change boolean params and fix bug with output files

src/snpeff/config.vsh.yaml

@@ -3,7 +3,8 @@ description: |
   Genetic variant annotation, and functional effect prediction toolbox. 
   It annotates and predicts the effects of genetic variants on genes and 
   proteins (such as amino acid changes).
-keywords: ["dna polymorphism", "genetic variation", "snp analysis", "next-generation dna sequencing"]
+keywords: [ "annotation", "effect prediction", "snp", "variant", "vcf"]
+
 links:
   repository: https://github.com/pcingola/SnpEff
   homepage: https://pcingola.github.io/SnpEff/
@@ -77,7 +78,7 @@ argument_groups:
         type: boolean_true
         description: Create HTML summary file.
       - name: --no_stats
-        type: boolean_false
+        type: boolean_true
         description: Do not create stats (summary) file.
   - name: Results filter options
     arguments:
@@ -88,19 +89,19 @@ argument_groups:
           Only analyze changes that intersect with the intervals 
           specified in this file. This option can be used several times.
       - name: --no_downstream 
-        type: boolean_false
+        type: boolean_true
         description: Do not show DOWNSTREAM changes
       - name: --no_intergenic
-        type: boolean_false
+        type: boolean_true
         description: Do not show INTERGENIC changes.
       - name: --no_intron
-        type: boolean_false
+        type: boolean_true
         description: Do not show INTRON changes.
       - name: --no_upstream
-        type: boolean_false
+        type: boolean_true
         description: Do not show UPSTREAM changes.
       - name: --no_utr
-        type: boolean_false
+        type: boolean_true
         description: Do not show 5_PRIME_UTR or 3_PRIME_UTR changes.
       - name: --no
         type: string
@@ -142,13 +143,13 @@ argument_groups:
         description: |
           Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
       - name: -no_hgvs
-        type: boolean_false
+        type: boolean_true
         description: Do not add HGVS annotations.
       - name: --no_lof
-        type: boolean_false
+        type: boolean_true
         description: Do not add LOF and NMD annotations.
       - name: --no_shift_hgvs
-        type: boolean_false
+        type: boolean_true
         description: |
           Do not shift variants according to HGVS notation (most 3prime end).
       - name: --oicr
@@ -173,14 +174,11 @@ argument_groups:
       - name: --data_dir
         type: file
         description: Override data_dir parameter from config file.
-      # - name: -download
-      #   type: boolean_true
-      #   description: Download a SnpEff database, if not available locally.
       - name: --no_download
-        type: boolean_false
+        type: boolean_true
         description: Do not download a SnpEff database, if not available locally.
       - name: --no_log
-        type: boolean_false
+        type: boolean_true
         description: Do not report usage statistics to server.
       - name: --quiet
         alternatives: [-q]
@@ -205,7 +203,7 @@ argument_groups:
         description: |
           Only use transcript having a tag 'tagName'. This option can be used multiple times.
       - name: --no_tag
-        type: boolean_false
+        type: boolean_true
         description: |
           Filter out transcript having a tag 'tagName'. This option can be used multiple times.
       - name: --interaction
@@ -225,19 +223,19 @@ argument_groups:
         type: boolean_true
         description: Annotate using NextProt (requires NextProt database).
       - name: --no_genome
-        type: boolean_false
+        type: boolean_true
         description: Do not load any genomic database (e.g. annotate using custom files).
       - name: --no_expand_iub
-        type: boolean_false
+        type: boolean_true
         description: Disable IUB code expansion in input variants.
       - name: --no_interaction
-        type: boolean_false
+        type: boolean_true
         description: Disable inteaction annotations.
       - name: --no_motif
-        type: boolean_false
+        type: boolean_true
         description: Disable motif annotations.
       - name: --no_nextprot
-        type: boolean_false
+        type: boolean_true
         description: Disable NextProt annotations.
       - name: --only_reg
         type: boolean_true

src/snpeff/script.sh

@@ -31,14 +31,6 @@ unset_if_false=(
     par_only_reg
     par_only_protein
     par_strict
-)
-for par in ${unset_if_false[@]}; do
-    test_val="${!par}" # contains the value of the 'par'
-    [[ "$test_val" == "false" ]] && unset $par
-done
-
-# Unset flags if 'true'
-unset_if_true=(
     par_no_stats
     par_no_downstream
     par_no_intergenic
@@ -57,11 +49,12 @@ unset_if_true=(
     par_no_motif
     par_no_nextprot
 )
-for par in ${unset_if_true[@]}; do
-    test_val="${!par}"
-    [[ "$test_val" == "true" ]] && unset $par
+for par in ${unset_if_false[@]}; do
+    test_val="${!par}" # contains the value of the 'par'
+    [[ "$test_val" == "false" ]] && unset $par
 done
 
+
 # Run SnpEff
 snpEff \
     ${par_chr:+-chr "$par_chr"} \
@@ -138,18 +131,18 @@ directory_path=$(dirname "$absolute_path")
 # Move the automatically generated outputs to their locations
 if [ -z "$par_no_stats" ]; then
     if [ ! -z "$par_summary" ]; then
-    mv -f snpEff_summary.html "$par_summary"
+        mv -n snpEff_summary.html "$par_summary"
     else
-    mv -f snpEff_summary.html "$directory_path"
+        mv -n snpEff_summary.html "$directory_path"
     fi
-fi
+fi 
 
 if [ -z "$par_no_stats" ]; then
     if [ ! -z "$par_genes" ]; then
-    mv -f snpEff_genes.txt "$par_genes"
+        mv -n snpEff_genes.txt "$par_genes"
     else
-    mv -f snpEff_genes.txt "$directory_path"
+        mv -n snpEff_genes.txt "$directory_path"
     fi
 fi
 
-exit 0
+exit 0

src/snpeff/test.sh

@@ -104,7 +104,7 @@ output_files=("snpEff_genes.txt" "snpEff_summary.html")
 # Check if any of the files do not exist
 for file in "${output_files[@]}"; do
     if [ ! -e "temp/$file" ]; then
-        echo "File $file does not exist in "temp" folder."
+        echo "File $file does not exist in 'temp' folder."
     fi
 done