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Update CONCOCT module(s): conda build bump, stub, and nf-test #5869

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merged 9 commits into from
Jun 25, 2024
Merged

Update CONCOCT module(s): conda build bump, stub, and nf-test #5869

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b381e9e
Version update, stub, nf-test for concoct/concoct
jfy133 Jun 21, 2024
142ce6c
Bump version, add nf-test, stub to concoct/mergecutupclustering
jfy133 Jun 21, 2024
66e0880
nf-test, stub, and version conda build version bump for concoct/extra…
jfy133 Jun 21, 2024
fa66b55
Remove a superfluous config and specify a used one
jfy133 Jun 21, 2024
4956d63
Update modules/nf-core/concoct/extractfastabins/main.nf
jfy133 Jun 24, 2024
af4b05f
Remove superfluous config file
jfy133 Jun 24, 2024
a1bcc97
Clean up code
jfy133 Jun 24, 2024
120ce9c
Repair all stub tests that were empty
jfy133 Jun 24, 2024
2fcd76f
Merge branch 'master' into concoct-module-updates2
jfy133 Jun 24, 2024
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21 changes: 19 additions & 2 deletions modules/nf-core/concoct/concoct/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -5,8 +5,8 @@ process CONCOCT_CONCOCT {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/concoct:1.1.0--py311h245ed52_4':
'biocontainers/concoct:1.1.0--py311h245ed52_4' }"
'https://depot.galaxyproject.org/singularity/concoct:1.1.0--py312h245ed52_6':
'biocontainers/concoct:1.1.0--py312h245ed52_6' }"

input:
tuple val(meta), path(coverage_file), path(fasta)
Expand Down Expand Up @@ -39,4 +39,21 @@ process CONCOCT_CONCOCT {
concoct: \$(echo \$(concoct --version 2>&1) | sed 's/concoct //g' )
END_VERSIONS
"""

stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}_args.txt
touch ${prefix}_clustering_gt1000.csv
touch ${prefix}_log.txt
touch ${prefix}_original_data_gt1000.csv
touch ${prefix}_PCA_components_data_gt1000.csv
touch ${prefix}_PCA_transformed_data_gt1000.csv

cat <<-END_VERSIONS > versions.yml
"${task.process}":
concoct: \$(echo \$(concoct --version 2>&1) | sed 's/concoct //g' )
END_VERSIONS
"""
}
4 changes: 2 additions & 2 deletions modules/nf-core/concoct/concoct/meta.yml
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Expand Up @@ -17,14 +17,14 @@ tools:
documentation: "https://concoct.readthedocs.io/en/latest/index.html"
tool_dev_url: "https://github.com/BinPro/CONCOCT"
doi: "10.1038/nmeth.3103"
licence: "['FreeBSD']"
licence: ["FreeBSD"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- coverage:
- coverage_file:
type: file
description: Subcontig coverage TSV table (typically generated with concoct_coverage_table.py)
pattern: "*.tsv"
Expand Down
105 changes: 105 additions & 0 deletions modules/nf-core/concoct/concoct/tests/main.nf.test
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@@ -0,0 +1,105 @@
nextflow_process {

name "Test Process CONCOCT_CONCOCT"
script "../main.nf"
process "CONCOCT_CONCOCT"

tag "modules"
tag "modules_nfcore"
tag "concoct"
tag "concoct/concoct"
tag "concoct/cutupfasta"
tag "concoct/concoctcoveragetable"

setup {
run("CONCOCT_CUTUPFASTA") {
script "../../cutupfasta/main.nf"
process {
"""
input[0] = [
[id: 'test', single_end: false],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
]
input[1] = true
"""
}
}

run("CONCOCT_CONCOCTCOVERAGETABLE") {
script "../../concoctcoveragetable/main.nf"
process {
"""
ch_bam_input = Channel
.fromList([
[
[ id:'test', single_end:false ], // meta map
[
file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true),
file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
],
[
file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai', checkIfExists: true),
file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
]
]
])


input[0] = CONCOCT_CUTUPFASTA.out.bed.join( ch_bam_input )
"""
}
}
}

test("sarscov2 - bam") {

when {
process {
"""
ch_input_for_concoctconcoct = CONCOCT_CONCOCTCOVERAGETABLE.out.tsv
.join(CONCOCT_CUTUPFASTA.out.fasta)

input[0] = ch_input_for_concoctconcoct
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.args_txt,
process.out.clustering_csv,
process.out.original_data_csv,
process.out.pca_components_csv,
process.out.pca_transformed_csv,
process.out.versions,
file(process.out.log_txt[0][1]).readLines().last().contains("CONCOCT Finished, the log shows how it went.")
).match() }
)
}

}

test("sarscov2 - bam - stub") {

options "-stub"

when {
process {
"""
input[0] = [ [id: 'test'], [], [] ]
"""
}
}

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

}

}
173 changes: 173 additions & 0 deletions modules/nf-core/concoct/concoct/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -0,0 +1,173 @@
{
"sarscov2 - bam - stub": {
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"content": [
{
"0": [
[
{
"id": "test"
},
"test_args.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
[
{
"id": "test"
},
"test_clustering_gt1000.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"2": [
[
{
"id": "test"
},
"test_log.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"3": [
[
{
"id": "test"
},
"test_original_data_gt1000.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"4": [
[
{
"id": "test"
},
"test_PCA_components_data_gt1000.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"5": [
[
{
"id": "test"
},
"test_PCA_transformed_data_gt1000.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"6": [
"versions.yml:md5,ed583fb0862e060844ceffee6bf0eeb7"
],
"args_txt": [
[
{
"id": "test"
},
"test_args.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"clustering_csv": [
[
{
"id": "test"
},
"test_clustering_gt1000.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"log_txt": [
[
{
"id": "test"
},
"test_log.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"original_data_csv": [
[
{
"id": "test"
},
"test_original_data_gt1000.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"pca_components_csv": [
[
{
"id": "test"
},
"test_PCA_components_data_gt1000.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"pca_transformed_csv": [
[
{
"id": "test"
},
"test_PCA_transformed_data_gt1000.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,ed583fb0862e060844ceffee6bf0eeb7"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-06-24T08:39:53.759611572"
},
"sarscov2 - bam": {
"content": [
[
[
{
"id": "test",
"single_end": false
},
"test_args.txt:md5,277d8a15f732ae1bd4d6839fd768113e"
]
],
[
[
{
"id": "test",
"single_end": false
},
"test_clustering_gt1000.csv:md5,8cb3e6901075bf07966d08e1816762ce"
]
],
[
[
{
"id": "test",
"single_end": false
},
"test_original_data_gt1000.csv:md5,7474c6a670a608c2c9c9b9edde724074"
]
],
[
[
{
"id": "test",
"single_end": false
},
"test_PCA_components_data_gt1000.csv:md5,e69fd8a810563e62cb0c3998842b3659"
]
],
[
[
{
"id": "test",
"single_end": false
},
"test_PCA_transformed_data_gt1000.csv:md5,558a35f720a9bfa54cbf7cdf099fd367"
]
],
[
"versions.yml:md5,ed583fb0862e060844ceffee6bf0eeb7"
],
true
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-06-21T20:25:56.619830843"
}
}
2 changes: 2 additions & 0 deletions modules/nf-core/concoct/concoct/tests/tags.yml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
concoct/concoct:
- "modules/nf-core/concoct/concoct/**"
17 changes: 1 addition & 16 deletions modules/nf-core/concoct/concoctcoveragetable/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -67,22 +67,7 @@ nextflow_process {
when {
process {
"""
ch_bam_input = Channel
.fromList([
[
[ id:'test', single_end:false ], // meta map
[
file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true),
file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
],
[
file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai', checkIfExists: true),
file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
]
]
])

input[0] = CONCOCT_CUTUPFASTA.out.bed.join( ch_bam_input )
input[0] = [ [id:'test'], [], [] ,[] ]
"""
}
}
Expand Down
20 changes: 15 additions & 5 deletions modules/nf-core/concoct/concoctcoveragetable/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -3,24 +3,34 @@
"content": [
{
"0": [

[
{
"id": "test"
},
"test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [

"versions.yml:md5,156a9a23e05b34188d03d52b39fae343"
],
"tsv": [

[
{
"id": "test"
},
"test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [

"versions.yml:md5,156a9a23e05b34188d03d52b39fae343"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-06-21T16:02:03.884676509"
"timestamp": "2024-06-24T08:41:27.166202038"
},
"sarscov2 - bam": {
"content": [
Expand Down
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