Avoid duplicate code when unsetting multiple boolean arguments (#133)

* Avoid duplicate code when unsetting multiple boolean arguments

* Add CHANGELOG entry [ci skip]

* Update CONTRIBUTING guide

CHANGELOG.md

@@ -36,6 +36,8 @@
 
 * Update CI to reusable workflow in `viash-io/viash-actions` (PR #86).
 
+* Update several components in order to avoid duplicate code when using `unset` on boolean arguments (PR #133).
+
 ## DOCUMENTATION
 
 * Extend the contributing guidelines (PR #82):

CONTRIBUTING.md

@@ -320,6 +320,31 @@ Notes:
 
 * If your tool allows for multiple inputs using a separator other than `;` (which is the default Viash multiple separator), you can substitute these values with a command like: `par_disable_filters=$(echo $par_disable_filters | tr ';' ',')`.
 
+* If you have a lot of boolean variables that you would like to unset when the value is `false`, you can avoid duplicate code by using the following syntax:
+
+```bash
+unset_if_false=(
+    par_argument_1
+    par_argument_2
+    par_argument_3
+    par_argument_4
+)
+
+for par in ${unset_if_false[@]}; do
+    test_val="${!par}"
+    [[ "$test_val" == "false" ]] && unset $par
+done
+```
+
+this code is equivalent to
+
+```bash
+[[ "$par_argument_1" == "false" ]] && unset par_argument_1
+[[ "$par_argument_2" == "false" ]] && unset par_argument_2
+[[ "$par_argument_3" == "false" ]] && unset par_argument_3
+[[ "$par_argument_4" == "false" ]] && unset par_argument_4
+```
+
 
 ### Step 12: Create test script
 

src/bedtools/bedtools_intersect/script.sh

@@ -3,27 +3,34 @@
 ## VIASH START
 ## VIASH END
 
-[[ "$par_write_a" == "false" ]] && unset par_write_a
-[[ "$par_write_b" == "false" ]] && unset par_write_b
-[[ "$par_left_outer_join" == "false" ]] && unset par_left_outer_join
-[[ "$par_write_overlap" == "false" ]] && unset par_write_overlap
-[[ "$par_write_overlap_plus" == "false" ]] && unset par_write_overlap_plus
-[[ "$par_report_A_if_no_overlap" == "false" ]] && unset par_report_A_if_no_overlap
-[[ "$par_number_of_overlaps_A" == "false" ]] && unset par_number_of_overlaps_A
-[[ "$par_report_no_overlaps_A" == "false" ]] && unset par_report_no_overlaps_A
-[[ "$par_uncompressed_bam" == "false" ]] && unset par_uncompressed_bam
-[[ "$par_same_strand" == "false" ]] && unset par_same_strand
-[[ "$par_opposite_strand" == "false" ]] && unset par_opposite_strand
-[[ "$par_reciprocal_overlap" == "false" ]] && unset par_reciprocal_overlap
-[[ "$par_either_overlap" == "false" ]] && unset par_either_overlap
-[[ "$par_split" == "false" ]] && unset par_split
-[[ "$par_nonamecheck" == "false" ]] && unset par_nonamecheck
-[[ "$par_sorted" == "false" ]] && unset par_sorted
-[[ "$par_filenames" == "false" ]] && unset par_filenames
-[[ "$par_sortout" == "false" ]] && unset par_sortout
-[[ "$par_bed" == "false" ]] && unset par_bed
-[[ "$par_header" == "false" ]] && unset par_header
-[[ "$par_no_buffer_output" == "false" ]] && unset par_no_buffer_output
+unset_if_false=(
+    par_write_a
+    par_write_b
+    par_left_outer_join
+    par_write_overlap
+    par_write_overlap_plus
+    par_report_A_if_no_overlap
+    par_number_of_overlaps_A
+    par_report_no_overlaps_A
+    par_uncompressed_bam
+    par_same_strand
+    par_opposite_strand
+    par_reciprocal_overlap
+    par_either_overlap
+    par_split
+    par_nonamecheck
+    par_sorted
+    par_filenames
+    par_sortout
+    par_bed
+    par_no_buffer_output
+)
+
+for par in ${unset_if_false[@]}; do
+    test_val="${!par}"
+    [[ "$test_val" == "false" ]] && unset $par
+done
+
 
 # Create input array 
 IFS=";" read -ra input <<< $par_input_b

src/bedtools/bedtools_sort/script.sh

@@ -4,13 +4,20 @@
 ## VIASH END
 
 # Unset parameters
-[[ "$par_sizeA" == "false" ]] && unset par_sizeA
-[[ "$par_sizeD" == "false" ]] && unset par_sizeD
-[[ "$par_chrThenSizeA" == "false" ]] && unset par_chrThenSizeA
-[[ "$par_chrThenSizeD" == "false" ]] && unset par_chrThenSizeD
-[[ "$par_chrThenScoreA" == "false" ]] && unset par_chrThenScoreA
-[[ "$par_chrThenScoreD" == "false" ]] && unset par_chrThenScoreD
-[[ "$par_header" == "false" ]] && unset par_header
+unset_if_false=(
+    par_sizeA
+    par_sizeD
+    par_chrThenSizeA
+    par_chrThenSizeD
+    par_chrThenScoreA
+    par_chrThenScoreD
+    par_header
+)
+
+for par in ${unset_if_false[@]}; do
+    test_val="${!par}"
+    [[ "$test_val" == "false" ]] && unset $par
+done
 
 # Execute bedtools sort with the provided arguments
 bedtools sort \

src/busco/busco_run/script.sh

@@ -3,18 +3,24 @@
 ## VIASH START
 ## VIASH END
 
+unset_if_false=(
+    par_tar
+    par_force
+    par_quiet
+    par_restart
+    par_auto_lineage
+    par_auto_lineage_euk
+    par_auto_lineage_prok
+    par_augustus
+    par_long
+    par_scaffold_composition
+    par_miniprot
+)
 
-[[ "$par_tar" == "false" ]] && unset par_tar
-[[ "$par_force" == "false" ]] && unset par_force
-[[ "$par_quiet" == "false" ]] && unset par_quiet
-[[ "$par_restart" == "false" ]] && unset par_restart
-[[ "$par_auto_lineage" == "false" ]] && unset par_auto_lineage
-[[ "$par_auto_lineage_euk" == "false" ]] && unset par_auto_lineage_euk
-[[ "$par_auto_lineage_prok" == "false" ]] && unset par_auto_lineage_prok
-[[ "$par_augustus" == "false" ]] && unset par_augustus
-[[ "$par_long" == "false" ]] && unset par_long
-[[ "$par_scaffold_composition" == "false" ]] && unset par_scaffold_composition
-[[ "$par_miniprot" == "false" ]] && unset par_miniprot
+for par in ${unset_if_false[@]}; do
+    test_val="${!par}"
+    [[ "$test_val" == "false" ]] && unset $par
+done
 
 tmp_dir=$(mktemp -d -p "$meta_temp_dir" busco_XXXXXXXXX)
 prefix=$(openssl rand -hex 8)

src/fastp/script.sh

@@ -4,25 +4,32 @@
 ## VIASH END
 
 # disable flags
-[[ "$par_disable_adapter_trimming" == "false" ]] && unset par_disable_adapter_trimming
-[[ "$par_detect_adapter_for_pe" == "false" ]] && unset par_detect_adapter_for_pe
-[[ "$par_merge" == "false" ]] && unset par_merge
-[[ "$par_include_unmerged" == "false" ]] && unset par_include_unmerged
-[[ "$par_interleaved_in" == "false" ]] && unset par_interleaved_in
-[[ "$par_fix_mgi_id" == "false" ]] && unset par_fix_mgi_id
-[[ "$par_phred64" == "false" ]] && unset par_phred64
-[[ "$par_dont_overwrite" == "false" ]] && unset par_dont_overwrite
-[[ "$par_verbose" == "false" ]] && unset par_verbose
-[[ "$par_dedup" == "false" ]] && unset par_dedup
-[[ "$par_dont_eval_duplication" == "false" ]] && unset par_dont_eval_duplication
-[[ "$par_trim_poly_g" == "false" ]] && unset par_trim_poly_g
-[[ "$par_disable_trim_poly_g" == "false" ]] && unset par_disable_trim_poly_g
-[[ "$par_trim_poly_x" == "false" ]] && unset par_trim_poly_x
-[[ "$par_disable_quality_filtering" == "false" ]] && unset par_disable_quality_filtering
-[[ "$par_disable_length_filtering" == "false" ]] && unset par_disable_length_filtering
-[[ "$par_low_complexity_filter" == "false" ]] && unset par_low_complexity_filter
-[[ "$par_umi" == "false" ]] && unset par_umi
-[[ "$par_overrepresentation_analysis" == "false" ]] && unset par_overrepresentation_analysis
+unset_if_false=(
+    par_disable_adapter_trimming
+    par_detect_adapter_for_pe
+    par_merge
+    par_include_unmerged
+    par_interleaved_in
+    par_fix_mgi_id
+    par_phred64
+    par_dont_overwrite
+    par_verbose
+    par_dedup
+    par_dont_eval_duplication
+    par_trim_poly_g
+    par_disable_trim_poly_g
+    par_trim_poly_x
+    par_disable_quality_filtering
+    par_disable_length_filtering
+    par_low_complexity_filter
+    par_umi
+    par_overrepresentation_analysis
+)
+
+for par in ${unset_if_false[@]}; do
+    test_val="${!par}"
+    [[ "$test_val" == "false" ]] && unset $par
+done
 
 # run command
 fastp \

src/featurecounts/script.sh

@@ -19,24 +19,31 @@ par_feature_type=$(echo $par_feature_type | tr ',' ';')
 par_extra_attributes=$(echo $par_extra_attributes | tr ',' ';')
 
 # unset flag variables
-[[ "$par_feature_level" == "false" ]] && unset par_feature_level
-[[ "$par_overlapping" == "false" ]] && unset par_overlapping
-[[ "$par_largest_overlap" == "false" ]] && unset par_largest_overlap
-[[ "$par_multi_mapping" == "false" ]] && unset par_multi_mapping
-[[ "$par_fraction" == "false" ]] && unset par_fraction
-[[ "$par_split_only" == "false" ]] && unset par_split_only
-[[ "$par_non_split_only" == "false" ]] && unset par_non_split_only
-[[ "$par_primary" == "false" ]] && unset par_primary
-[[ "$par_ignore_dup" == "false" ]] && unset par_ignore_dup
-[[ "$par_paired" == "false" ]] && unset par_paired
-[[ "$par_count_read_pairs" == "false" ]] && unset par_count_read_pairs
-[[ "$par_both_aligned" == "false" ]] && unset par_both_aligned
-[[ "$par_check_pe_dist" == "false" ]] && unset par_check_pe_dist
-[[ "$par_same_strand" == "false" ]] && unset par_same_strand
-[[ "$par_donotsort" == "false" ]] && unset par_donotsort
-[[ "$par_by_read_group" == "false" ]] && unset par_by_read_group
-[[ "$par_long_reads" == "false" ]] && unset par_long_reads
-[[ "$par_verbose" == "false" ]] && unset par_verbose
+unset_if_false=(
+    par_feature_level
+    par_overlapping
+    par_largest_overlap
+    par_multi_mapping
+    par_fraction
+    par_split_only
+    par_non_split_only
+    par_primary
+    par_ignore_dup
+    par_paired
+    par_count_read_pairs
+    par_both_aligned
+    par_check_pe_dist
+    par_same_strand
+    par_donotsort
+    par_by_read_group
+    par_long_reads
+    par_verbose
+)
+
+for par in ${unset_if_false[@]}; do
+    test_val="${!par}"
+    [[ "$test_val" == "false" ]] && unset $par
+done
 
 IFS=";" read -ra input <<< $par_input
 

src/gffread/script.sh

@@ -4,51 +4,58 @@
 ## VIASH END
 
 # unset flags
-[[ "$par_coding" == "false" ]] && unset par_coding
-[[ "$par_strict_range" == "false" ]] && unset par_strict_range
-[[ "$par_no_single_exon" == "false" ]] && unset par_no_single_exon
-[[ "$par_no_exon_attrs" == "false" ]] && unset par_no_exon_attrs
-[[ "$par_nc" == "false" ]] && unset par_nc
-[[ "$par_ignore_locus" == "false" ]] && unset par_ignore_locus
-[[ "$par_description" == "false" ]] && unset par_description
-[[ "$par_sort_alpha" == "false" ]] && unset par_sort_alpha
-[[ "$par_keep_genes" == "false" ]] && unset par_keep_genes
-[[ "$par_keep_attrs" == "false" ]] && unset par_keep_attrs
-[[ "$par_keep_exon_attrs" == "false" ]] && unset par_keep_exon_attrs
-[[ "$par_keep_comments" == "false" ]] && unset par_keep_comments
-[[ "$par_process_other" == "false" ]] && unset par_process_other
-[[ "$par_rm_stop_codons" == "false" ]] && unset par_rm_stop_codons
-[[ "$par_adj_cds_start" == "false" ]] && unset par_adj_cds_start
-[[ "$par_opposite_strand" == "false" ]] && unset par_opposite_strand
-[[ "$par_coding_status" == "false" ]] && unset par_coding_status
-[[ "$par_add_hasCDS" == "false" ]] && unset par_add_hasCDS
-[[ "$par_adj_stop" == "false" ]] && unset par_adj_stop
-[[ "$par_rm_noncanon" == "false" ]] && unset par_rm_noncanon
-[[ "$par_complete_cds" == "false" ]] && unset par_complete_cds
-[[ "$par_no_pseudo" == "false" ]] && unset par_no_pseudo
-[[ "$par_in_bed" == "false" ]] && unset par_in_bed
-[[ "$par_in_tlf" == "false" ]] && unset par_in_tlf
-[[ "$par_stream" == "false" ]] && unset par_stream
-[[ "$par_merge" == "false" ]] && unset par_merge
-[[ "$par_rm_redundant" == "false" ]] && unset par_rm_redundant
-[[ "$par_no_boundary" == "false" ]] && unset par_no_boundary
-[[ "$par_no_overlap" == "false" ]] && unset par_no_overlap
-[[ "$par_force_exons" == "false" ]] && unset par_force_exons
-[[ "$par_gene2exon" == "false" ]] && unset par_gene2exon
-[[ "$par_t_adopt" == "false" ]] && unset par_t_adopt
-[[ "$par_decode" == "false" ]] && unset par_decode
-[[ "$par_merge_exons" == "false" ]] && unset par_merge_exons
-[[ "$par_junctions" == "false" ]] && unset par_junctions
-[[ "$par_w_nocds" == "false" ]] && unset par_w_nocds
-[[ "$par_tr_cds" == "false" ]] && unset par_tr_cds
-[[ "$par_w_coords" == "false" ]] && unset par_w_coords
-[[ "$par_stop_dot" == "false" ]] && unset par_stop_dot
-[[ "$par_id_version" == "false" ]] && unset par_id_version
-[[ "$par_gtf_output" == "false" ]] && unset par_gtf_output
-[[ "$par_bed" == "false" ]] && unset par_bed
-[[ "$par_tlf" == "false" ]] && unset par_tlf
-[[ "$par_expose_dups" == "false" ]] && unset par_expose_dups
-[[ "$par_cluster_only" == "false" ]] && unset par_cluster_only
+unset_if_false=(
+    par_coding
+    par_strict_range
+    par_no_single_exon
+    par_no_exon_attrs
+    par_nc
+    par_ignore_locus
+    par_description
+    par_sort_alpha
+    par_keep_genes
+    par_keep_attrs
+    par_keep_exon_attrs
+    par_keep_comments
+    par_process_other
+    par_rm_stop_codons
+    par_adj_cds_start
+    par_opposite_strand
+    par_coding_status
+    par_add_hasCDS
+    par_adj_stop
+    par_rm_noncanon
+    par_complete_cds
+    par_no_pseudo
+    par_in_bed
+    par_in_tlf
+    par_stream
+    par_merge
+    par_rm_redundant
+    par_no_boundary
+    par_no_overlap
+    par_force_exons
+    par_gene2exon
+    par_t_adopt
+    par_decode
+    par_merge_exons
+    par_junctions
+    par_w_nocds
+    par_tr_cds
+    par_w_coords
+    par_stop_dot
+    par_id_version
+    par_gtf_output
+    par_bed
+    par_tlf
+    par_expose_dups
+    par_cluster_only
+)
+
+for par in ${unset_if_false[@]}; do
+    test_val="${!par}"
+    [[ "$test_val" == "false" ]] && unset $par
+done
 
 # if par_table is not empty, replace ";" with ","
 par_table=$(echo "$par_table" | tr ';' ',')