From d5fc46b1d9ef8313c06e369bc881f6de75c53dd4 Mon Sep 17 00:00:00 2001
From: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>
Date: Tue, 13 Aug 2024 10:14:59 +0200
Subject: [PATCH] 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                              |  2 +
 CONTRIBUTING.md                           | 25 ++++++
 src/bedtools/bedtools_intersect/script.sh | 49 +++++++-----
 src/bedtools/bedtools_sort/script.sh      | 21 +++--
 src/busco/busco_run/script.sh             | 28 ++++---
 src/fastp/script.sh                       | 45 ++++++-----
 src/featurecounts/script.sh               | 43 +++++-----
 src/gffread/script.sh                     | 97 ++++++++++++-----------
 src/lofreq/call/script.sh                 | 37 +++++----
 src/multiqc/script.sh                     | 44 +++++-----
 src/salmon/salmon_index/script.sh         | 19 +++--
 src/salmon/salmon_quant/script.sh         | 90 +++++++++++----------
 src/samtools/samtools_fastq/script.sh     | 17 ++--
 src/samtools/samtools_sort/script.sh      | 25 +++---
 src/samtools/samtools_view/script.sh      | 38 +++++----
 src/umi_tools/umi_tools_dedup/script.sh   | 33 +++++---
 src/umi_tools/umi_tools_extract/script.sh | 19 +++--
 17 files changed, 380 insertions(+), 252 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3c2f347a..5030894c 100644
--- a/CHANGELOG.md
+++ b/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):
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index cee4249a..a32b680c 100644
--- a/CONTRIBUTING.md
+++ b/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
 
diff --git a/src/bedtools/bedtools_intersect/script.sh b/src/bedtools/bedtools_intersect/script.sh
index 2141859d..04a8d854 100644
--- a/src/bedtools/bedtools_intersect/script.sh
+++ b/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
diff --git a/src/bedtools/bedtools_sort/script.sh b/src/bedtools/bedtools_sort/script.sh
index e7f712d7..0d0b9b54 100644
--- a/src/bedtools/bedtools_sort/script.sh
+++ 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 \
diff --git a/src/busco/busco_run/script.sh b/src/busco/busco_run/script.sh
index a0ef24de..673ccd0b 100644
--- a/src/busco/busco_run/script.sh
+++ b/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)
diff --git a/src/fastp/script.sh b/src/fastp/script.sh
index 4bb37c87..557f7ac3 100644
--- a/src/fastp/script.sh
+++ b/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 \
diff --git a/src/featurecounts/script.sh b/src/featurecounts/script.sh
index 2e54feb3..53f8c63f 100644
--- a/src/featurecounts/script.sh
+++ b/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
 
diff --git a/src/gffread/script.sh b/src/gffread/script.sh
index cd4abf14..fab9e521 100644
--- a/src/gffread/script.sh
+++ b/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 ';' ',')
diff --git a/src/lofreq/call/script.sh b/src/lofreq/call/script.sh
index 863fe986..ca229194 100644
--- a/src/lofreq/call/script.sh
+++ b/src/lofreq/call/script.sh
@@ -4,21 +4,28 @@
 ## VIASH END
 
 # Unset all parameters that are set to "false"
-[[ "$par_no_baq" == "false" ]] && unset par_no_baq
-[[ "$par_no_idaq" == "false" ]] && unset par_no_idaq
-[[ "$par_del_baq" == "false" ]] && unset par_del_baq
-[[ "$par_no_ext_baq" == "false" ]] && unset par_no_ext_baq
-[[ "$par_no_mq" == "false" ]] && unset par_no_mq
-[[ "$par_call_indels" == "false" ]] && unset par_call_indels
-[[ "$par_only_indels" == "false" ]] && unset par_only_indels
-[[ "$par_src_qual" == "false" ]] && unset par_src_qual
-[[ "$par_illumina_13" == "false" ]] && unset par_illumina_13
-[[ "$par_use_orphan" == "false" ]] && unset par_use_orphan
-[[ "$par_plp_summary_only" == "false" ]] && unset par_plp_summary_only
-[[ "$par_no_default_filter" == "false" ]] && unset par_no_default_filter
-[[ "$par_force_overwrite" == "false" ]] && unset par_force_overwrite
-[[ "$par_verbose" == "false" ]] && unset par_verbose
-[[ "$par_debug" == "false" ]] && unset par_debug
+unset_if_false=(
+    par_no_baq
+    par_no_idaq
+    par_del_baq
+    par_no_ext_baq
+    par_no_mq
+    par_call_indels
+    par_only_indels
+    par_src_qual
+    par_illumina_13
+    par_use_orphan
+    par_plp_summary_only
+    par_no_default_filter
+    par_force_overwrite
+    par_verbose
+    par_debug
+)
+
+for par in ${unset_if_false[@]}; do
+    test_val="${!par}"
+    [[ "$test_val" == "false" ]] && unset $par
+done
 
 # Run lofreq call
 lofreq call \
diff --git a/src/multiqc/script.sh b/src/multiqc/script.sh
index ad8c1c0c..5806fa1d 100755
--- a/src/multiqc/script.sh
+++ b/src/multiqc/script.sh
@@ -1,26 +1,32 @@
 #!/bin/bash
 
 # disable flags
-[[ "$par_ignore_symlinks" == "false" ]] && unset par_ignore_symlinks
-[[ "$par_dirs" == "false" ]] && unset par_dirs
-[[ "$par_full_names" == "false" ]] && unset par_full_names
-[[ "$par_fn_as_s_name" == "false" ]] && unset par_fn_as_s_name
-[[ "$par_profile_runtime" == "false" ]] && unset par_profile_runtime
-[[ "$par_verbose" == "false" ]] && unset par_verbose
-[[ "$par_quiet" == "false" ]] && unset par_quiet
-[[ "$par_strict" == "false" ]] && unset par_strict
-[[ "$par_development" == "false" ]] && unset par_development
-[[ "$par_require_logs" == "false" ]] && unset par_require_logs
-[[ "$par_no_megaqc_upload" == "false" ]] && unset par_no_megaqc_upload
-[[ "$par_no_ansi" == "false" ]] && unset par_no_ansi
-[[ "$par_flat" == "false" ]] && unset par_flat
-[[ "$par_interactive" == "false" ]] && unset par_interactive
-[[ "$par_static_plot_export" == "false" ]] && unset par_static_plot_export
-[[ "$par_data_dir" == "false" ]] && unset par_data_dir
-[[ "$par_no_data_dir" == "false" ]] && unset par_no_data_dir
-[[ "$par_zip_data_dir" == "false" ]] && unset par_zip_data_dir
-[[ "$par_pdf" == "false" ]] && unset par_pdf
+unset_if_false=(
+    par_ignore_symlinks
+    par_dirs
+    par_full_names
+    par_fn_as_s_name
+    par_profile_runtime
+    par_verbose
+    par_quiet
+    par_strict
+    par_development
+    par_require_logs
+    par_no_megaqc_upload
+    par_no_ansi
+    par_flat
+    par_interactive
+    par_static_plot_export
+    par_data_dir
+    par_no_data_dir
+    par_zip_data_dir
+    par_pdf
+)
 
+for par in ${unset_if_false[@]}; do
+    test_val="${!par}"
+    [[ "$test_val" == "false" ]] && unset $par
+done
 
 # handle inputs
 out_dir=$(dirname "$par_output_report")
diff --git a/src/salmon/salmon_index/script.sh b/src/salmon/salmon_index/script.sh
index c2b9e7a0..5b1c4d76 100644
--- a/src/salmon/salmon_index/script.sh
+++ b/src/salmon/salmon_index/script.sh
@@ -5,12 +5,19 @@ set -e
 ## VIASH START
 ## VIASH END
 
-[[ "$par_gencode" == "false" ]] && unset par_gencode
-[[ "$par_features" == "false" ]] && unset par_features
-[[ "$par_keep_duplicates" == "false" ]] && unset par_keep_duplicates
-[[ "$par_keep_fixed_fasta" == "false" ]] && unset par_keep_fixed_fasta
-[[ "$par_sparse" == "false" ]] && unset par_sparse
-[[ "$par_no_clip" == "false" ]] && unset par_no_clip
+unset_if_false=(
+    par_gencode
+    par_features
+    par_keep_duplicates
+    par_keep_fixed_fasta
+    par_sparse
+    par_no_clip
+)
+
+for par in ${unset_if_false[@]}; do
+    test_val="${!par}"
+    [[ "$test_val" == "false" ]] && unset $par
+done
 
 tmp_dir=$(mktemp -d -p "$meta_temp_dir" "${meta_functionality_name}_XXXXXX")
 mkdir -p "$tmp_dir/temp"
diff --git a/src/salmon/salmon_quant/script.sh b/src/salmon/salmon_quant/script.sh
index 4c9f69d5..47cba1b9 100644
--- a/src/salmon/salmon_quant/script.sh
+++ b/src/salmon/salmon_quant/script.sh
@@ -4,49 +4,55 @@ set -e
 
 ## VIASH START
 ## VIASH END
+unset_if_false=(
+    par_discard_orphans
+    par_ont
+    par_seq_bias
+    par_gc_bias
+    par_pos_bias
+    par_meta
+    par_discard_orphans_quasi
+    par_disable_chaining_heuristic
+    par_allow_dovetail
+    par_recover_orphans
+    par_mimicBT2
+    par_mimic_strictBT2
+    par_softclip
+    par_softclip_overhangs
+    par_full_length_alignment
+    par_hard_filter
+    par_write_mappings
+    par_write_qualities
+    par_alternative_init_mode
+    par_skip_quant
+    par_dump_eq
+    par_dump_eq_weights
+    par_reduce_GC_memory
+    par_init_uniform
+    par_no_length_correction
+    par_no_effective_length_correction
+    par_no_single_frag_prob
+    par_no_frag_length_dist
+    par_no_bias_length_threshold
+    par_useEM
+    par_useVBOpt
+    par_no_Gamma_draw
+    par_bootstrap_reproject
+    par_quiet
+    par_per_transcript_prior
+    par_per_nucleotide_prior
+    par_write_orphan_links
+    par_write_unmapped_names
+    par_no_error_model
+    par_sample_out
+    par_sample_unaligned
+    par_gencode
+)
 
-[[ "$par_discard_orphans" == "false" ]] && unset par_discard_orphans
-[[ "$par_ont" == "false" ]] && unset par_ont
-[[ "$par_seq_bias" == "false" ]] && unset par_seq_bias
-[[ "$par_gc_bias" == "false" ]] && unset par_gc_bias
-[[ "$par_pos_bias" == "false" ]] && unset par_pos_bias
-[[ "$par_meta" == "false" ]] && unset par_meta
-[[ "$par_discard_orphans_quasi" == "false" ]] && unset par_discard_orphans_quasi
-[[ "$par_disable_chaining_heuristic" == "false" ]] && unset par_disable_chaining_heuristic
-[[ "$par_allow_dovetail" == "false" ]] && unset par_allow_dovetail
-[[ "$par_recover_orphans" == "false" ]] && unset par_recover_orphans
-[[ "$par_mimicBT2" == "false" ]] && unset par_mimicBT2
-[[ "$par_mimic_strictBT2" == "false" ]] && unset par_mimic_strictBT2
-[[ "$par_softclip" == "false" ]] && unset par_softclip
-[[ "$par_softclip_overhangs" == "false" ]] && unset par_softclip_overhangs
-[[ "$par_full_length_alignment" == "false" ]] && unset par_full_length_alignment
-[[ "$par_hard_filter" == "false" ]] && unset par_hard_filter
-[[ "$par_write_mappings" == "false" ]] && unset par_write_mappings
-[[ "$par_write_qualities" == "false" ]] && unset par_write_qualities
-[[ "$par_alternative_init_mode" == "false" ]] && unset par_alternative_init_mode
-[[ "$par_skip_quant" == "false" ]] && unset par_skip_quant
-[[ "$par_dump_eq" == "false" ]] && unset par_dump_eq
-[[ "$par_dump_eq_weights" == "false" ]] && unset par_dump_eq_weights
-[[ "$par_reduce_GC_memory" == "false" ]] && unset par_reduce_GC_memory
-[[ "$par_init_uniform" == "false" ]] && unset par_init_uniform
-[[ "$par_no_length_correction" == "false" ]] && unset par_no_length_correction
-[[ "$par_no_effective_length_correction" == "false" ]] && unset par_no_effective_length_correction
-[[ "$par_no_single_frag_prob" == "false" ]] && unset par_no_single_frag_prob
-[[ "$par_no_frag_length_dist" == "false" ]] && unset par_no_frag_length_dist
-[[ "$par_no_bias_length_threshold" == "false" ]] && unset par_no_bias_length_threshold
-[[ "$par_useEM" == "false" ]] && unset par_useEM
-[[ "$par_useVBOpt" == "false" ]] && unset par_useVBOpt
-[[ "$par_no_Gamma_draw" == "false" ]] && unset par_no_Gamma_draw
-[[ "$par_bootstrap_reproject" == "false" ]] && unset par_bootstrap_reproject
-[[ "$par_quiet" == "false" ]] && unset par_quiet
-[[ "$par_per_transcript_prior" == "false" ]] && unset par_per_transcript_prior
-[[ "$par_per_nucleotide_prior" == "false" ]] && unset par_per_nucleotide_prior
-[[ "$par_write_orphan_links" == "false" ]] && unset par_write_orphan_links
-[[ "$par_write_unmapped_names" == "false" ]] && unset par_write_unmapped_names
-[[ "$par_no_error_model" == "false" ]] && unset par_no_error_model
-[[ "$par_sample_out" == "false" ]] && unset par_sample_out
-[[ "$par_sample_unaligned" == "false" ]] && unset par_sample_unaligned
-[[ "$par_gencode" == "false" ]] && unset par_gencode
+for par in ${unset_if_false[@]}; do
+    test_val="${!par}"
+    [[ "$test_val" == "false" ]] && unset $par
+done
 
 IFS=";" read -ra unmated_reads <<< $par_unmated_reads
 IFS=";" read -ra mates1 <<< $par_mates1
diff --git a/src/samtools/samtools_fastq/script.sh b/src/samtools/samtools_fastq/script.sh
index 0cad9cfe..e05da9b0 100644
--- a/src/samtools/samtools_fastq/script.sh
+++ b/src/samtools/samtools_fastq/script.sh
@@ -5,11 +5,18 @@
 
 set -e
 
-[[ "$par_no_suffix" == "false" ]] && unset par_no_suffix
-[[ "$par_suffix" == "false" ]] && unset par_suffix
-[[ "$par_use_oq" == "false" ]] && unset par_use_oq
-[[ "$par_copy_tags" == "false" ]] && unset par_copy_tags
-[[ "$par_casava" == "false" ]] && unset par_casava
+unset_if_false=(
+  par_no_suffix
+  par_suffix
+  par_use_oq
+  par_copy_tags
+  par_casava
+)
+
+for par in ${unset_if_false[@]}; do
+    test_val="${!par}"
+    [[ "$test_val" == "false" ]] && unset $par
+done
 
 if [[ "$meta_name" == "samtools_fasta" ]]; then
   subcommand=fasta
diff --git a/src/samtools/samtools_sort/script.sh b/src/samtools/samtools_sort/script.sh
index 94836c18..a8b3ce0f 100644
--- a/src/samtools/samtools_sort/script.sh
+++ b/src/samtools/samtools_sort/script.sh
@@ -5,15 +5,22 @@
 
 set -e
 
-[[ "$par_uncompressed" == "false" ]] && unset par_uncompressed
-[[ "$par_minimiser" == "false" ]] && unset par_minimiser
-[[ "$par_not_reverse" == "false" ]] && unset par_not_reverse
-[[ "$par_homopolymers" == "false" ]] && unset par_homopolymers
-[[ "$par_natural_sort" == "false" ]] && unset par_natural_sort
-[[ "$par_ascii_sort" == "false" ]] && unset par_ascii_sort
-[[ "$par_template_coordinate" == "false" ]] && unset par_template_coordinate
-[[ "$par_write_index" == "false" ]] && unset par_write_index
-[[ "$par_no_PG" == "false" ]] && unset par_no_PG
+unset_if_false=(
+   par_uncompressed
+   par_minimiser
+   par_not_reverse
+   par_homopolymers
+   par_natural_sort
+   par_ascii_sort
+   par_template_coordinate
+   par_write_index
+   par_no_PG
+)
+
+for par in ${unset_if_false[@]}; do
+    test_val="${!par}"
+    [[ "$test_val" == "false" ]] && unset $par
+done
 
 
 samtools sort \
diff --git a/src/samtools/samtools_view/script.sh b/src/samtools/samtools_view/script.sh
index c3911b48..7608844b 100644
--- a/src/samtools/samtools_view/script.sh
+++ b/src/samtools/samtools_view/script.sh
@@ -5,21 +5,29 @@
 
 set -e
 
-[[ "$par_bam" == "false" ]] && unset par_bam
-[[ "$par_cram" == "false" ]] && unset par_cram
-[[ "$par_fast" == "false" ]] && unset par_fast
-[[ "$par_uncompressed" == "false" ]] && unset par_uncompressed
-[[ "$par_with_header" == "false" ]] && unset par_with_header
-[[ "$par_header_only" == "false" ]] && unset par_header_only
-[[ "$par_no_header" == "false" ]] && unset par_no_header
-[[ "$par_count" == "false" ]] && unset par_count
-[[ "$par_unmap" == "false" ]] && unset par_unmap
-[[ "$par_use_index" == "false" ]] && unset par_use_index
-[[ "$par_fetch_pairs" == "false" ]] && unset par_fetch_pairs
-[[ "$par_customized_index" == "false" ]] && unset par_customized_index
-[[ "$par_no_PG" == "false" ]] && unset par_no_PG
-[[ "$par_write_index" == "false" ]] && unset par_write_index
-[[ "$par_remove_B" == "false" ]] && unset par_remove_B
+unset_if_false=(
+   par_bam
+   par_cram
+   par_fast
+   par_uncompressed
+   par_with_header
+   par_header_only
+   par_no_header
+   par_count
+   par_unmap
+   par_use_index
+   par_fetch_pairs
+   par_customized_index
+   par_no_PG
+   par_write_index
+   par_remove_B
+)
+
+for par in ${unset_if_false[@]}; do
+    test_val="${!par}"
+    [[ "$test_val" == "false" ]] && unset $par
+done
+
 
 samtools view \
     ${par_bam:+-b} \
diff --git a/src/umi_tools/umi_tools_dedup/script.sh b/src/umi_tools/umi_tools_dedup/script.sh
index d57a5e76..3f3bdc89 100644
--- a/src/umi_tools/umi_tools_dedup/script.sh
+++ b/src/umi_tools/umi_tools_dedup/script.sh
@@ -7,19 +7,26 @@ set -e
 
 test_dir="${metal_executable}/test_data"
 
-[[ "$par_paired" == "false" ]] && unset par_paired
-[[ "$par_in_sam" == "false" ]] && unset par_in_sam
-[[ "$par_out_sam" == "false" ]] && unset par_out_sam
-[[ "$par_spliced_is_unique" == "false" ]] && unset par_spliced_is_unique
-[[ "$par_per_gene" == "false" ]] && unset par_per_gene
-[[ "$par_per_contig" == "false" ]] && unset par_per_contig
-[[ "$par_per_cell" == "false" ]] && unset par_per_cell
-[[ "$par_no_sort_output" == "false" ]] && unset par_no_sort_output
-[[ "$par_buffer_whole_contig" == "false" ]] && unset par_buffer_whole_contig
-[[ "$par_ignore_umi" == "false" ]] && unset par_ignore_umi
-[[ "$par_subset" == "false" ]] && unset par_subset
-[[ "$par_log2stderr" == "false" ]] && unset par_log2stderr
-[[ "$par_read_length" == "false" ]] && unset par_read_length
+unset_if_false=(
+   par_paired
+   par_in_sam
+   par_out_sam
+   par_spliced_is_unique
+   par_per_gene
+   par_per_contig
+   par_per_cell
+   par_no_sort_output
+   par_buffer_whole_contig
+   par_ignore_umi
+   par_subset
+   par_log2stderr
+   par_read_length
+)
+
+for par in ${unset_if_false[@]}; do
+    test_val="${!par}"
+    [[ "$test_val" == "false" ]] && unset $par
+done
 
 umi_tools dedup \
     --stdin "$par_input" \
diff --git a/src/umi_tools/umi_tools_extract/script.sh b/src/umi_tools/umi_tools_extract/script.sh
index 5e41865d..4514860e 100644
--- a/src/umi_tools/umi_tools_extract/script.sh
+++ b/src/umi_tools/umi_tools_extract/script.sh
@@ -5,14 +5,19 @@
 
 set -exo pipefail
 
-test_dir="${metal_executable}/test_data"
+unset_if_false=(
+   par_error_correct_cell
+   par_reconcile_pairs
+   par_three_prime
+   par_ignore_read_pair_suffixes
+   par_timeit_header
+   par_log2stderr
+)
 
-[[ "$par_error_correct_cell" == "false" ]] && unset par_error_correct_cell
-[[ "$par_reconcile_pairs" == "false" ]] && unset par_reconcile_pairs
-[[ "$par_three_prime" == "false" ]] && unset par_three_prime
-[[ "$par_ignore_read_pair_suffixes" == "false" ]] && unset par_ignore_read_pair_suffixes
-[[ "$par_timeit_header" == "false" ]] && unset par_timeit_header
-[[ "$par_log2stderr" == "false" ]] && unset par_log2stderr
+for par in ${unset_if_false[@]}; do
+    test_val="${!par}"
+    [[ "$test_val" == "false" ]] && unset $par
+done
 
 
 # Check if we have the correct number of input files and patterns for paired-end or single-end reads