Merge pull request #51 from karinlag/master

Prokka removal

asm_annot.nf

@@ -12,8 +12,6 @@ else {
   version = "v0.2.0 local"
 }
 
-// TODO I need to incorporate some options for prokka here
-// Also strip genome
 
 log.info ''
 log.info "================================================="
@@ -231,7 +229,6 @@ process run_pilon {
 
     output:
     set pair_id, file("${pair_id}_pilon_spades.*") into pilon_results
-    set pair_id, file("${pair_id}_pilon_spades.fasta") into to_prokka
     file "${pair_id}_pilon_spades.fasta" into asms_for_quast
 
     """
@@ -242,29 +239,6 @@ process run_pilon {
     """
 }
 
-/*
-* Annotation using PROKKA
-*/
-process run_prokka {
-    publishDir "${params.out_dir}/prokka", mode: "${params.savemode}"
-    tag { pair_id }
-
-    input:
-    set pair_id, file("${pair_id}_pilon_spades.fasta") from to_prokka
-
-    output:
-    set pair_id, file("${pair_id}.*") into annotation_results
-    file "${pair_id}.*" into annotation_multiqc
-
-    """
-    prokka --compliant --force --usegenus --cpus $task.cpus \
-    --centre ${params.centre} --prefix ${pair_id} --locustag ${params.locustag} \
-    --genus ${params.genus} --species ${params.species} \
-    --kingdom ${params.kingdom} --strain ${pair_id}_prokka_info ${params.prokka_additional} \
-    --outdir . ${pair_id}_pilon_spades.fasta
-    """
-}
-
 /*
  * Evaluate ALL assemblies with QUAST
  */
@@ -297,7 +271,6 @@ process run_multiqc_final {
     file "bbduk/*" from bbduk_stats_stripped_multiqc.collect()
     file "bbduk_trimmed/*" from bbduk_trimmed_multiqc.collect()
     file "bbduk_trimmed_fastqc/*" from fastqc_bbduk_trimmed_multiqc.collect()
-    file "prokka/*" from annotation_multiqc.collect()
     file quast_evaluation_all from quast_multiqc
 
     output:

bin/printversions.sh

@@ -13,7 +13,6 @@ if [[ "$STR" == *"$SUBSTR"* ]]; then
         conda list -n bifrost2022-spades >> ${output_file}
         conda list -n bifrost2022-bwa >> ${output_file}
         conda list -n bifrost2022-pilon >> ${output_file}
-        conda list -n bifrost2022-prokka >> ${output_file}
         conda list -n bifrost2022-quast >> ${output_file}
         conda list -n bifrost2022-ariba >> ${output_file}
 
@@ -28,7 +27,6 @@ if [[ "$STR" == *"$SUBSTR"* ]]; then
         rm tmpfile
         samtools --version |head  -1 >> ${output_file}
         pilon --version >> ${output_file} 
-        prokka -v >> ${output_file}
         quast -v >> ${output_file}
         ariba version |head -1 >> ${output_file}
 

conf/asm_annot_template.config

@@ -24,7 +24,7 @@ params.savemode = "copy"
 
 // Directory to where data is stored
 params.data_dir = "/cluster/projects/nn9305k/vi_pipeline_data/bifrost_data"
-params.multiqc_config = "/cluster/projects/nn9305k/Bifrost22/conf/multiqc_config.yaml"
+params.multiqc_config = "/cluster/projects/nn9305k/vi_src/Bifrost22/conf/multiqc_config.yaml"
 
 // BBDuk params, has to be absolute paths
 params.stripgenome = "${params.data_dir}/genome_references/genomes/PhiX/PhiX.fasta"
@@ -47,17 +47,6 @@ params.assembly = "spades_asm"
 params.cov_cutoff = "auto"
 params.min_contig_len = "500"
 
-// PROKKA configuration variables
-params.locustag = "locustag"
-params.genus = "Escherichia"
-params.species = "coli"
-params.kingdom = "Bacteria"
-// If you have additional options to set, put them here.
-params.prokka_additional = ""
-params.centre = "NVI"
-
-
-
 // QUAST variables
 params.quast_ref = "${params.data_dir}/genome_references/genomes/ecoli/GCF_000005845.2_ASM584v2_genomic.fna"
 params.quast_genes = "${params.data_dir}/genome_references/genomes/ecoli/GCF_000005845.2_ASM584v2_genomic.gff"

conf/conda.config

@@ -43,10 +43,6 @@ process {
   conda = "${params.condahome}/bifrost2022-pilon"
   }
 
-  withName: run_prokka {
-  conda = "${params.condahome}/bifrost2022-prokka"
-  }
-
   withName: run_quast {
   conda = "${params.condahome}/bifrost2022-quast"
   }