.nf'
include { METABAT2_METABAT2 } from '../../../../modules/metabat2/metabat2/main.nf'
include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../modules/metabat2/jgisummarizebamcontigdepths/main.nf'
include { DASTOOL_FASTATOCONTIG2BIN } from '../../../../modules/dastool/fastatocontig2bin/main.nf'
workflow test_dastool_fastatocontig2bin {
input_depth = [ [ id:'test', single_end:false ], // meta map
file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_sorted_bam_bai'], checkIfExists: true) ]
METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS ( input_depth )
Channel.fromPath(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
.map { it -> [[ id:'test', single_end:false ], it] }
.join(METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS.out.depth)
.set { input_metabat2 }
METABAT2_METABAT2 ( input_metabat2 )
DASTOOL_FASTATOCONTIG2BIN ( METABAT2_METABAT2.out.fasta.collect(), "fa")
}
workflow test_dastool_fastatocontig2bin_ungzipped {
input_depth = [ [ id:'test', single_end:false ], // meta map
file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_sorted_bam_bai'], checkIfExists: true) ]
METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS ( input_depth )
Channel.fromPath(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
.map { it -> [[ id:'test', single_end:false ], it] }
.join(METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS.out.depth)
.set { input_metabat2 }
METABAT2_METABAT2 ( input_metabat2 )
// TODO test unzipped input files
ch_input_2_fastatocontig2bin = GUNZIP( METABAT2_METABAT2.out.fasta ).gunzip
DASTOOL_FASTATOCONTIG2BIN ( ch_input_2_fastatocontig2bin, "fa")
}

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

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@ -0,0 +1,20 @@
- name: dastool fastatocontig2bin test_dastool_fastatocontig2bin
command: nextflow run tests/modules/dastool/fastatocontig2bin -entry test_dastool_fastatocontig2bin -c tests/config/nextflow.config
tags:
- dastool
- dastool/fastatocontig2bin
files:
- path: output/dastool/test.tsv
md5sum: 6e46c0be14dded7cb13af38f54feea47
- path: output/dastool/versions.yml
md5sum: ff4b6f14bee4548bf09b5e602c306595
- name: dastool fastatocontig2bin test_dastool_fastatocontig2bin_ungzipped
command: nextflow run tests/modules/dastool/fastatocontig2bin -entry test_dastool_fastatocontig2bin_ungzipped -c tests/config/nextflow.config
tags:
- dastool
- dastool/fastatocontig2bin
files:
- path: output/dastool/test.tsv
md5sum: 6e46c0be14dded7cb13af38f54feea47
- path: output/dastool/versions.yml