Skip to content

a3m msa input for colabfold #174

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

Open
vagkaratzas wants to merge 1 commit into
base: dev
Choose a base branch
from
+118 −47
Open

a3m msa input for colabfold #174

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
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
6 changes: 6 additions & 0 deletions assets/test_msa/test_msa.a3m
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
>1
ALDLKLRKDMQYELKTMQQELGITFIYVTHDQEEALTMSDRIVVMKDGYIQQIGTPEDIYNEPVNKFVADFIGESNILDGIM
>2
NLDVALRNRLRKELKELQRKTGVTMVFVTHDQEEALSLSDRLVVMEHGKIVQINTPEEVYYHPVNHYVASFVGKSNFMRGED
>3
GLHQRDNEKLIATLKKL-RDLGNTVIVVEHDEDTMYA-ADQIIDIGpgpgvhGGKVIAQGTAEQIKQI---peSITGQYLSgkkqipi-----PEKR
25 changes: 25 additions & 0 deletions conf/test_full_colabfold_local_msa.config
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,25 @@
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Nextflow config file for running full-size tests
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Defines input files and everything required to run a full size pipeline test.

Use as follows:
nextflow run nf-core/proteinfold -profile test_full_colabfold_local_msa,<docker/singularity> --outdir <OUTDIR>

----------------------------------------------------------------------------------------
*/

params {
config_profile_name = 'Full test profile for colabfold local with msa input'
config_profile_description = 'Minimal test dataset to check pipeline function'


// Input data to test colabfold with a local server analysis
mode = 'colabfold'
colabfold_server = 'local'
colabfold_model_preset = 'alphafold2_ptm'
input = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.0/samplesheet.csv'
colabfold_db = 's3://proteinfold-dataset/test-data/db/colabfold_mini'
msa_folder_path = "${projectDir}/assets/test_msa"
}
2 changes: 2 additions & 0 deletions nextflow.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -57,6 +57,7 @@ params {
host_url = null
use_templates = true
create_colabfold_index = false
msa_folder_path = null

// Colabfold links
colabfold_db_link = null
Expand Down Expand Up @@ -261,6 +262,7 @@ profiles {
test_full_alphafold2_split { includeConfig 'conf/test_full_alphafold_split.config' }
test_full_alphafold2_multimer { includeConfig 'conf/test_full_alphafold_multimer.config' }
test_full_colabfold_local { includeConfig 'conf/test_full_colabfold_local.config' }
test_full_colabfold_local_msa { includeConfig 'conf/test_full_colabfold_local_msa.config' }
test_full_colabfold_webserver { includeConfig 'conf/test_full_colabfold_webserver.config' }
test_full_colabfold_multimer { includeConfig 'conf/test_full_colabfold_webserver_multimer.config' }
test_full_esmfold { includeConfig 'conf/test_full_esmfold.config' }
Expand Down
7 changes: 7 additions & 0 deletions nextflow_schema.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -164,6 +164,13 @@
"type": "boolean",
"description": "Create databases indexes when running colabfold_local mode",
"fa_icon": "fas fa-bezier-curve"
},
"msa_folder_path": {
"type": "string",
"format": "path",
"exists": true,
"description": "Specifies the path to a folder with precalcualted MSA files for 'colabfold' mode",
"fa_icon": "fas fa-folder-open"
}
}
},
Expand Down
125 changes: 78 additions & 47 deletions workflows/colabfold.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -57,17 +57,18 @@ workflow COLABFOLD {
.fromSamplesheet("input")
.set { ch_fasta }

if (params.msa_folder_path) {
Channel.fromPath(params.msa_folder_path)
.map { filepath ->
return [ [id:"msa"], file(filepath) ]
}
.set { ch_msa }
}

if (params.colabfold_server == 'webserver') {
//
// MODULE: Run colabfold
//
if (params.colabfold_model_preset != 'alphafold2_ptm' && params.colabfold_model_preset != 'alphafold2') {
MULTIFASTA_TO_CSV(
ch_fasta
)
ch_versions = ch_versions.mix(MULTIFASTA_TO_CSV.out.versions)
if (params.msa_folder_path) {
COLABFOLD_BATCH(
MULTIFASTA_TO_CSV.out.input_csv,
ch_msa,
colabfold_model_preset,
ch_colabfold_params,
[],
Expand All @@ -76,55 +77,85 @@ workflow COLABFOLD {
)
ch_versions = ch_versions.mix(COLABFOLD_BATCH.out.versions)
} else {
//
// MODULE: Run colabfold
//
if (params.colabfold_model_preset != 'alphafold2_ptm' && params.colabfold_model_preset != 'alphafold2') {
MULTIFASTA_TO_CSV(
ch_fasta
)
ch_versions = ch_versions.mix(MULTIFASTA_TO_CSV.out.versions)
COLABFOLD_BATCH(
MULTIFASTA_TO_CSV.out.input_csv,
colabfold_model_preset,
ch_colabfold_params,
[],
[],
num_recycles
)
ch_versions = ch_versions.mix(COLABFOLD_BATCH.out.versions)
} else {
COLABFOLD_BATCH(
ch_fasta,
colabfold_model_preset,
ch_colabfold_params,
[],
[],
num_recycles
)
ch_versions = ch_versions.mix(COLABFOLD_BATCH.out.versions)
}
}
} else if (params.colabfold_server == 'local') {
if (params.msa_folder_path) {
COLABFOLD_BATCH(
ch_fasta,
ch_msa,
colabfold_model_preset,
ch_colabfold_params,
[],
[],
ch_colabfold_db,
ch_uniref30,
num_recycles
)
ch_versions = ch_versions.mix(COLABFOLD_BATCH.out.versions)
}

} else if (params.colabfold_server == 'local') {
//
// MODULE: Run mmseqs
//
if (params.colabfold_model_preset != 'AlphaFold2-ptm') {
MULTIFASTA_TO_CSV(
ch_fasta
)
ch_versions = ch_versions.mix(MULTIFASTA_TO_CSV.out.versions)
MMSEQS_COLABFOLDSEARCH (
MULTIFASTA_TO_CSV.out.input_csv,
ch_colabfold_params,
ch_colabfold_db,
ch_uniref30
)
ch_versions = ch_versions.mix(MMSEQS_COLABFOLDSEARCH.out.versions)
} else {
MMSEQS_COLABFOLDSEARCH (
ch_fasta,
//
// MODULE: Run mmseqs
//
if (params.colabfold_model_preset != 'AlphaFold2-ptm') {
MULTIFASTA_TO_CSV(
ch_fasta
)
ch_versions = ch_versions.mix(MULTIFASTA_TO_CSV.out.versions)
MMSEQS_COLABFOLDSEARCH (
MULTIFASTA_TO_CSV.out.input_csv,
ch_colabfold_params,
ch_colabfold_db,
ch_uniref30
)
ch_versions = ch_versions.mix(MMSEQS_COLABFOLDSEARCH.out.versions)
} else {
MMSEQS_COLABFOLDSEARCH (
ch_fasta,
ch_colabfold_params,
ch_colabfold_db,
ch_uniref30
)
ch_versions = ch_versions.mix(MMSEQS_COLABFOLDSEARCH.out.versions)
}

//
// MODULE: Run colabfold
//
COLABFOLD_BATCH(
MMSEQS_COLABFOLDSEARCH.out.a3m,
colabfold_model_preset,
ch_colabfold_params,
ch_colabfold_db,
ch_uniref30
ch_uniref30,
num_recycles
)
ch_versions = ch_versions.mix(MMSEQS_COLABFOLDSEARCH.out.versions)
ch_versions = ch_versions.mix(COLABFOLD_BATCH.out.versions)
}

//
// MODULE: Run colabfold
//
COLABFOLD_BATCH(
MMSEQS_COLABFOLDSEARCH.out.a3m,
colabfold_model_preset,
ch_colabfold_params,
ch_colabfold_db,
ch_uniref30,
num_recycles
)
ch_versions = ch_versions.mix(COLABFOLD_BATCH.out.versions)
}

//
Expand Down