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feat: Add annotation tools param #134

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merged 2 commits into from
Jun 16, 2023
Merged

feat: Add annotation tools param #134

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bfa843a
feat: Add annotation tools param
jvfe Jun 16, 2023
dc152c5
test: Add missing tool in ann test
jvfe Jun 16, 2023
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3 changes: 1 addition & 2 deletions conf/test.config
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Original file line number Diff line number Diff line change
Expand Up @@ -24,8 +24,7 @@ params {
use_prokka = true
skip_kraken = true
skip_poppunk = true
skip_phispy = true
light = true
annotation_tools = 'mobsuite,rgi,vfdb'
}

process {
Expand Down
3 changes: 1 addition & 2 deletions nextflow.config
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Expand Up @@ -34,8 +34,7 @@ params {
// Annotation parameters
use_prokka = false
bakta_db = null
light = false
run_integronfinder = false
annotation_tools = 'mobsuite,rgi,cazy,vfdb,iceberg,bacmet,islandpath,phispy'
min_pident = 60
min_qcover = 0.6
skip_phispy = false
Expand Down
18 changes: 7 additions & 11 deletions nextflow_schema.json
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Expand Up @@ -82,28 +82,24 @@
"default": "",
"fa_icon": "fas fa-edit",
"properties": {
"annotation_tools": {
"type": "string",
"default": "mobsuite,rgi,cazy,vfdb,iceberg,bacmet,islandpath,phispy",
"fa_icon": "fas fa-tools",
"description": "Comma-separated list of annotation tools to run",
"pattern": "^((rgi|mobsuite|islandpath|phispy|vfdb|cazy|bacmet|iceberg|integronfinder)?,?)*(?<!,)$"
},
"bakta_db": {
"type": "string",
"default": "None",
"fa_icon": "fas fa-database",
"description": "Path to the BAKTA database"
},
"light": {
"type": "boolean",
"description": "Only run one DIAMOND annotation step - against VFDB",
"hidden": true,
"fa_icon": "fas fa-feather-alt"
},
"use_prokka": {
"type": "boolean",
"fa_icon": "fas fa-bacterium",
"description": "Use Prokka (not Bakta) for annotating assemblies"
},
"run_integronfinder": {
"type": "boolean",
"fa_icon": "fas fa-puzzle-piece",
"description": "Run Integron Finder as part of the annotation workflow"
},
"min_pident": {
"type": "integer",
"default": 60,
Expand Down
158 changes: 86 additions & 72 deletions subworkflows/local/annotation.nf
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Expand Up @@ -66,6 +66,7 @@ workflow ANNOTATE_ASSEMBLIES {
ch_multiqc_files = Channel.empty()
ch_software_versions = Channel.empty()

tools_to_run = params.annotation_tools.split(',')
min_pident = params.min_pident
min_qcover = params.min_qcover
/*
Expand All @@ -83,32 +84,34 @@ workflow ANNOTATE_ASSEMBLIES {
if (vfdb_cache){
vfdb_cache.set { ch_vfdb }
}
else{
else if (tools_to_run.contains('vfdb')) {
GET_VFDB()
GET_VFDB.out.vfdb.set { ch_vfdb }
}
if (!params.light) {
if(bacmet_cache){
bacmet_cache.set { ch_bacmet_db }
}
else{
GET_BACMET()
GET_BACMET.out.bacmet.set { ch_bacmet_db }
}
if (cazydb_cache){
cazydb_cache.set{ ch_cazy_db }
}
else{
GET_CAZYDB()
GET_CAZYDB.out.cazydb.set { ch_cazy_db }
}
if (icebergdb_cache){
icebergdb_cache.set{ ch_iceberg_db }
}
else{
GET_ICEBERG()
GET_ICEBERG.out.iceberg.set { ch_iceberg_db }
}

if(bacmet_cache){
bacmet_cache.set { ch_bacmet_db }
}
else if (tools_to_run.contains('bacmet')) {
GET_BACMET()
GET_BACMET.out.bacmet.set { ch_bacmet_db }
}

if (cazydb_cache){
cazydb_cache.set{ ch_cazy_db }
}
else if (tools_to_run.contains('cazy')) {
GET_CAZYDB()
GET_CAZYDB.out.cazydb.set { ch_cazy_db }
}

if (icebergdb_cache){
icebergdb_cache.set{ ch_iceberg_db }
}

else if (tools_to_run.contains('iceberg')){
GET_ICEBERG()
GET_ICEBERG.out.iceberg.set { ch_iceberg_db }
}
/*
* Load RGI for AMR annotation
Expand All @@ -117,7 +120,7 @@ workflow ANNOTATE_ASSEMBLIES {
card_json_cache.set { ch_card_json }
ch_software_versions = ch_software_versions.mix(card_version_cache)
}
else{
else if (tools_to_run.contains('rgi')) {
UPDATE_RGI_DB()
UPDATE_RGI_DB.out.card_json.set { ch_card_json }
ch_software_versions = ch_software_versions.mix(UPDATE_RGI_DB.out.card_version.ifEmpty(null))
Expand Down Expand Up @@ -184,34 +187,37 @@ workflow ANNOTATE_ASSEMBLIES {
/*
* Run RGI
*/
RGI(ch_ffn_files, ch_card_json)
ch_software_versions = ch_software_versions.mix(RGI.out.version.first().ifEmpty(null))

RGI_ADD_COLUMN(
RGI.out.tsv,
"RGI",
0
)
if (tools_to_run.contains('rgi')) {
RGI(ch_ffn_files, ch_card_json)
ch_software_versions = ch_software_versions.mix(RGI.out.version.first().ifEmpty(null))

RGI_ADD_COLUMN(
RGI.out.tsv,
"RGI",
0
)

RGI_ADD_COLUMN.out.txt
.collect{ id, paths -> paths }
.set { rgi_tsvs }
RGI_ADD_COLUMN.out.txt
.collect{ id, paths -> paths }
.set { rgi_tsvs }

CONCAT_RGI(rgi_tsvs, "RGI", 1)
CONCAT_RGI(rgi_tsvs, "RGI", 1)
}

/*
* Module: Mob-Suite. Database is included in singularity container
*/
MOB_RECON(assemblies)
ch_software_versions = ch_software_versions.mix(MOB_RECON.out.version.first().ifEmpty(null))

MOB_RECON.out.contig_report
.collect{ id, paths -> paths }
.set { mobrecon_tsvs }
if (tools_to_run.contains('mobsuite')) {
MOB_RECON(assemblies)
ch_software_versions = ch_software_versions.mix(MOB_RECON.out.version.first().ifEmpty(null))

CONCAT_MOBSUITE(mobrecon_tsvs, "MOBSUITE", 1)
MOB_RECON.out.contig_report
.collect{ id, paths -> paths }
.set { mobrecon_tsvs }

if (params.run_integronfinder){
CONCAT_MOBSUITE(mobrecon_tsvs, "MOBSUITE", 1)
}
if (tools_to_run.contains('integronfinder')){
INTEGRON_FINDER(assemblies)
ch_software_versions = ch_software_versions.mix(INTEGRON_FINDER.out.versions.first())

Expand All @@ -223,7 +229,7 @@ workflow ANNOTATE_ASSEMBLIES {
}

ch_phispy_out = []
if (!params.skip_phispy) {
if (tools_to_run.contains('phispy')) {
PHISPY(ch_gbk_files)
ch_software_versions = ch_software_versions.mix(PHISPY.out.versions.first())

Expand All @@ -239,36 +245,39 @@ workflow ANNOTATE_ASSEMBLIES {

CONCAT_PHISPY(phispy_tsvs, "PHISPY", 1)
}
if (tools_to_run.contains('islandpath')) {
ISLANDPATH(ch_gbk_files)
ch_software_versions = ch_software_versions.mix(ISLANDPATH.out.versions.first())

ISLANDPATH(ch_gbk_files)
ch_software_versions = ch_software_versions.mix(ISLANDPATH.out.versions.first())

ISLANDPATH.out.gff
.collect{ id, paths -> paths }
.set { islandpath_gffs }

CONCAT_ISLANDS(islandpath_gffs, "ISLANDPATH", 1)
ISLANDPATH.out.gff
.collect{ id, paths -> paths }
.set { islandpath_gffs }

CONCAT_ISLANDS(islandpath_gffs, "ISLANDPATH", 1)
}
/*
* Run DIAMOND blast annotation with databases
*/
ch_diamond_outs = Channel.empty()
def blast_columns = "qseqid sseqid pident slen qlen length mismatch gapopen qstart qend sstart send evalue bitscore full_qseq"

if (tools_to_run.contains('vfdb')) {
DIAMOND_MAKE_VFDB(ch_vfdb)
DIAMOND_BLAST_VFDB(ch_ffn_files, DIAMOND_MAKE_VFDB.out.db, "txt", blast_columns)
VFDB_FILTER(
DIAMOND_BLAST_VFDB.out.txt,
"VFDB",
blast_columns,
min_pident,
min_qcover
)

DIAMOND_MAKE_VFDB(ch_vfdb)
DIAMOND_BLAST_VFDB(ch_ffn_files, DIAMOND_MAKE_VFDB.out.db, "txt", blast_columns)
VFDB_FILTER(
DIAMOND_BLAST_VFDB.out.txt,
"VFDB",
blast_columns,
min_pident,
min_qcover
)

ch_diamond_outs.mix(VFDB_FILTER.out.concatenated).set{ ch_diamond_outs }
ch_diamond_outs.mix(VFDB_FILTER.out.concatenated)
.set{ ch_diamond_outs }

if (!params.light) {
ch_software_versions = ch_software_versions.mix(DIAMOND_MAKE_VFDB.out.versions.ifEmpty(null))
}
if (tools_to_run.contains('bacmet')) {
DIAMOND_MAKE_BACMET(ch_bacmet_db)
DIAMOND_BLAST_BACMET(ch_ffn_files, DIAMOND_MAKE_BACMET.out.db, "txt", blast_columns)
BACMET_FILTER(
Expand All @@ -279,6 +288,10 @@ workflow ANNOTATE_ASSEMBLIES {
min_qcover
)

ch_diamond_outs.mix(BACMET_FILTER.out.concatenated)
.set{ ch_diamond_outs }
}
if (tools_to_run.contains('cazy')) {
DIAMOND_MAKE_CAZY(ch_cazy_db)
DIAMOND_BLAST_CAZY(ch_ffn_files, DIAMOND_MAKE_CAZY.out.db, "txt", blast_columns)
CAZY_FILTER(
Expand All @@ -289,6 +302,10 @@ workflow ANNOTATE_ASSEMBLIES {
min_qcover
)

ch_diamond_outs.mix(CAZY_FILTER.out.concatenated)
.set{ ch_diamond_outs }
}
if (tools_to_run.contains('iceberg')) {
DIAMOND_MAKE_ICEBERG(ch_iceberg_db)
DIAMOND_BLAST_ICEBERG(ch_ffn_files, DIAMOND_MAKE_ICEBERG.out.db, "txt", blast_columns)
ICEBERG_FILTER(
Expand All @@ -299,16 +316,13 @@ workflow ANNOTATE_ASSEMBLIES {
min_qcover
)

ch_diamond_outs
.mix(BACMET_FILTER.out.concatenated)
.mix(CAZY_FILTER.out.concatenated)
.mix(ICEBERG_FILTER.out.concatenated)
ch_diamond_outs.mix(ICEBERG_FILTER.out.concatenated)
.set { ch_diamond_outs }
}

ch_software_versions = ch_software_versions.mix(DIAMOND_MAKE_VFDB.out.versions.ifEmpty(null))

if (!params.use_prokka) {
needed_for_report = ['vfdb', 'rgi', 'mobsuite']
if (!params.use_prokka && needed_for_report.every { it in tools_to_run }) {
CREATE_REPORT(
CONCAT_BAKTA.out.txt,
ch_diamond_outs.collect(),
Expand All @@ -317,7 +331,7 @@ workflow ANNOTATE_ASSEMBLIES {
ch_phispy_out,
CONCAT_MOBSUITE.out.txt
)
} else {
} else if (needed_for_report.every { it in tools_to_run }) {
CREATE_REPORT(
CONCAT_PROKKA.out.txt,
ch_diamond_outs.collect(),
Expand Down
2 changes: 1 addition & 1 deletion tests/subworkflows/local/annotation.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ nextflow_workflow {
when {
params {
// define parameters here. Example:
light = true
annotation_tools = 'mobsuite,rgi,vfdb,islandpath'
use_prokka = true
min_pident = 80
min_qcover = 0.8
Expand Down