Add bakta missing ick4

assets/sample_fastas/Cdiphtheriae/BX248355.fasta

@@ -1,4 +1,4 @@
->BX248355.1 Corynebacterium diphtheriae gravis NCTC13129, complete genome; segment 2/8
+>BX248355.1-segment2 Corynebacterium diphtheriae gravis NCTC13129, complete genome; segment 2/8
 TTATATGAGCCCTTCCTTATCGAGTCATCTGCATCAGCGGCCTCGGTATCGGCCACCTGCGGTTCACTTG
 GTGGCAGATCCATCGTTACTGGCTCGCCACGAACACTCACTACTGTAGTAAGTAGGGGGCTAGGCCACAT
 AAGTGGGAAAGGGTGAGTTATATCATATGAAAATTGCCCGAAATAGGAGTAAAGAATTTTGCCTGCGATA
@@ -4072,7 +4072,7 @@ ACCTCACCTCACCTGCGAGAGGTGAGGTAGAAAACGTAACTGCGACCGATTACAGCGGGATGTTGCCGTG
 CTTCTTCGCAGGAACGTTAACAACCTTGCGGTCCAAGAGGCGTAGCGCTTCAATGATCTGACCACGGGTT
 TCGCTTGGTGGAATAACGGCGTCGACGTAACCACGCTCGGCTGCCATGTAAGGGTTGACCAAAGTTTCTT
 CGTACTCGCGCTCGTATTCCTTAGCTACAGCGAGCATGTCCTTGCCTTCGGCAGCAGCGGCCTTGATTTC
->BX248355.1 Corynebacterium diphtheriae gravis NCTC13129, complete genome; segment 3/8
+>BX248355.1-segment3 Corynebacterium diphtheriae gravis NCTC13129, complete genome; segment 3/8
 CTTGCGGTAGATGAATCCCACGGCACCAGCGGCGCCCATGACAGCGATCTGTGCGGTTGGCCATGCCAAG
 ACGAGGTCGGCGCCCATGTCCTTCGAACCCATCACGCAGTAAGCGCCACCGTAGGACTTGCGGGTAATCA
 CAGTGATCTTGCCGACGGTTGCTTCAGAGTAGGCGTAGAGGAGCTTGGCGCCACGGCGAATGATTCCGTC
@@ -4442,7 +4442,7 @@ CGATTATTGGGCATGGTGCTCGTATTGGAGCCAATGCTCGCATTACCGGCTGTGTGATTGGTGAAGGCGC
 GGAAATCGGTGCACGTTGTGAGCTTCGCGACGGCATGCGTGTGTGGCCAGGAGTTGTGATTCCAACTGCT
 GGTATCCGTTTTAGTTCGGATGCCTAAGTTGCAGTAATACCTAGTGCAACCTAGTCATAGGCTCCCACCA
 CGGCAGGGTAGACCCCCTCGTTGTGGTGGGAGCTTTCGCATTTTATGGAGGCTGGCTGAAGCGATTTCTT
->BX248355.1 Corynebacterium diphtheriae gravis NCTC13129, complete genome; segment 4/8
+>BX248355.1-segment4 Corynebacterium diphtheriae gravis NCTC13129, complete genome; segment 4/8
 AGTAGCTGCTGAGTGCTAGCACGTTTGTGTTCAAACACTTTTATGCGACACGCCGATAATGAGCCGACTA
 GCGAAGTATTTTTAGAGGCACCACTATATGTAGTACCCCCACCGTATACCCCTATGGTGGTGGCAATGTT
 ACTGGTGTGACTAATGAAGTTAACAACCTGCGGAAATGCAATTTTTCCGATCGGAATTACATGTTCAGGT

modules/nf-core/bakta/bakta/main.nf

@@ -21,6 +21,22 @@ process BAKTA {
 
     script:
     def args = task.ext.args  ?: ''
+    def prefix   = task.ext.prefix ?: "${meta.id}"
+    def proteins = params.bakta_proteins ? "--proteins ${proteins[0]}" : ""
+    def prodigal_tf = params.bakta_prodigal_tf ? "--prodigal-tf ${prodigal_tf[0]}" : ""
+    def skip_trna = params.bakta_skip_trna ? "--skip-trna" : ""
+    def skip_tmrna = params.bakta_skip_tmrna ? "--skip-tmrna" : ""
+    def skip_rrna = params.bakta_skip_rrna ? "--skip-rrna" : ""
+    def skip_ncrna = params.bakta_skip_ncrna ? "--skip-ncrna" : ""
+    def skip_ncrna_region = params.bakta_skip_ncrna_region ? "--skip-ncrna-region" : ""
+    def skip_crispr = params.bakta_skip_crispr ? "--skip-crispr" : ""
+    def skip_cds = params.bakta_skip_cds ? "--skip-cds" : ""
+    def skip_sorf = params.bakta_skip_sorf ? "--skip-sorf" : ""
+    def skip_gap = params.bakta_skip_gap ? "--skip-gap" : ""
+    def skip_ori = params.bakta_skip_ori ? "--skip-ori" : ""
+    def compliant = params.bakta_compliant ? "--compliant" : ""
+    def complete = params.bakta_complete ? "--complete" : ""
+    def keep_contig_headers = params.bakta_keep_contig_headers ? "--keep-contig-headers" : ""
 
     """
     bakta --db $db_path  \
@@ -34,30 +50,23 @@ process BAKTA {
         --complete $params.bakta_complete \
         --translation-table $params.bakta_translation_table \
         --gram $params.bakta_gram \
-        --compliant \
         --locus $params.bakta_locus \
         --locus-tag $params.bakta_locus_tag \
-        --keep-contig-headers \
+        $compliant \
+        $keep_contig_headers \
+        $proteins \
+        $prodigal_tf \
+        $skip_trna \
+        $skip_rrna \
+        $skip_ncrna \
+        $skip_ncrna_region \
+        $skip_crispr \
+        $skip_cds \
+        $skip_sorf \
+        $skip_gap \
+        $skip_ori \
         $fasta_path
     """
-    // optional args
-    // --prodigal-tf $params.bakta_prodigal_tf 
-    // --replicons $params.bakta_replicons 
-    // --proteins $params.bakta_proteins 
-    // --skip-trna  
-    // --skip-tmrna 
-    // --skip-rrna
-    // --skip-ncrna 
-    // --skip-ncrna-region 
-    // --skip-crispr 
-    // --skip-cds 
-    // --skip-pseudo
-    // --skip-sorf
-    // --skip-gap 
-    // --skip-ori 
-    // --skip-plot
-
-
 
     output:
     path "${fasta_path.getSimpleName()}/*.fna",   emit: fna

nextflow.config

@@ -9,9 +9,9 @@
 params {
     // input paths
     fasta_path            = "" // path to dir with fasta files that match metadata
-    fastq_path            = "" //
+    fastq_path            = "" // path to dir with fastq files that match metadata (for SRA upload of raw sequences)
     ref_fasta_path        = "${projectDir}/assets/ref/ref.MPXV.NC063383.v7.fasta"
-    meta_path             = "${projectDir}/assets/custom_meta_fields/custom_fields_MPXV_metadata_Sample_Run_1.xlsx"
+    meta_path             = "${projectDir}/assets/metadata_template.xlsx"
     ref_gff_path          = "${projectDir}/assets/ref/ref.MPXV.NC063383.v7.gff"
 
     // validation subworkflow
@@ -22,17 +22,10 @@ params {
 
     // viral annotation params
     annotation             = true 
-    repeatmasker_liftoff   = false 
+    repeatmasker_liftoff   = true 
     liftoff                = false
     vadr                   = false
 
-    if ( params.annotation == false ) {
-        repeatmasker_liftoff   = false 
-        liftoff                = false
-        vadr                   = false
-        bakta                  = false
-    }
-
     // organism specific repeat library settings
     // if you want to add your own custom library, if you choose to use one of ours state 'varv' to use the 'varv' custom lib or 'mpox' to use the mpox custom lib
     if ( params.variola ) {
@@ -60,16 +53,16 @@ params {
     send_submission_email  = false 
 
     // general params
-    help                   = false
-    output_dir             = ""
-    overwrite_output = false
-    publish_dir_mode           = 'copy'
+    help                     = false
+    publish_dir_mode         = 'copy'
+    output_dir               = ""
+    overwrite_output         = false
     // To Do check if we need these three dirs
     final_liftoff_output_dir = "liftoff"
-    bakta_output_dir       = ""
-    vadr_output_dir        = ""
+    bakta_output_dir         = ""
+    vadr_output_dir          = ""
     final_liftoff_output_dir = "liftoff_outputs"
-    val_output_dir         = "validation_outputs"
+    val_output_dir           = "validation_outputs"
 
     // taxon-specific params
     variola                = false
@@ -93,26 +86,24 @@ params {
     clear_nf_results       = false
     overwrite_output       = true
 
-    // batka annotation
-    bakta_output_dir          = ""
-    bakta_db_type             = "light" // light or full
-    download_bakta_db         = false
-    bakta_db_path             = ""
-    bakta_min_contig_length   = 200 // due to compliant mode default, otherwise default is 1
-    bakta_genus               = ""
-    bakta_species             = ""
-    bakta_strain              = ""
-    bakta_plasmid             = "unnamed"
-    bakta_complete            = ""
+    // required bakta params
+    bakta_db_type           = "light" // light or full
+    download_bakta_db       = ""
+    bakta_db_path           = ""
+    bakta_min_contig_length = 5
+    bakta_threads           = 2
+    bakta_genus             = 'N/A'
+    bakta_species           = 'N/A'
+    bakta_strain            = 'N/A'
+    bakta_plasmid           = 'unnamed' 
+    bakta_locus             = 'contig'
+    bakta_locus_tag         = 'autogenerated'
+    bakta_translation_table = 11
+
+    // optional bakta params
     bakta_compliant           = ""
-    bakta_translation_table   = 11
-    bakta_gram                = ""
-    bakta_locus               = "contig"
-    bakta_locus_tag           = "LOCUSTAG123" // set a meaningful locus tag here for compliant mode
     bakta_keep_contig_headers = ""
-
-    // optional bakta params, for now need to add these to modules/nf-core/bakta/bakta/main.nf
-    bakta_prodigal_df         = ""
+    bakta_prodigal_tf         = ""
     bakta_replicons           = ""
     bakta_proteins            = ""
     bakta_skip_trna           = ""
@@ -128,7 +119,6 @@ params {
     bakta_skip_ori            = ""
     bakta_skip_plot           = ""
 
-
     // liftoff annotation
     lift_print_version_exit            = false 
     lift_print_help_exit               = false 
@@ -156,14 +146,11 @@ params {
 
 }
 
-//includeConfig 'conf/modules.config'
-
 try {
     includeConfig 'conf/modules.config'
 } catch (Exception e) {
     System.err.println("WARNING:Could not load conf/modules.config")
-}
-
+}  
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -173,7 +160,6 @@ try {
 
 // To Do: align these profiles with nf-core style, also align rest of this config
 profiles {    
-    // standard { includeConfig "conf/standard_params.config" }
     test { includeConfig "conf/test_params.config" }
 
     // run docker + specify settings 
@@ -235,8 +221,9 @@ profiles {
     }
 }
 
+// todo: not sure about this - it's already somewhere else
 // Load modules.config for DSL2 module specific options
-includeConfig 'conf/modules.config'
+//includeConfig 'conf/modules.config'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -257,5 +244,4 @@ manifest {
     mainScript = 'main.nf'
     nextflowVersion = '>=20.07.1'
     version = 'latest'
-}
-
+}