fix logo and params

conda/process_trimmomatic.yml → conda/process_prokka.yml

 # conda env create -f environment.yml
-name: trimmomatic
+name: prokka
 channels:
   - conda-forge
   - bioconda
   - defaults
 
 dependencies:
-  - trimmomatic=0.39
+  - prokka=1.14.6=pl5321hdfd78af_4

config/software_packages.config

 process {
-    withName: 'prokka' {
-        conda = { singularity.enabled || docker.enabled ? '' : "$baseDir/conda/process_fastqc.yml" }
-        container = 'quay.io/biocontainers/fastqc:0.11.8--2'
-    }
+
     withName: 'agat' {
         conda = { singularity.enabled || docker.enabled ? '' : "$baseDir/conda/process_fastp.yml" }
-        container = 'quay.io/biocontainers/fastp:0.20.0--hdbcaa40_0'
+        container = 'docker://quay.io/biocontainers/agat:1.0.0--pl5321hdfd78af_0'
+    }
+
+   withName: bakta {
+     conda = { singularity.enabled || docker.enabled ? '' : "$baseDir/conda/process_bakta.yml" }
+     container = 'docker://oschwengers/bakta:v1.6.0'
+    }
+
+    withLabel: busco {
+      conda = { singularity.enabled || docker.enabled ? '' : "$baseDir/conda/process_busco.yml" }
+      container = 'docker://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'
     }
 }

bactos.nf → main.nf

@@ -30,15 +30,19 @@ if(!params.genus){
 
 
 log.info """
-NBIS
-  _   _ ____ _____  _____
- | \\ | |  _ \\_   _|/ ____|
- |  \\| | |_) || | | (___
- | . ` |  _ < | |  \\___ \\
- | |\\  | |_) || |_ ____) |
- |_| \\_|____/_____|_____/  Annotation Service
-
- Transcript assembly using Hisat2/Stringtie workflow
+IRD
+.-./`) .-------.     ______
+\\ .-.')|  _ _   \\   |    _ `''.
+/ `-' \\| ( ' )  |   | _ | ) _  \\
+ `-'`\"`|(_ o _) /   |( ''_'  ) |
+ .---. | (_,_).' __ | . (_) `. |
+ |   | |  |\\ \\  |  ||(_    ._) '
+ |   | |  | \\ `'   /|  (_.\\.' /
+ |   | |  |  \\    / |       .'
+ '---' ''-'   `'-'  '-----'`
+
+
+MbaP - Mutualize Bacterial Predictors
  ===================================================
 
  General Parameters
@@ -63,10 +67,10 @@ workflow {
         Channel.fromPath(params.assembly, checkIfExists: true)
             .ifEmpty { exit 1, "Cannot find assembly file matching ${params.assembly}!\n" }
             .set {assembly}
-        bactos(assembly)
+        mbap(assembly)
 }
 
-workflow bactos {
+workflow mbap {
 
     take:
         assembly
@@ -81,7 +85,6 @@ process prokka {
 
     tag "$sample_id"
     publishDir "${params.outdir}/prokka", mode: 'copy'
-    conda 'prokka'
 
     input:
     path(assembly)

nextflow.config

 manifest {
-    name = 'TranscriptAssembly'
-    author = 'Mahesh Binzer-Panchal'
+    name = 'MbaP'
+    author = 'Jacques Dainat'
     homePage = ''
-    description = 'Nextflow Transcript assembly pipeline'
-    mainScript = 'TranscriptAssembly.nf'
-    nextflowVersion = '!>=20.01.0'
+    description = 'Nextflow prokaryote annotation pipeline'
+    mainScript = 'main.nf'
+    nextflowVersion = '!>=22.04.0'
     version = '0.2'
 }
 
 profiles {
 
-    uppmax {
-        executor {
-            name = 'slurm'
-        }
-        process {
-            scratch = '$SNIC_TMP'
-        }
-        includeConfig "$baseDir/config/compute_resources.config"
-        singularity.enabled = true
-        singularity.envWhitelist = 'SNIC_TMP'
-        includeConfig "$baseDir/config/software_packages.config"
-    }
-
     conda {
         includeConfig "$baseDir/config/software_packages.config"
     }
@@ -31,6 +18,7 @@ profiles {
 
     docker {
         docker.enabled = true
+        docker.runOptions='-u "$( id -u ):$( id -g )"'
         includeConfig "$baseDir/config/software_packages.config"
     }
 
@@ -39,7 +27,7 @@ profiles {
         includeConfig "$baseDir/config/software_packages.config"
     }
 
-    nbis {
+    itrop {
         executor {
             name = 'slurm'
         }
@@ -49,13 +37,6 @@ profiles {
         includeConfig "$baseDir/config/compute_resources.config"
     }
 
-    bils {
-        executor {
-            name = 'lsf'
-        }
-        includeConfig "$baseDir/config/compute_resources.config"
-    }
-
     test {
         includeConfig "$baseDir/config/test_profile.config"
     }

workflow.config

+// Set your work directory to a folder on the /active partition
+workDir = '/scratch/dainat/work'
+// Restart workflows from last successful execution (i.e. use cached results where possible).
+resume = true
+// Use a shared cache folder singularity images
+singularity.cacheDir = '/scratch/dainat/nxf_singularity_cachedir'
+// If using conda, use a shared cache for conda environments
+conda.cacheDir = '/scratch/dainat/nxf_conda_cachedir'
+// Use mamba for speed over conda
+conda.useMamba = true