add busco and fix main

config/compute_resources.config

+// limit the system resources against which nextflow schedules processes
+executor {
+    name   = 'local'
+    cpus   = 4
+    memory = '8GB'
+}
+
 process {
     cpus = 1
     maxForks = 20
     shell = ['/bin/bash', '-euo', 'pipefail']
     stageOutMode = 'rsync'
-    withName: 'fastqc' {
-        cpus = 2
+    withName: 'agat' {
+        cpus = 1
     }
-    withName: 'fastp' {
+    withName: 'prokka' {
         cpus = 2
     }
-    withName: 'trimmomatic' {
+    withName: 'bakta' {
         cpus = 2
     }
-    withName: 'hisat2_index' {
-        cpus = 4
-    }
-    withName: 'hisat2' {
-        cpus = 8
-    }
-    withName: 'stringtie' {
-        cpus = 8
+    withName: 'busco' {
+        cpus = 2
     }
 }

config/software_packages.config

@@ -2,21 +2,21 @@ process {
 
     withName: 'agat' {
         conda = { singularity.enabled || docker.enabled ? '' : "$baseDir/conda/process_fastp.yml" }
-        container = 'docker://quay.io/biocontainers/agat:1.0.0--pl5321hdfd78af_0'
+        container = 'quay.io/biocontainers/agat:1.0.0--pl5321hdfd78af_0'
     }
 
    withName: bakta {
      conda = { singularity.enabled || docker.enabled ? '' : "$baseDir/conda/process_bakta.yml" }
-     container = 'docker://oschwengers/bakta:v1.6.0'
+     container = 'oschwengers/bakta:v1.6.0'
     }
 
     withLabel: busco {
       conda = { singularity.enabled || docker.enabled ? '' : "$baseDir/conda/process_busco.yml" }
-      container = 'docker://quay.io/biocontainers/busco:5.3.2--pyhdfd78af_0'
+      container = 'quay.io/biocontainers/busco:5.3.2--pyhdfd78af_0'
     }
 
     withName: 'prokka' {
         conda = { singularity.enabled || docker.enabled ? '' : "$baseDir/conda/process_prokka.yml" }
-        container = 'docker://quay.io/biocontainers/prokka:1.14.6--pl5321hdfd78af_4'
+        container = 'quay.io/biocontainers/prokka:1.14.6--pl5321hdfd78af_4'
     }
 }

main.nf

@@ -9,25 +9,48 @@ nextflow.enable.dsl=2
 
 params.assembly = "/path/to/assembly.fasta"
 params.outdir = "results"
-params.locus_prefix = "BACTOS"
+params.locus_prefix = "MBaP"
 params.genus = "Escherichia"
 params.species = "coli"
 params.strain = "POO247"
 params.codon_table = 11
 params.evalue = 1e-9
 
-// Prokka params
-params.prokka = ''
-if(!params.strain){
+params.bakta_db="/path/to/bakta_db" // optional
+params.busco_db = "/path/to/busco_db" // optional
+params.busco_lineage = "" // optional
+
+// *************  DEAL with provided params ****************
+// Deal with Prokka Parameters
+params.prokka = ' '
+if(params.strain){
 	params.prokka = '--strain ${params.strain}'
 }
-if(!params.species){
+if(params.species){
 	params.prokka = '${params.prokka} --species ${params.species}'
 }
-if(!params.genus){
+if(params.genus){
 	params.prokka = '${params.prokka} --genus ${params.genus} --usegenus'
 }
 
+// Deal with BAKTA Parameters
+params.bakta = ' '
+File bakta_db_file = new File( params.bakta_db );
+if (bakta_db_file.exists() ){
+  params.bakta = '--db ${bakta_db}'
+}
+
+// Deal with BUSCO Parameters
+params.busco = ' '
+File busco_db_file = new File( params.busco_db );
+if (busco_db_file.exists() ){
+  params.busco = '--offline --download_path ${busco_db}}'
+}
+if(params.busco_lineage){
+  params.busco = '${params.busco} --lineage_dataset ${busco_lineage}'
+} else {
+  params.busco = '${params.busco} --auto-lineage-prok'
+}
 
 log.info """
 IRD
@@ -43,7 +66,7 @@ IRD
 
 
 MbaP - Mutualize Bacterial Predictors
- ===================================================
+===================================================
 
  General Parameters
      assembly                   : ${params.assembly}
@@ -78,13 +101,14 @@ workflow mbap {
     main:
         //busco(assembly)
         prokka(assembly)
+        bakta(assembly)
 
 }
 
 process prokka {
 
-    tag "$sample_id"
-    publishDir "${params.outdir}/prokka", mode: 'copy'
+    tag "${assembly}"
+    publishDir "${params.outdir}/${assembly}/prokka", mode: 'copy'
 
     input:
     path(assembly)
@@ -94,40 +118,69 @@ process prokka {
 
     script:
     """
-		prokka \
-        --addgenes --locustag ${params.locus_prefix}
+    prokka \
+        --addgenes --locustag ${params.locus_prefix} \
         --increment 10 --compliant \
         --kingdom Bacteria --gcode ${params.codon_table} \
         --evalue ${params.evalue} --rfam \
-        assembly
+        ${params.prokka} \
+        ${assembly}
     """
 
 }
 
 process bakta {
 
-    tag "$sample_id"
-    publishDir "${params.outdir}/bakta", mode: 'copy'
+    tag "$assembly"
+    publishDir "${params.outdir}/${assembly}/bakta", mode: 'copy'
     conda 'bakta'
 
     input:
     path(assembly)
 
     output:
-    file('*')
+    path("${assembly}_bakta")
 
     script:
     """
-		bakta \
-        --addgenes --locustag ${params.locus_prefix}
-        --increment 10 --compliant \
-        --kingdom Bacteria --gcode ${params.codon_table} \
-        --evalue ${params.evalue} --rfam \
-        assembly
+    bakta \
+      --keep-contig-headers --genus ${params.genus} \
+      --species ${params.species} --prefix ${assembly} --locus-tag ${params.locus_prefix} --output ${assembly}_bakta \
+      --verbose \
+      ${params.bakta} \
+      ${assembly}
     """
+}
+
+process busco {
+    label 'busco'
+    publishDir "${params.output}/${assembly}/assembly", mode: 'copy'
+    input:
+        tuple val(id), path(contigs)
+        val(lineage)
+    output:
+        path("busco_${assembly}")
 
+    script:
+        """
+        busco -i ${assembly} -o busco_${assembly} --mode genome -f ${params.busco}
+        """
 }
 
+
+/**************         onComplete         ****************/
+
 workflow.onComplete {
-    log.info ( workflow.success ? "\nTranscript assembly complete!\n" : "Oops .. something went wrong\n" )
+    log.info ( workflow.success ? "\nMbaP pipeline complete!\n" : "Oops .. something went wrong\n" )
+
+    log.info """
+    MbaP Pipeline execution summary
+    --------------------------------------
+    Completed at : ${workflow.complete}
+    UUID         : ${workflow.sessionId}
+    Duration     : ${workflow.duration}
+    Success      : ${workflow.success}
+    Exit Status  : ${workflow.exitStatus}
+    Error report : ${workflow.errorReport ?: '-'}
+    """
 }

nextflow.config

@@ -55,6 +55,7 @@ report {
 }
 
 trace {
+    overwrite = true
     enabled = true
     file = "pipeline_report/execution_trace.txt"
 }