remove rst lint

.pre-commit-config.yaml

@@ -28,10 +28,3 @@ repos:
         language: node
         types: [markdown]
         minimum_pre_commit_version: 0.15.0
-
-  - repo: https://github.com/Lucas-C/pre-commit-hooks-markup
-    rev: v1.0.0
-    hooks:
-      - id: rst-linter
-        description: "rst-linter"
-        entry: "rst-linter"

pipeline.nf

@@ -353,16 +353,15 @@ if (!params.skip_reference_download){
      reference_genome_gb_ftp (fasta.gz): The reference genome gbff accessed by url via FTP.
 
      Output:
-     ch_reference_genome_snippy_pairwise (fasta): The compressed reference genome for process snippy_pairwise.
      ch_reference_detect_repeats (fasta): The reference genome for process detect_repeats.
      ch_reference_genome_detect_low_complexity (fasta): The reference genome for process detect_low_complexity.
-     ch_reference_gb_snippy_pairwise (gb): The reference genome for process snippy_pairwise.
-     ch_reference_gb_snippy_multi (gb): The reference genome for process snippy_multi.
-     ch_reference_genome_snpeff_build_db (gb): The reference genome for process snpeff_build_db
+     ch_reference_gb_snippy_pairwise (gbff): The reference genome for process snippy_pairwise.
+     ch_reference_gb_snippy_multi (gbff): The reference genome for process snippy_multi.
+     ch_reference_genome_snpeff_build_db (gbff): The reference genome for process snpeff_build_db.
 
      Publish:
      reference_genome_fna_local (fasta): The locally downloaded reference fasta.
-     reference_genome_gb_local (fasta): The locally downloaded reference annotations.
+     reference_genome_gb_local (gbff): The locally downloaded reference annotations.
     */
 
     // Other variables and config
@@ -376,7 +375,7 @@ if (!params.skip_reference_download){
     file reference_genome_gb_local from file(params.reference_genome_gb_ftp)
 
     output:
-    file "${reference_genome_fna_local.baseName}" into ch_reference_genome_snippy_pairwise, ch_reference_genome_detect_repeats, ch_reference_genome_low_complexity
+    file "${reference_genome_fna_local.baseName}" into ch_reference_genome_detect_repeats, ch_reference_genome_low_complexity
     file "${reference_genome_gb_local.baseName}" into ch_reference_gb_snippy_pairwise, ch_reference_gb_snippy_multi, ch_reference_genome_snpeff_build_db
 
     // Shell script to execute
@@ -398,16 +397,17 @@ if (!params.skip_reference_download){
 
   process snpeff_build_db{
     /*
-     Build a SnpEff database for the reference genome annotations
+     Build a SnpEff database for the reference genome annotations.
 
      Input:
-     reference_genome_gb (gb): The reference genome gbff from process reference_download.
+     reference_genome_gb (gbff): The reference genome gbff from process reference_download.
 
      Output:
-     snpEff.config (text): Edited SnpEff configuration file for process snippy_pairwise.
+     ch_snpeff_config_snippy_pairwise (text): Edited SnpEff configuration file for process snippy_pairwise.
 
      Publish:
      snpEff.config (text): Edited SnpEff configuration file.
+     snpEffectPredictor.bin (gzip text): SnpEff database.
 
     */
     // Other variables and config
@@ -420,6 +420,7 @@ if (!params.skip_reference_download){
 
     output:
     file "snpEff.config" into ch_snpeff_config_snippy_pairwise
+    file "data/${reference_genome_gb.baseName}/snpEffectPredictor.bin"
 
     // Shell script to execute
     script:
@@ -428,18 +429,29 @@ if (!params.skip_reference_download){
     ref=${reference_genome_gb.baseName}
     snpeffDir=~/miniconda3/envs/${params.conda_env}/share/snpeff-4.3.1t-3
     snpeffData=\$snpeffDir/data;
+
     # Create a new reference data directory
     mkdir -p \$snpeffData/\$ref;
+
     # Move over the ref genome genbank annotations and rename
     cp ${outdir}/reference_genome/${reference_genome_gb} \$snpeffData/\$ref/genes.gbk;
+
     # Add the new annotation entry to the snpeff config file
     configLine="${reference_genome_gb.baseName}.genome : ${reference_genome_gb.baseName}"
+
     # Search for the genome entry in the snpEff config file
     if [[ -z `grep "\$configLine" \$snpeffDir/snpEff.config` ]]; then
       echo "\$configLine" >> \$snpeffDir/snpEff.config;
     fi;
-    # Copy over snpEff.config just to track it
+
+    # Copy over snpEff.config to become an output channel
+    snpEff build -v -genbank ${reference_genome_gb.baseName}
     cp \$snpeffDir/snpEff.config `pwd`
+
+    # Move SnpEff database to the correct path
+    mkdir -p data/
+    mkdir -p data/${reference_genome_gb.baseName}/
+    cp \$snpeffData/${reference_genome_gb.baseName}/snpEffectPredictor.bin data/${reference_genome_gb.baseName}/
     """
   }
 
@@ -557,7 +569,7 @@ if(!params.skip_snippy_pairwise && !params.skip_assembly_download && (params.sql
 
     Input:
     ch_assembly_fna_snippy_pairwise (fasta): The genomic assembly from process assembly_download.
-    ch_reference_gb_snippy_pairwise (gb): The reference annotations from process reference_download.
+    ch_reference_gb_snippy_pairwise (gbff): The reference annotations from process reference_download.
     ch_snpeff_config_snippy_pairwise (text): Edited SnpEff configuration file from process snpeff_build_db.
 
     Output:
@@ -622,7 +634,7 @@ if(!params.skip_snippy_pairwise && !params.skip_assembly_download && (params.sql
 
     # SnpEff csv Stats
     mv \$snippy_snps_csv \$snippy_snps_rename
-    snpEff -v -csvStats \$snippy_snps_csv ${params.snpeff_db} \$snippy_snps_filt
+    snpEff -c ${snpeff_config} -v -csvStats \$snippy_snps_csv ${reference_genome_gb.baseName} \$snippy_snps_filt
     """
   }