FEAT: avoid using boolean_false (#160)

CHANGELOG.md

@@ -19,6 +19,10 @@
 
 ## MINOR CHANGES
 
+* `agat_convert_bed2gff`: change type of argument `inflate_off` from `boolean_false` to `boolean_true` (PR #160).
+
+* `cutadapt`: change type of argument `no_indels` and `no_match_adapter_wildcards` from `boolean_false` to `boolean_true` (PR #160).
+
 * Upgrade to Viash 0.9.0.
 
 # biobox 0.2.0

CONTRIBUTING.md

@@ -231,6 +231,12 @@ Finally, add all other arguments to the config file. There are a few exceptions:
 
 * If the help lists defaults, do not add them as defaults but to the description. Example: `description: <Explanation of parameter>. Default: 10.`
 
+Note:
+
+* Prefer using `boolean_true` over `boolean_false`. This avoids confusion when specifying values for this argument in a Nextflow workflow.
+  For example, consider the CLI option `--no-indels` for `cutadapt`. If the config for `cutadapt` would specify an argument `no_indels` of type `boolean_false`,
+  the script of the component must pass a `--no-indels` argument to `cutadapt` when `par_no_indels` is set to `false`. This becomes problematic setting a value for this argument using `fromState` in a nextflow workflow: with `fromState: ["no_indels": true]`, the value that gets passed to the script is `true` and the `--no-indels` flag would *not* be added to the options for `cutadapt`. This is inconsitent to what one might expect when interpreting `["no_indels": true]`.
+  When using `boolean_true`, the reasoning becomes simpler because its value no longer represents the effect of the argument, but wether or not the flag is set.
 
 ### Step 10: Add a Docker engine
 

src/agat/agat_convert_bed2gff/config.vsh.yaml

@@ -49,7 +49,7 @@ argument_groups:
       - name: --inflate_off
         description: |
           By default we inflate the block fields (blockCount, blockSizes, blockStarts) to create subfeatures of the main feature (primary_tag). The type of subfeature created is based on the inflate_type parameter. If you do not want this inflating behaviour you can deactivate it by using the --inflate_off option.
-        type: boolean_false
+        type: boolean_true
       - name: --inflate_type
         description: |
           Feature type (3rd column in gff) created when inflate parameter activated [default: exon].

src/agat/agat_convert_bed2gff/script.sh

@@ -4,7 +4,7 @@
 ## VIASH END
 
 # unset flags
-[[ "$par_inflate_off" == "true" ]] && unset par_inflate_off
+[[ "$par_inflate_off" == "false" ]] && unset par_inflate_off
 [[ "$par_verbose" == "false" ]] && unset par_verbose
 
 # run agat_convert_sp_bed2gff.pl

src/cutadapt/config.vsh.yaml

@@ -196,7 +196,7 @@ argument_groups:
           length of matching region. Default: 0.1 (10%).
         example: 0.1
       - name: --no_indels
-        type: boolean_false
+        type: boolean_true
         description: |
           Allow only mismatches in alignments.
 
@@ -218,7 +218,7 @@ argument_groups:
         description: |
           Interpret IUPAC wildcards in reads.
       - name: --no_match_adapter_wildcards
-        type: boolean_false
+        type: boolean_true
         description: |
           Do not interpret IUPAC wildcards in adapters.
       - name: --action

src/cutadapt/script.sh

@@ -96,9 +96,9 @@ debug
 # Input arguments 
 ###########################################################
 echo ">> Parsing input arguments"
-[[ "$par_no_indels" == "true" ]] && unset par_no_indels
+[[ "$par_no_indels" == "false" ]] && unset par_no_indels
 [[ "$par_match_read_wildcards" == "false" ]] && unset par_match_read_wildcards
-[[ "$par_no_match_adapter_wildcards" == "true" ]] && unset par_no_match_adapter_wildcards
+[[ "$par_no_match_adapter_wildcards" == "false" ]] && unset par_no_match_adapter_wildcards
 [[ "$par_revcomp" == "false" ]] && unset par_revcomp
 
 input_args=$(echo \