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* initial trycycler subsample commit * Update modules/nf-core/trycycler/subsample/main.nf to resolve issue with nf-test and empty gzipped files Co-authored-by: Simon Pearce <[email protected]> * addressing comments on initial commit, fixed version number, added stub tests * initial commit for trycycler cluster module --------- Co-authored-by: Simon Pearce <[email protected]>
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--- | ||
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json | ||
name: "trycycler_cluster" | ||
channels: | ||
- conda-forge | ||
- bioconda | ||
- defaults | ||
dependencies: | ||
- "bioconda::trycycler=0.5.3" |
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process TRYCYCLER_CLUSTER { | ||
tag "$meta.id" | ||
label 'process_medium' | ||
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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' }" | ||
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input: | ||
tuple val(meta), path(contigs), path(reads) | ||
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output: | ||
tuple val(meta), path("*") , emit: cluster_dir | ||
path "versions.yml" , emit: versions | ||
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when: | ||
task.ext.when == null || task.ext.when | ||
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script: | ||
def args = task.ext.args ?: '' | ||
def args2 = task.ext.args2 ?: '' | ||
def prefix = task.ext.prefix ?: "${meta.id}" | ||
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""" | ||
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 | ||
""" | ||
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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 | ||
""" | ||
} |
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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"] | ||
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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 | ||
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- assemblies: | ||
type: file | ||
description: Input assemblies whose contigs will be clustered | ||
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- out_dir: | ||
type: directory | ||
description: Output directory for clustering results | ||
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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 | ||
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||
- versions: | ||
type: file | ||
description: File containing software versions | ||
pattern: "versions.yml" | ||
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authors: | ||
- "@watsonar" | ||
maintainers: | ||
- "@watsonar" |
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nextflow_process { | ||
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name "Test Process TRYCYCLER_CLUSTER" | ||
script "../main.nf" | ||
process "TRYCYCLER_CLUSTER" | ||
config './nextflow.config' | ||
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tag "modules" | ||
tag "modules_nfcore" | ||
tag "trycycler" | ||
tag "trycycler/cluster" | ||
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test("custom test data") { | ||
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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 | ||
] | ||
""" | ||
} | ||
} | ||
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then { | ||
assertAll( | ||
{ assert process.success }, | ||
{ assert snapshot(process.out).match() } | ||
) | ||
} | ||
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} | ||
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test("custom test data - stub") { | ||
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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 | ||
] | ||
""" | ||
} | ||
} | ||
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then { | ||
assertAll( | ||
{ assert process.success }, | ||
{ assert snapshot(process.out).match() } | ||
) | ||
} | ||
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} | ||
} |
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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" | ||
} | ||
} |
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process { | ||
withName: TRYCYCLER_CLUSTER { | ||
ext.args = '--min_contig_len 0 --min_contig_depth 0' | ||
} | ||
} |
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trycycler/cluster: | ||
- "modules/nf-core/trycycler/cluster/**" |
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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" |
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