Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update BUSCO module #7199

Merged
merged 8 commits into from
Dec 11, 2024
Merged

Update BUSCO module #7199

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
8 commits
Select commit Hold shift + click to select a range
5674aad
Update BUSCO
dialvarezs Dec 11, 2024
8a908ee
Merge branch 'master' into update-busco
dialvarezs Dec 11, 2024
904dbe5
Update docs
dialvarezs Dec 11, 2024
d48f35b
Merge branch 'update-busco' of github.com:dialvarezs/nf-core-modules …
dialvarezs Dec 11, 2024
f3184f4
Fix very strange linting bug
jfy133 Dec 11, 2024
c048d45
Update checksum
dialvarezs Dec 11, 2024
c44ff08
Merge branch 'update-busco' of github.com:dialvarezs/nf-core-modules …
dialvarezs Dec 11, 2024
5bb5e0e
Update test to remove variability
dialvarezs Dec 11, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 2 additions & 1 deletion modules/nf-core/busco/busco/environment.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
channels:
- conda-forge
- bioconda

dependencies:
- bioconda::busco=5.7.1
- bioconda::busco=5.8.2
14 changes: 8 additions & 6 deletions modules/nf-core/busco/busco/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,14 +4,14 @@ process BUSCO_BUSCO {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/busco:5.7.1--pyhdfd78af_0':
'biocontainers/busco:5.7.1--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/busco:5.8.2--pyhdfd78af_0':
'biocontainers/busco:5.8.2--pyhdfd78af_0' }"

input:
tuple val(meta), path(fasta, stageAs:'tmp_input/*')
val mode // Required: One of genome, proteins, or transcriptome
val lineage // Required: lineage to check against, "auto" enables --auto-lineage instead
path busco_lineages_path // Recommended: path to busco lineages - downloads if not set
val lineage // Required: lineage for checking against, or "auto/auto_prok/auto_euk" for enabling auto-lineage
path busco_lineages_path // Recommended: busco lineages file - downloads if not set
path config_file // Optional: busco configuration file

output:
Expand All @@ -35,8 +35,10 @@ process BUSCO_BUSCO {
}
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}-${lineage}"
def busco_config = config_file ? "--config $config_file" : ''
def busco_lineage = lineage.equals('auto') ? '--auto-lineage' : "--lineage_dataset ${lineage}"
def busco_config = config_file ? "--config ${config_file}" : ''
def busco_lineage = lineage in [ 'auto', 'auto_prok', 'auto_euk']
? lineage.replaceFirst('auto', '--auto-lineage').replaceAll('_', '-')
: "--lineage_dataset ${lineage}"
def busco_lineage_dir = busco_lineages_path ? "--download_path ${busco_lineages_path}" : ''
"""
# Nextflow changes the container --entrypoint to /bin/bash (container default entrypoint: /usr/local/env-execute)
Expand Down
3 changes: 2 additions & 1 deletion modules/nf-core/busco/busco/meta.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,8 @@ input:
pattern: "{genome,proteins,transcriptome}"
- - lineage:
type: string
description: The BUSCO lineage to use, or "auto" to automatically select lineage
description: The BUSCO lineage to use, or "auto", "auto_prok" or "auto_euk"
to automatically select lineage
- - busco_lineages_path:
type: directory
description: Path to local BUSCO lineages directory.
Expand Down
13 changes: 6 additions & 7 deletions modules/nf-core/busco/busco/tests/main.nf.test
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@ nextflow_process {
file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz', checkIfExists: true)
]
input[1] = 'genome'
input[2] = 'bacteria_odb10' // Launch with 'auto' to use --auto-lineage, and specified lineages // 'auto' removed from test due to memory issues
input[2] = 'bacteria_odb12' // Launch with 'auto' to use --auto-lineage, and specified lineages // 'auto' removed from test due to memory issues
input[3] = [] // Download busco lineage
input[4] = [] // No config
"""
Expand Down Expand Up @@ -85,7 +85,7 @@ nextflow_process {
]
]
input[1] = 'genome'
input[2] = 'bacteria_odb10'
input[2] = 'bacteria_odb12'
input[3] = []
input[4] = []
"""
Expand Down Expand Up @@ -126,7 +126,6 @@ nextflow_process {
}

assert snapshot(
process.out.batch_summary[0][1],
process.out.full_table[0][1],
process.out.missing_busco_list[0][1],
process.out.versions[0]
Expand Down Expand Up @@ -274,7 +273,7 @@ nextflow_process {
file(params.modules_testdata_base_path + 'genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/proteome.fasta', checkIfExists: true)
]
input[1] = 'proteins'
input[2] = 'bacteria_odb10'
input[2] = 'bacteria_odb12'
input[3] = []
input[4] = []
"""
Expand Down Expand Up @@ -336,7 +335,7 @@ nextflow_process {
file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz', checkIfExists: true)
]
input[1] = 'transcriptome'
input[2] = 'bacteria_odb10'
input[2] = 'bacteria_odb12'
input[3] = []
input[4] = []
"""
Expand Down Expand Up @@ -397,7 +396,7 @@ nextflow_process {
file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz', checkIfExists: true)
]
input[1] = 'genome'
input[2] = 'bacteria_odb10'
input[2] = 'bacteria_odb12'
input[3] = []
input[4] = []
"""
Expand All @@ -412,4 +411,4 @@ nextflow_process {
}
}

}
}
160 changes: 90 additions & 70 deletions modules/nf-core/busco/busco/tests/main.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@
{
"id": "test"
},
"test-bacteria_odb10-busco.batch_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
"test-bacteria_odb12-busco.batch_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
Expand Down Expand Up @@ -55,14 +55,14 @@
]
],
"9": [
"versions.yml:md5,3fc94714b95c2dc15399a4229d9dd1d9"
"versions.yml:md5,c6e638f981761c13cd9ff7663cf707e6"
],
"batch_summary": [
[
{
"id": "test"
},
"test-bacteria_odb10-busco.batch_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
"test-bacteria_odb12-busco.batch_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"busco_dir": [
Expand Down Expand Up @@ -110,121 +110,141 @@

],
"versions": [
"versions.yml:md5,3fc94714b95c2dc15399a4229d9dd1d9"
"versions.yml:md5,c6e638f981761c13cd9ff7663cf707e6"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.2",
"nextflow": "24.10.1"
},
"timestamp": "2024-05-03T13:28:04.451297"
"timestamp": "2024-12-11T12:45:52.045550047"
},
"test_busco_eukaryote_augustus": {
"content": [
"test-eukaryota_odb10-busco.batch_summary.txt:md5,3ea3bdc423a461dae514d816bdc61c89",
"versions.yml:md5,3fc94714b95c2dc15399a4229d9dd1d9"
"versions.yml:md5,c6e638f981761c13cd9ff7663cf707e6"
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.2",
"nextflow": "24.10.1"
},
"timestamp": "2024-05-03T13:26:36.974986"
"timestamp": "2024-12-11T13:07:45.550722277"
},
"test_busco_genome_single_fasta": {
"content": [
"test-bacteria_odb10-busco.batch_summary.txt:md5,21b3fb771cf36be917cc451540d999be",
"full_table.tsv:md5,638fe7590f442c57361554dae330eca1",
"missing_busco_list.tsv:md5,1530af4fe7673a6d001349537bcd410a",
"versions.yml:md5,3fc94714b95c2dc15399a4229d9dd1d9"
"test-bacteria_odb12-busco.batch_summary.txt:md5,e3e503e1540b633d95c273c465945740",
"full_table.tsv:md5,e2a08fdd9b2596322e70c5549d1affc7",
"missing_busco_list.tsv:md5,25417462f2c484f1942c86b21bcf77d0",
"versions.yml:md5,c6e638f981761c13cd9ff7663cf707e6"
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.2",
"nextflow": "24.10.1"
},
"timestamp": "2024-05-03T13:22:45.07816"
"timestamp": "2024-12-11T12:43:40.359736221"
},
"test_busco_genome_multi_fasta": {
"content": [
"test-bacteria_odb10-busco.batch_summary.txt:md5,fcd3c208913e8abda3d6742c43fec5fa",
[
"full_table.tsv:md5,c657edcc7d0de0175869717551df6e83",
"full_table.tsv:md5,638fe7590f442c57361554dae330eca1"
"full_table.tsv:md5,5e7df014f2804789f0d98ae2e09734ad",
"full_table.tsv:md5,e2a08fdd9b2596322e70c5549d1affc7"
],
[
"missing_busco_list.tsv:md5,aceb66e347a353cb7fca8e2a725f9112",
"missing_busco_list.tsv:md5,1530af4fe7673a6d001349537bcd410a"
"missing_busco_list.tsv:md5,d902f10173b463f81e4892ef64f63c50",
"missing_busco_list.tsv:md5,25417462f2c484f1942c86b21bcf77d0"
],
"versions.yml:md5,3fc94714b95c2dc15399a4229d9dd1d9"
"versions.yml:md5,c6e638f981761c13cd9ff7663cf707e6"
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.2",
"nextflow": "24.10.1"
},
"timestamp": "2024-05-03T13:23:50.255602"
"timestamp": "2024-12-11T17:17:42.175675858"
},
"test_busco_eukaryote_metaeuk": {
"content": [
"test-eukaryota_odb10-busco.batch_summary.txt:md5,ff6d8277e452a83ce9456bbee666feb6",
"full_table.tsv:md5,92b1b1d5cb5ea0e2093d16f00187e8c7",
"missing_busco_list.tsv:md5,0352e563de290bf804c708323c35a9e3",
"versions.yml:md5,3fc94714b95c2dc15399a4229d9dd1d9"
"full_table.tsv:md5,9bfa9ef7d54ca6ad8bcf8e87729720b1",
"missing_busco_list.tsv:md5,325b529e5a8af2a392d747b4eddc150c",
"versions.yml:md5,c6e638f981761c13cd9ff7663cf707e6"
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.2",
"nextflow": "24.10.1"
},
"timestamp": "2024-05-03T13:25:38.159041"
"timestamp": "2024-12-11T13:07:17.335085326"
},
"test_busco_transcriptome": {
"content": [
"test-bacteria_odb10-busco.batch_summary.txt:md5,8734b3f379c4c0928e5dd4ea1873dc64",
"full_table.tsv:md5,1b2ce808fdafa744c56b5f781551272d",
"missing_busco_list.tsv:md5,a6931b6470262b997b8b99ea0f1d14a4",
"test-bacteria_odb12-busco.batch_summary.txt:md5,6cd69d8a66b5f8b7fd4a9de758e7a739",
"full_table.tsv:md5,73a3a90c2fa8fef41cafed5a607fab66",
"missing_busco_list.tsv:md5,4778855c345f4e409750c9bbd38c5a0c",
[
"1024388at2.faa:md5,797d603d262a6595a112e25b73e878b0",
"1054741at2.faa:md5,cd4b928cba6b19b4437746ba507e7195",
"1093223at2.faa:md5,df9549708e5ffcfaee6a74dd70a0e5dc",
"1151822at2.faa:md5,12726afc1cdc40c13392e1596e93df3a",
"143460at2.faa:md5,d887431fd988a5556a523440f02d9594",
"1491686at2.faa:md5,d03362d19979b27306c192f1c74a84e5",
"1504821at2.faa:md5,4f5f6e5c57bac0092c1d85ded73d7e67",
"1574817at2.faa:md5,1153e55998c2929eacad2aed7d08d248",
"1592033at2.faa:md5,bb7a59e5f3a57ba12d10dabf4c77ab57",
"1623045at2.faa:md5,8fe38155feb1802beb97ef7714837bf5",
"1661836at2.faa:md5,6c6d592c2fbb0d7a4e5e1f47a15644f0",
"1674344at2.faa:md5,bb41b44e53565a54cadf0b780532fe08",
"1698718at2.faa:md5,f233860000028eb00329aa85236c71e5",
"1990650at2.faa:md5,34a2d29c5f8b6253159ddb7a43fa1829",
"223233at2.faa:md5,dec6705c7846c989296e73942f953cbc",
"402899at2.faa:md5,acc0f271f9a586d2ce1ee41669b22999",
"505485at2.faa:md5,aa0391f8fa5d9bd19b30d844d5a99845",
"665824at2.faa:md5,47f8ad43b6a6078206feb48c2e552793",
"776861at2.faa:md5,f8b90c13f7c6be828dea3bb920195e3d",
"874197at2.faa:md5,8d22a35a768debe6f376fc695d233a69",
"932854at2.faa:md5,2eff2de1ab83b22f3234a529a44e22bb",
"95696at2.faa:md5,247bfd1aef432f7b5456307768e9149c"
"9767721at2.faa:md5,1731738ca153959391f8302fd5a3679f",
"9778364at2.faa:md5,7a19a6b6696ae53efce30457b4dd1ab2",
"9782003at2.faa:md5,65d2a613c903852681981f8e8427dc70",
"9790352at2.faa:md5,5e18cfb68122dff7a61c5517246223fc",
"9791908at2.faa:md5,707ef4501f93a6e0dc217e037f26da54",
"9793681at2.faa:md5,e361d654145e70f06c386e75ad90f943",
"9800696at2.faa:md5,9e2f431e4aada7bdc2c317747105b874",
"9801107at2.faa:md5,83933b1426fc9abfe8891c49838cd02f",
"9801213at2.faa:md5,ec340354a86728189c3d1a294c0ccbad",
"9801753at2.faa:md5,39c09bd8a831c90aab44ded14c56d0e6",
"9802065at2.faa:md5,8361fa013dc1cd29af938c9d5ffebfe4",
"9802219at2.faa:md5,9e23aed07790f460da634f7f6132e73d",
"9802304at2.faa:md5,86b259197441716075f3d3d18f8743ba",
"9802309at2.faa:md5,b4b4613e9b69baa9274140c1b26cc27b",
"9802672at2.faa:md5,6c6d592c2fbb0d7a4e5e1f47a15644f0",
"9803420at2.faa:md5,eec6f7189ce9a596ed6ead06f2229c8a",
"9803541at2.faa:md5,132954cc7bfcb1c1fe9da105867c4b78",
"9803667at2.faa:md5,ec31d499f6b523cb081af6a3284a5a5c",
"9803773at2.faa:md5,efbe4c35075dd8c871827d4e5ac72922",
"9804006at2.faa:md5,fca5b560714ba37be0be3e2597f74c5a",
"9804243at2.faa:md5,3280570e4357fb4daedaea8a066dbf0b",
"9804478at2.faa:md5,98c2cfd8f089812a41a1e66fea630b2d",
"9804933at2.faa:md5,de648025c49061c614c77e7c9ce7ab62",
"9805026at2.faa:md5,eea9da88f3cd718514493d6890bf7660",
"9806637at2.faa:md5,c8a9e0c37a8aeb1fd44db64fd93aa3e1",
"9806651at2.faa:md5,f5abacf8930d78c81fdeb0c91c8681a7",
"9807064at2.faa:md5,1167d5c4c044b4eb82fac5d1955e7130",
"9807233at2.faa:md5,7c8adb6556a7f9a0244e7c7e5f75f20d",
"9807240at2.faa:md5,2eff2de1ab83b22f3234a529a44e22bb",
"9807458at2.faa:md5,bee695d260b2b7f8980a636fed6aa0c0",
"9808036at2.faa:md5,797ca476d2c7820151fec98d2815d6cb",
"9808348at2.faa:md5,4e8573a5d287e01aa4f5de8b48feaa42",
"9808936at2.faa:md5,30333f3f62f8e3d0ea6f6544d49572c6",
"9809052at2.faa:md5,0590efbf94fce0ad212513dcb2e8176f",
"9809084at2.faa:md5,37e6214b4204dc31858e2ef2bad5db4a",
"9809356at2.faa:md5,e18c1d5a4931a25baf7dbd1a40c417dc",
"9809796at2.faa:md5,857aac8a22c00472bfc9add7fde94c5c",
"9810191at2.faa:md5,72b63933bb045b680e0635eb03915cc0",
"9811804at2.faa:md5,da341c24e763a949d16432bb052af321",
"9812272at2.faa:md5,7a54f872dd8243c6814852d40cf1bfc0",
"9812943at2.faa:md5,149da17f067cdce328a73f6364a95b26",
"9813375at2.faa:md5,49835b9f3188434c771a840b628b07f6",
"9814755at2.faa:md5,9b4c4648d250c2e6d04acb78f9cf6df0"
],
"single_copy_proteins.faa:md5,73e2c5d6a9b0f01f2deea3cc5f21b764",
"versions.yml:md5,3fc94714b95c2dc15399a4229d9dd1d9"
"single_copy_proteins.faa:md5,14124def13668c6d9b0d589207754b31",
"versions.yml:md5,c6e638f981761c13cd9ff7663cf707e6"
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.2",
"nextflow": "24.10.1"
},
"timestamp": "2024-05-03T13:27:53.992893"
"timestamp": "2024-12-11T12:45:43.336777509"
},
"test_busco_protein": {
"content": [
"test-bacteria_odb10-busco.batch_summary.txt:md5,f5a782378f9f94a748aa907381fdef91",
"full_table.tsv:md5,812ab6a0496fccab774643cf40c4f2a8",
"missing_busco_list.tsv:md5,aceb66e347a353cb7fca8e2a725f9112",
"versions.yml:md5,3fc94714b95c2dc15399a4229d9dd1d9"
"test-bacteria_odb12-busco.batch_summary.txt:md5,44d4cdebd61a3c8e8981ddf1829f83b3",
"full_table.tsv:md5,696bae3f377fd5dbaf19f1c522088d93",
"missing_busco_list.tsv:md5,d902f10173b463f81e4892ef64f63c50",
"versions.yml:md5,c6e638f981761c13cd9ff7663cf707e6"
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.2",
"nextflow": "24.10.1"
},
"timestamp": "2024-05-03T13:27:12.724862"
"timestamp": "2024-12-11T12:45:16.960592213"
}
}
Loading
Loading