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Trycycler cluster #5670

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merged 5 commits into from
May 25, 2024
Merged

Trycycler cluster #5670

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90a4ec9
initial trycycler subsample commit
watsonar May 21, 2024
228c76c
Update modules/nf-core/trycycler/subsample/main.nf
watsonar May 22, 2024
d9cc745
addressing comments on initial commit, fixed version number, added st…
watsonar May 22, 2024
27f7ea9
initial commit for trycycler cluster module
watsonar May 22, 2024
361def8
Merge branch 'master' into trycycler-cluster
watsonar May 22, 2024
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9 changes: 9 additions & 0 deletions modules/nf-core/trycycler/cluster/environment.yml
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---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
name: "trycycler_cluster"
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- "bioconda::trycycler=0.5.3"
56 changes: 56 additions & 0 deletions modules/nf-core/trycycler/cluster/main.nf
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process TRYCYCLER_CLUSTER {
tag "$meta.id"
label 'process_medium'

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/trycycler:0.5.3--pyhdfd78af_0':
'biocontainers/trycycler:0.5.3--pyhdfd78af_0' }"

input:
tuple val(meta), path(contigs), path(reads)

output:
tuple val(meta), path("*") , emit: cluster_dir
path "versions.yml" , emit: versions

when:
task.ext.when == null || task.ext.when

script:
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"

"""
trycycler \\
cluster \\
$args \\
--assemblies ${contigs} \\
--reads ${reads} \\
--threads $task.cpus \\
--out_dir ${prefix}

gzip $args2 ${prefix}/cluster_*/*/*.fasta

cat <<-END_VERSIONS > versions.yml
"${task.process}":
trycycler: \$(trycycler --version | sed 's/Trycycler v//')
END_VERSIONS
"""

stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
mkdir -p ${prefix}/cluster_001/1_contigs
echo "" | gzip > ${prefix}/cluster_001/1_contigs/A_contig_2a.fasta.gz
touch ${prefix}/contigs.newick
touch ${prefix}/contigs.phylip

cat <<-END_VERSIONS > versions.yml
"${task.process}":
trycycler: \$(trycycler --version | sed 's/Trycycler v//')
END_VERSIONS
"""
}
55 changes: 55 additions & 0 deletions modules/nf-core/trycycler/cluster/meta.yml
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name: "trycycler_cluster"
description: Cluster contigs from multiple assemblies by similarity
keywords:
- cluster
- alignment
- fastq
- fasta
- genomics
tools:
- "trycycler":
description: Trycycler is a tool for generating consensus long-read assemblies for bacterial genomes
homepage: https://github.com/rrwick/Trycycler
documentation: https://github.com/rrwick/Trycycler/wiki
doi: 10.1186/s13059-021-02483-z
licence: ["GPL v3"]

input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. `[ id:'sample1', single_end:false ]`

- reads:
type: file
description: Long-read FASTQ file, optionally gzip compressed

- assemblies:
type: file
description: Input assemblies whose contigs will be clustered

- out_dir:
type: directory
description: Output directory for clustering results

output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. `[ id:'sample1', single_end:false ]`

- cluster_dir:
type: directory
description: Output directory containing clustering results

- versions:
type: file
description: File containing software versions
pattern: "versions.yml"

authors:
- "@watsonar"
maintainers:
- "@watsonar"
77 changes: 77 additions & 0 deletions modules/nf-core/trycycler/cluster/tests/main.nf.test
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nextflow_process {

name "Test Process TRYCYCLER_CLUSTER"
script "../main.nf"
process "TRYCYCLER_CLUSTER"
config './nextflow.config'

tag "modules"
tag "modules_nfcore"
tag "trycycler"
tag "trycycler/cluster"

test("custom test data") {

when {
process {
"""
def contigs1 = file("contigs1.fasta")
contigs1.text = '>contig_1a\\nATCCCCTTGGACTCCTAGCTAGGCTCTAGAGCCTTCTCTCGACTACGAGCTAGCAGCTACGATCACGACTACAGCACAGCACTACAGCATCAGCACAGCAGTCAGCGA\\n>contig_2a\\nGCTAGGCTCTAACGCGCCATCAGCCGCTCAGCTACGACTATCGCAGCTACGATCAGCATCGATCTAGCAGAGCCTTCTGGTAACGCGACTCAGTCTCTACAGCACGGTAACCAGCACTACAGGGGTTAAGCCCATCA\\n'

def contigs2 = file("contigs2.fasta")
contigs2.text = '>contig_1b\\nATCCCCTTGGACTCCTAGCTAGGCTCTAGAGCCTTCTCTCGACTACCCAGCTAGCAGCTACGATCACGTCTACAGCACAGCACTACAGCATCAGCACAGCAGTA\\n>contig_2b\\nGCTAGGCTCTAACGCGCCATCAGCCGCTCAGCTACGACTAGCGCAGCTACGATCAGCATCCATCTAGCAGAGCCAACTGGTAACGCGACTCAGTCTCTACAGCACGGTAACCAGCACTACAGGGGTTAAGCCCATCA\\n'

def reads = file("reads.fastq")
reads.text = '@NC-000913.3_646515_unaligned_0_F_0_1238_0\\nCTCTAGAGCCTTCTCTCGACTACGAGCTAGCAGCTACGA\\n+\\nIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\\[email protected]_646518_unaligned_0_F_0_1238_0\\nTAGGCTCTAACGCGCCATCAGCCGCTCAGCTACGACTAGCGC\\n+\\nIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\\n'

input[0] = [
[ id:'test' ], // meta map
[ file('contigs1.fasta', checkIfExists: true), file('contigs2.fasta', checkIfExists: true) ], // contigs
file('reads.fastq', checkIfExists: true) // reads
]
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}

}

test("custom test data - stub") {

when {
process {
options "-stub-run"
"""
def contigs1 = file("contigs1.fasta")
contigs1.text = '>contig_1a\\nATCCCCTTGGACTCCTAGCTAGGCTCTAGAGCCTTCTCTCGACTACGAGCTAGCAGCTACGATCACGACTACAGCACAGCACTACAGCATCAGCACAGCAGTCAGCGA\\n>contig_2a\\nGCTAGGCTCTAACGCGCCATCAGCCGCTCAGCTACGACTATCGCAGCTACGATCAGCATCGATCTAGCAGAGCCTTCTGGTAACGCGACTCAGTCTCTACAGCACGGTAACCAGCACTACAGGGGTTAAGCCCATCA\\n'

def contigs2 = file("contigs2.fasta")
contigs2.text = '>contig_1b\\nATCCCCTTGGACTCCTAGCTAGGCTCTAGAGCCTTCTCTCGACTACCCAGCTAGCAGCTACGATCACGTCTACAGCACAGCACTACAGCATCAGCACAGCAGTA\\n>contig_2b\\nGCTAGGCTCTAACGCGCCATCAGCCGCTCAGCTACGACTAGCGCAGCTACGATCAGCATCCATCTAGCAGAGCCAACTGGTAACGCGACTCAGTCTCTACAGCACGGTAACCAGCACTACAGGGGTTAAGCCCATCA\\n'

def reads = file("reads.fastq")
reads.text = '@NC-000913.3_646515_unaligned_0_F_0_1238_0\\nCTCTAGAGCCTTCTCTCGACTACGAGCTAGCAGCTACGA\\n+\\nIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\\[email protected]_646518_unaligned_0_F_0_1238_0\\nTAGGCTCTAACGCGCCATCAGCCGCTCAGCTACGACTAGCGC\\n+\\nIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\\n'

input[0] = [
[ id:'test' ], // meta map
[ file('contigs1.fasta', checkIfExists: true), file('contigs2.fasta', checkIfExists: true) ], // contigs
file('reads.fastq', checkIfExists: true) // reads
]
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}

}
}
142 changes: 142 additions & 0 deletions modules/nf-core/trycycler/cluster/tests/main.nf.test.snap
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{
"custom test data - stub": {
"content": [
{
"0": [
[
{
"id": "test"
},
[
[
[
[
"A_contig_2a.fasta.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"contigs.newick:md5,d41d8cd98f00b204e9800998ecf8427e",
"contigs.phylip:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"versions.yml:md5,616584ce01fb659316a99b1329e047aa"
]
]
],
"1": [
"versions.yml:md5,616584ce01fb659316a99b1329e047aa"
],
"cluster_dir": [
[
{
"id": "test"
},
[
[
[
[
"A_contig_2a.fasta.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"contigs.newick:md5,d41d8cd98f00b204e9800998ecf8427e",
"contigs.phylip:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"versions.yml:md5,616584ce01fb659316a99b1329e047aa"
]
]
],
"versions": [
"versions.yml:md5,616584ce01fb659316a99b1329e047aa"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
},
"timestamp": "2024-05-22T14:59:36.502272455"
},
"custom test data": {
"content": [
{
"0": [
[
{
"id": "test"
},
[
[
[
[
"A_contig_2a.fasta.gz:md5,2c579f9cc210a544772daa7f4a16d0d5"
]
],
[
[
"B_contig_2b.fasta.gz:md5,4b4819e6b8f996d387216450b314798e"
]
],
[
[
"A_contig_1a.fasta.gz:md5,6d49552461c330871cecac80635c1798"
]
],
[
[
"B_contig_1b.fasta.gz:md5,f012c88fa34c176735737485eb730d71"
]
],
"contigs.newick:md5,1793ccb2bff4a79525a1ce60fb90f8ab",
"contigs.phylip:md5,984639efc8ae4b4cbe6e53bdb0b8b8c1"
],
"versions.yml:md5,616584ce01fb659316a99b1329e047aa"
]
]
],
"1": [
"versions.yml:md5,616584ce01fb659316a99b1329e047aa"
],
"cluster_dir": [
[
{
"id": "test"
},
[
[
[
[
"A_contig_2a.fasta.gz:md5,2c579f9cc210a544772daa7f4a16d0d5"
]
],
[
[
"B_contig_2b.fasta.gz:md5,4b4819e6b8f996d387216450b314798e"
]
],
[
[
"A_contig_1a.fasta.gz:md5,6d49552461c330871cecac80635c1798"
]
],
[
[
"B_contig_1b.fasta.gz:md5,f012c88fa34c176735737485eb730d71"
]
],
"contigs.newick:md5,1793ccb2bff4a79525a1ce60fb90f8ab",
"contigs.phylip:md5,984639efc8ae4b4cbe6e53bdb0b8b8c1"
],
"versions.yml:md5,616584ce01fb659316a99b1329e047aa"
]
]
],
"versions": [
"versions.yml:md5,616584ce01fb659316a99b1329e047aa"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
},
"timestamp": "2024-05-22T14:59:28.088111496"
}
}
5 changes: 5 additions & 0 deletions modules/nf-core/trycycler/cluster/tests/nextflow.config
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process {
withName: TRYCYCLER_CLUSTER {
ext.args = '--min_contig_len 0 --min_contig_depth 0'
}
}
2 changes: 2 additions & 0 deletions modules/nf-core/trycycler/cluster/tests/tags.yml
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trycycler/cluster:
- "modules/nf-core/trycycler/cluster/**"
9 changes: 9 additions & 0 deletions modules/nf-core/trycycler/subsample/environment.yml
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---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
name: "trycycler_subsample"
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- "bioconda::trycycler=0.5.3"