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Upgrade the blast/makedb module - took it from nf-core
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‎README.md

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Original file line numberDiff line numberDiff line change
@@ -46,6 +46,10 @@ Then import the desired module in your pipeline script:
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include { <subworkflow_name> } from '../subworkflows/ebi-metagenomics/<subworkflow_name>.nf'
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```
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## nf-core modules
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The [nf-core](https://nf-co.re/) team supports a large number of high-quality modules, and our team contributes whenever we can. At the moment, the [nf-core tools](https://github.com/nf-core/tools/) don't support subworkflows that install modules from different repos ([#3083](https://github.com/nf-core/tools/pull/3083)). That is why we decided to copy some modules from nf-core into this repo (a nasty hack, but it works). The nf-core team has been making impressive progress on supporting this use case (subworkflows with modules from different repos), and we will remove the duplicated modules once they reach that point. In the meantime, you will find duplicated modules from nf-core here.
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## References
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This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/LICENSE).

‎modules/ebi-metagenomics/blast/blastn/tests/main.nf.test

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@@ -6,6 +6,7 @@ nextflow_process {
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config "./nextflow.config"
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tag "modules"
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tag "modules_nfcore"
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tag "modules_ebimetagenomics"
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tag "blast"
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tag "blast/blastn"
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tag "blast/makeblastdb"

‎modules/ebi-metagenomics/blast/makeblastdb/environment.yml

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@@ -0,0 +1,7 @@
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---
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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
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channels:
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- conda-forge
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- bioconda
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dependencies:
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- bioconda::blast=2.15.0

‎modules/ebi-metagenomics/blast/makeblastdb/main.nf

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Original file line numberDiff line numberDiff line change
@@ -1,30 +1,62 @@
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process BLAST_MAKEBLASTDB {
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tag "$fasta"
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tag "$meta.id"
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label 'process_medium'
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conda "bioconda::blast=2.13.0"
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conda "${moduleDir}/environment.yml"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/blast:2.13.0--hf3cf87c_0' :
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'biocontainers/blast:2.13.0--hf3cf87c_0' }"
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'https://depot.galaxyproject.org/singularity/blast:2.15.0--pl5321h6f7f691_1':
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'biocontainers/blast:2.15.0--pl5321h6f7f691_1' }"
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input:
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path fasta
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tuple val(meta), path(fasta)
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output:
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path 'blast_db' , emit: db
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path "versions.yml" , emit: versions
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tuple val(meta), path("${meta.id}"), emit: db
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path "versions.yml" , emit: versions
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1717
when:
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task.ext.when == null || task.ext.when
1919

2020
script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def is_compressed = fasta.getExtension() == "gz" ? true : false
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def fasta_name = is_compressed ? fasta.getBaseName() : fasta
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"""
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if [ "${is_compressed}" == "true" ]; then
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gzip -c -d ${fasta} > ${fasta_name}
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fi
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2330
makeblastdb \\
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-in $fasta \\
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$args
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mkdir blast_db
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mv ${fasta}* blast_db
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-in ${fasta_name} \\
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${args}
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mkdir ${prefix}
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mv ${fasta_name}* ${prefix}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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blast: \$(blastn -version 2>&1 | sed 's/^.*blastn: //; s/ .*\$//')
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END_VERSIONS
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"""
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stub:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def is_compressed = fasta.getExtension() == "gz" ? true : false
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def fasta_name = is_compressed ? fasta.getBaseName() : fasta
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"""
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touch ${fasta_name}.fasta
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touch ${fasta_name}.fasta.ndb
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touch ${fasta_name}.fasta.nhr
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touch ${fasta_name}.fasta.nin
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touch ${fasta_name}.fasta.njs
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touch ${fasta_name}.fasta.not
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touch ${fasta_name}.fasta.nsq
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touch ${fasta_name}.fasta.ntf
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touch ${fasta_name}.fasta.nto
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mkdir ${prefix}
58+
mv ${fasta_name}* ${prefix}
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2860
cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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blast: \$(blastn -version 2>&1 | sed 's/^.*blastn: //; s/ .*\$//')

‎modules/ebi-metagenomics/blast/makeblastdb/meta.yml

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Original file line numberDiff line numberDiff line change
@@ -12,20 +12,37 @@ tools:
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documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs
1313
doi: 10.1016/S0022-2836(05)80360-2
1414
licence: ["US-Government-Work"]
15+
identifier: ""
1516
input:
16-
- fasta:
17-
type: file
18-
description: Input fasta file
19-
pattern: "*.{fa,fasta}"
17+
- - meta:
18+
type: map
19+
description: |
20+
Groovy Map containing sample information
21+
e.g. [ id:'test', single_end:false ]
22+
- fasta:
23+
type: file
24+
description: Input fasta file
25+
pattern: "*.{fa,fasta,fa.gz,fasta.gz}"
2026
output:
2127
- db:
22-
type: directory
23-
description: Output directory containing blast database files
24-
pattern: "*"
28+
- meta:
29+
type: map
30+
description: |
31+
Groovy Map containing sample information
32+
e.g. [ id:'test', single_end:false ]
33+
- ${meta.id}:
34+
type: directory
35+
description: Output directory containing blast database files
36+
pattern: "*"
2537
- versions:
26-
type: file
27-
description: File containing software versions
28-
pattern: "versions.yml"
38+
- versions.yml:
39+
type: file
40+
description: File containing software versions
41+
pattern: "versions.yml"
2942
authors:
3043
- "@joseespinosa"
3144
- "@drpatelh"
45+
maintainers:
46+
- "@joseespinosa"
47+
- "@drpatelh"
48+
- "@vagkaratzas"

‎modules/ebi-metagenomics/blast/makeblastdb/tests/main.nf.test

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@@ -0,0 +1,93 @@
1+
nextflow_process {
2+
3+
name "Test Process BLAST_MAKEBLASTDB"
4+
script "../main.nf"
5+
process "BLAST_MAKEBLASTDB"
6+
config "./nextflow.config"
7+
tag "modules"
8+
tag "modules_nfcore"
9+
tag "modules_ebimetagenomics"
10+
tag "blast"
11+
tag "blast/makeblastdb"
12+
13+
test("Should build a blast db folder from a fasta file") {
14+
15+
when {
16+
process {
17+
"""
18+
input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]
19+
"""
20+
}
21+
}
22+
23+
then {
24+
assertAll(
25+
{ assert process.success },
26+
{
27+
assert process.out.db.size() == 1
28+
29+
def all_files = ( new File(process.out.db[0][1]) ).listFiles()
30+
def stable_file_names = [
31+
'genome.fasta',
32+
'genome.fasta.ndb',
33+
'genome.fasta.nhr',
34+
'genome.fasta.not',
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'genome.fasta.nsq',
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'genome.fasta.ntf',
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'genome.fasta.nto'
38+
]
39+
40+
def stable_files = all_files.findAll { it.name in stable_file_names }.toSorted()
41+
42+
assert snapshot(
43+
all_files.collect { it.name }.toSorted(),
44+
stable_files,
45+
process.out.versions[0]
46+
).match()
47+
}
48+
)
49+
}
50+
51+
}
52+
53+
test("Should build a blast db folder from a zipped fasta file") {
54+
55+
when {
56+
process {
57+
"""
58+
input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) ]
59+
"""
60+
}
61+
}
62+
63+
then {
64+
assertAll(
65+
{ assert process.success },
66+
{
67+
assert process.out.db.size() == 1
68+
69+
def all_files = ( new File(process.out.db[0][1]) ).listFiles()
70+
def stable_file_names = [
71+
'genome.fasta',
72+
'genome.fasta.ndb',
73+
'genome.fasta.nhr',
74+
'genome.fasta.not',
75+
'genome.fasta.nsq',
76+
'genome.fasta.ntf',
77+
'genome.fasta.nto'
78+
]
79+
80+
def stable_files = all_files.findAll { it.name in stable_file_names }.toSorted()
81+
82+
assert snapshot(
83+
all_files.collect { it.name }.toSorted(),
84+
stable_files,
85+
process.out.versions[0]
86+
).match()
87+
}
88+
)
89+
}
90+
91+
}
92+
93+
}

‎modules/ebi-metagenomics/blast/makeblastdb/tests/main.nf.test.snap

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@@ -0,0 +1,64 @@
1+
2+
{
3+
"Should build a blast db folder from a fasta file": {
4+
"content": [
5+
[
6+
"genome.fasta",
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"genome.fasta.ndb",
8+
"genome.fasta.nhr",
9+
"genome.fasta.nin",
10+
"genome.fasta.njs",
11+
"genome.fasta.not",
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"genome.fasta.nsq",
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"genome.fasta.ntf",
14+
"genome.fasta.nto"
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],
16+
[
17+
"genome.fasta:md5,6e9fe4042a72f2345f644f239272b7e6",
18+
"genome.fasta.ndb:md5,0d553c830656469211de113c5022f06d",
19+
"genome.fasta.nhr:md5,f4b4ddb034fd3dd7b25c89e9d50c004e",
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"genome.fasta.not:md5,1e53e9d08f1d23af0299cfa87478a7bb",
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"genome.fasta.nsq:md5,982cbc7d9e38743b9b1037588862b9da",
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"genome.fasta.ntf:md5,de1250813f0c7affc6d12dac9d0fb6bb",
23+
"genome.fasta.nto:md5,33cdeccccebe80329f1fdbee7f5874cb"
24+
],
25+
"versions.yml:md5,cb63396fd8d8f4df57913b63452d6ba8"
26+
],
27+
"meta": {
28+
"nf-test": "0.8.4",
29+
"nextflow": "24.04.4"
30+
},
31+
"timestamp": "2024-08-09T15:40:32.52079"
32+
},
33+
"Should build a blast db folder from a zipped fasta file": {
34+
"content": [
35+
[
36+
"genome.fasta",
37+
"genome.fasta.gz",
38+
"genome.fasta.ndb",
39+
"genome.fasta.nhr",
40+
"genome.fasta.nin",
41+
"genome.fasta.njs",
42+
"genome.fasta.not",
43+
"genome.fasta.nsq",
44+
"genome.fasta.ntf",
45+
"genome.fasta.nto"
46+
],
47+
[
48+
"genome.fasta:md5,6e9fe4042a72f2345f644f239272b7e6",
49+
"genome.fasta.ndb:md5,0d553c830656469211de113c5022f06d",
50+
"genome.fasta.nhr:md5,f4b4ddb034fd3dd7b25c89e9d50c004e",
51+
"genome.fasta.not:md5,1e53e9d08f1d23af0299cfa87478a7bb",
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"genome.fasta.nsq:md5,982cbc7d9e38743b9b1037588862b9da",
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"genome.fasta.ntf:md5,de1250813f0c7affc6d12dac9d0fb6bb",
54+
"genome.fasta.nto:md5,33cdeccccebe80329f1fdbee7f5874cb"
55+
],
56+
"versions.yml:md5,cb63396fd8d8f4df57913b63452d6ba8"
57+
],
58+
"meta": {
59+
"nf-test": "0.8.4",
60+
"nextflow": "24.04.4"
61+
},
62+
"timestamp": "2024-08-09T15:40:37.45154"
63+
}
64+
}

‎modules/ebi-metagenomics/blast/makeblastdb/tests/nextflow.config

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@@ -0,0 +1,5 @@
1+
process {
2+
withName: BLAST_MAKEBLASTDB {
3+
ext.args = '-dbtype nucl'
4+
}
5+
}

‎modules/ebi-metagenomics/blast/makeblastdb/tests/tags.yml

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1+
blast/makeblastdb:
2+
- modules/ebi-metagenomics/blast/makeblastdb/**

‎subworkflows/ebi-metagenomics/assembly_decontamination/tests/main.nf.test

+1-1
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
nextflow_workflow {
2-
2+
33
name "Test subworkflow ASSEMBLY_DECONTAMINATION"
44
script "../main.nf"
55
config "./nextflow.config"

‎tests/config/pytest_modules.yml

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@@ -1,11 +1,3 @@
1-
blast/blastp:
2-
- modules/ebi-metagenomics/blast/blastp/**
3-
- tests/modules/ebi-metagenomics/blast/blastp/**
4-
5-
blast/makeblastdb:
6-
- modules/ebi-metagenomics/blast/makeblastdb/**
7-
- tests/modules/ebi-metagenomics/blast/makeblastdb/**
8-
91
bmtagger/bmtagger:
102
- modules/ebi-metagenomics/bmtagger/bmtagger/**
113
- tests/modules/ebi-metagenomics/bmtagger/bmtagger/**

‎tests/modules/ebi-metagenomics/blast/blastp/main.nf

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This file was deleted.

‎tests/modules/ebi-metagenomics/blast/blastp/nextflow.config

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This file was deleted.

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