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Add support for Bakta expert systems annotation #7

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6 changes: 5 additions & 1 deletion main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -65,6 +65,7 @@ workflow {
infiles = Channel.fromPath("${params.indir}/*${params.infile_extension}") // TODO: add input file extension as a parameter

infiles
.take(5)
.combine(bakta_db)
.set { infiles_and_bakta_db }

Expand Down Expand Up @@ -96,7 +97,10 @@ workflow {
.combine(bakta_db)
.set { rep_proteins_and_bakta_db }

ANNOTATE_PROTEINS(rep_proteins_and_bakta_db)
hmm_ch = params.user_hmms ? Channel.of(file(params.user_hmms)) : []
prots_ch = params.user_proteins ? Channel.of(file(params.user_proteins)) : []

ANNOTATE_PROTEINS(rep_proteins_and_bakta_db, hmm_ch, prots_ch)

//-----------------------------
// Merge annotations
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6 changes: 6 additions & 0 deletions modules/annotate_proteins.nf
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Expand Up @@ -7,15 +7,21 @@ process ANNOTATE_PROTEINS {

input:
tuple path(proteins_fa), path(bakta_db)
path(user_hmms)
path(user_proteins)

output:
path("annotated_proteins_bakta/unique_proteins_annotation.json")

script:
user_proteins_bakta = user_proteins ? "--proteins ${user_proteins}" : ""
hmms_bakta = user_hmms ? "--hmms ${user_hmms}" : ""
"""
bakta_proteins --db ${bakta_db} \
--output annotated_proteins_bakta \
--prefix unique_proteins_annotation \
${user_proteins_bakta} \
${hmms_bakta} \
--threads ${task.cpus} \
${proteins_fa}
"""
Expand Down
8 changes: 6 additions & 2 deletions nextflow.config
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Expand Up @@ -47,6 +47,10 @@ params {

bakta_args = ""

// Bakta expert systems parameters
user_proteins = null
user_hmms = null

// Sequence clustering
mmseqs_clusterPrefix = "mmseqs_clustering"
mmseqs_tmpDir = "mmseqs_clustering"
Expand Down Expand Up @@ -74,7 +78,7 @@ process {

withName: ANNOTATE_PROTEINS_MODULE {
cpus = { 8 * task.attempt } // cpu_48
memory = { 32.GB * task.attempt } // mem_32
memory = { 8.GB * task.attempt } // mem_32
time = { 2.h * task.attempt } // time_2
}

Expand All @@ -85,7 +89,7 @@ process {

withName: DETECT_PSEUDOGENES_MODULE {
cpus = { 8 * task.attempt } // cpu_16
memory = { 32.GB * task.attempt } // mem_32
memory = { 16.GB * task.attempt } // mem_32
}
}

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6 changes: 4 additions & 2 deletions subworkflows/annotate_proteins.nf
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Expand Up @@ -2,10 +2,12 @@ include { ANNOTATE_PROTEINS as ANNOTATE_PROTEINS_MODULE; PARSE_BAKTA_JSON_ANNOTA

workflow ANNOTATE_PROTEINS {
take:
unique_proteins_channel // path(proteins_fa)
unique_proteins_channel // path(proteins_fa), path(bakta_db)
hmm_ch //path(user_hmms)
prots_ch // path(user_proteins)

main:
ANNOTATE_PROTEINS_MODULE(unique_proteins_channel)
ANNOTATE_PROTEINS_MODULE(unique_proteins_channel, hmm_ch, prots_ch)
ANNOTATE_PROTEINS_MODULE.out
.set { protein_annotations }

Expand Down