diff --git a/CHANGELOG.md b/CHANGELOG.md
index c4575cb9..36681056 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -21,6 +21,9 @@
 
 * `agat/agat_convert_sp_gff2gtf`: convert any GTF/GFF file into a proper GTF file (PR #76).
 
+* `bedtools`:
+    - `bedtools/bedtools_intersect`: Allows one to screen for overlaps between two sets of genomic features (PR #94).
+
 ## MINOR CHANGES
 
 * `busco` components: update BUSCO to `5.7.1` (PR #72).
diff --git a/src/bedtools/bedtools_intersect/config.vsh.yaml b/src/bedtools/bedtools_intersect/config.vsh.yaml
new file mode 100644
index 00000000..73dc0047
--- /dev/null
+++ b/src/bedtools/bedtools_intersect/config.vsh.yaml
@@ -0,0 +1,255 @@
+name: bedtools_intersect
+namespace: bedtools
+description: |
+  bedtools intersect allows one to screen for overlaps between two sets of genomic features. 
+  Moreover, it allows one to have fine control as to how the intersections are reported. 
+  bedtools intersect works with both BED/GFF/VCF and BAM files as input.
+keywords: [feature intersection, BAM, BED, GFF, VCF]
+links:
+  documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html
+  repository: https://github.com/arq5x/bedtools2
+references:
+  doi: 10.1093/bioinformatics/btq033
+license: GPL-2.0, MIT
+requirements:
+  commands: [bedtools]
+authors:
+  - __merge__: /src/_authors/theodoro_gasperin.yaml
+    roles: [ author, maintainer ]
+
+argument_groups:
+  - name: Inputs
+    arguments:
+      - name: --input_a
+        alternatives: -a
+        type: file
+        direction: input
+        description: |
+          The input file (BED/GFF/VCF/BAM) to be used as the -a file.
+        required: true
+        example: input_a.bed
+        
+      - name: --input_b
+        alternatives: -b
+        type: file
+        direction: input
+        multiple: true
+        description: | 
+          The input file(s) (BED/GFF/VCF/BAM) to be used as the -b file(s).
+        required: true
+        example: input_b.bed
+    
+  - name: Outputs
+    arguments:
+      - name: --output
+        type: file
+        direction: output
+        description: | 
+          The output BED file. 
+        required: true
+        example: output.bed
+  
+  - name: Options
+    arguments:
+      - name: --write_a
+        alternatives: -wa
+        type: boolean_true
+        description: Write the original A entry for each overlap.      
+      
+      - name: --write_b
+        alternatives: -wb
+        type: boolean_true
+        description: | 
+          Write the original B entry for each overlap. 
+          Useful for knowing _what_ A overlaps. Restricted by -f and -r.
+      
+      - name: --left_outer_join
+        alternatives: -loj
+        type: boolean_true
+        description: |
+          Perform a "left outer join". That is, for each feature in A report each overlap with B. 
+          If no overlaps are found, report a NULL feature for B.
+      
+      - name: --write_overlap
+        alternatives: -wo
+        type: boolean_true
+        description: | 
+          Write the original A and B entries plus the number of base pairs of overlap between the two features.
+          - Overlaps restricted by -f and -r. 
+            Only A features with overlap are reported.
+      
+      - name: --write_overlap_plus
+        alternatives: -wao
+        type: boolean_true
+        description: | 
+          Write the original A and B entries plus the number of base pairs of overlap between the two features.
+          - Overlaps restricted by -f and -r. 
+            However, A features w/o overlap are also reported with a NULL B feature and overlap = 0.
+
+      - name: --report_A_if_no_overlap
+        alternatives: -u
+        type: boolean_true
+        description: | 
+          Write the original A entry _if_ no overlap is found. 
+          - In other words, just report the fact >=1 hit was found.
+          - Overlaps restricted by -f and -r. 
+      
+      - name: --number_of_overlaps_A
+        alternatives: -c
+        type: boolean_true
+        description: | 
+          For each entry in A, report the number of overlaps with B.
+          - Reports 0 for A entries that have no overlap with B.
+          - Overlaps restricted by -f and -r.
+
+      - name: --report_no_overlaps_A
+        alternatives: -v
+        type: boolean_true
+        description: | 
+          Only report those entries in A that have _no overlaps_ with B.
+          - Similar to "grep -v" (an homage).
+      
+      - name: --uncompressed_bam
+        alternatives: -ubam
+        type: boolean_true
+        description: Write uncompressed BAM output. Default writes compressed BAM.
+
+      - name: --same_strand
+        alternatives: -s
+        type: boolean_true
+        description: | 
+          Require same strandedness.  That is, only report hits in B.
+          that overlap A on the _same_ strand.
+          - By default, overlaps are reported without respect to strand.
+
+      - name: --opposite_strand
+        alternatives: -S
+        type: boolean_true
+        description: | 
+          Require different strandedness.  That is, only report hits in B
+          that overlap A on the _opposite_ strand.
+          - By default, overlaps are reported without respect to strand.
+
+      - name: --min_overlap_A
+        alternatives: -f
+        type: double
+        description: | 
+          Minimum overlap required as a fraction of A.
+          - Default is 1E-9 (i.e., 1bp).
+          - FLOAT (e.g. 0.50)
+        example: 0.50
+
+      - name: --min_overlap_B
+        alternatives: -F
+        type: double
+        description: | 
+          Minimum overlap required as a fraction of B.
+          - Default is 1E-9 (i.e., 1bp).
+          - FLOAT (e.g. 0.50)
+        example: 0.50
+
+      - name: --reciprocal_overlap
+        alternatives: -r
+        type: boolean_true
+        description: | 
+          Require that the fraction overlap be reciprocal for A AND B.
+          - In other words, if -f is 0.90 and -r is used, this requires
+          that B overlap 90% of A and A _also_ overlaps 90% of B.
+      
+      - name: --either_overlap
+        alternatives: -e
+        type: boolean_true
+        description: | 
+          Require that the minimum fraction be satisfied for A OR B.
+          - In other words, if -e is used with -f 0.90 and -F 0.10 this requires
+          that either 90% of A is covered OR 10% of B is covered.
+          Without -e, both fractions would have to be satisfied.
+
+      - name: --split
+        type: boolean_true
+        description: Treat "split" BAM or BED12 entries as distinct BED intervals.
+
+      - name: --genome
+        alternatives: -g
+        type: file
+        description: | 
+          Provide a genome file to enforce consistent chromosome 
+          sort order across input files. Only applies when used 
+          with -sorted option.
+        example: genome.txt
+
+      - name: --nonamecheck
+        type: boolean_true
+        description: | 
+          For sorted data, don't throw an error if the file 
+          has different naming conventions for the same chromosome 
+          (e.g., "chr1" vs "chr01").
+
+      - name: --sorted
+        type: boolean_true
+        description: | 
+          Use the "chromsweep" algorithm for sorted (-k1,1 -k2,2n) input.
+
+      - name: --names
+        type: string
+        description: | 
+          When using multiple databases, provide an alias 
+          for each that will appear instead of a fileId when 
+          also printing the DB record.
+
+      - name: --filenames
+        type: boolean_true
+        description: When using multiple databases, show each complete filename instead of a fileId when also printing the DB record.
+
+      - name: --sortout
+        type: boolean_true
+        description: When using multiple databases, sort the output DB hits for each record.
+
+      - name: --bed
+        type: boolean_true
+        description: If using BAM input, write output as BED.
+
+      - name: --header
+        type: boolean_true
+        description: Print the header from the A file prior to results.
+
+      - name: --no_buffer_output
+        alternatives: --nobuf
+        type: boolean_true
+        description: | 
+          Disable buffered output. Using this option will cause each line
+          of output to be printed as it is generated, rather than saved
+          in a buffer. This will make printing large output files 
+          noticeably slower, but can be useful in conjunction with
+          other software tools and scripts that need to process one
+          line of bedtools output at a time.
+
+      - name: --io_buffer_size
+        alternatives: --iobuf
+        type: integer
+        description: | 
+          Specify amount of memory to use for input buffer.
+          Takes an integer argument. Optional suffixes K/M/G supported.
+          Note: currently has no effect with compressed files.       
+
+resources:
+  - type: bash_script
+    path: script.sh
+
+test_resources:
+  - type: bash_script
+    path: test.sh
+
+engines:
+  - type: docker
+    image: debian:stable-slim
+    setup:
+      - type: apt
+        packages: [bedtools, procps]
+      - type: docker
+        run: |
+          echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var/software_versions.txt
+
+runners:
+  - type: executable
+  - type: nextflow
diff --git a/src/bedtools/bedtools_intersect/help.txt b/src/bedtools/bedtools_intersect/help.txt
new file mode 100644
index 00000000..d1bbdc20
--- /dev/null
+++ b/src/bedtools/bedtools_intersect/help.txt
@@ -0,0 +1,119 @@
+```bash
+bedtools intersect
+```
+
+Tool:    bedtools intersect (aka intersectBed)
+Version: v2.30.0
+Summary: Report overlaps between two feature files.
+
+Usage:   bedtools intersect [OPTIONS] -a <bed/gff/vcf/bam> -b <bed/gff/vcf/bam>
+
+	Note: -b may be followed with multiple databases and/or 
+	wildcard (*) character(s). 
+Options: 
+	-wa	Write the original entry in A for each overlap.
+
+	-wb	Write the original entry in B for each overlap.
+		- Useful for knowing _what_ A overlaps. Restricted by -f and -r.
+
+	-loj	Perform a "left outer join". That is, for each feature in A
+		report each overlap with B.  If no overlaps are found, 
+		report a NULL feature for B.
+
+	-wo	Write the original A and B entries plus the number of base
+		pairs of overlap between the two features.
+		- Overlaps restricted by -f and -r.
+		  Only A features with overlap are reported.
+
+	-wao	Write the original A and B entries plus the number of base
+		pairs of overlap between the two features.
+		- Overlapping features restricted by -f and -r.
+		  However, A features w/o overlap are also reported
+		  with a NULL B feature and overlap = 0.
+
+	-u	Write the original A entry _once_ if _any_ overlaps found in B.
+		- In other words, just report the fact >=1 hit was found.
+		- Overlaps restricted by -f and -r.
+
+	-c	For each entry in A, report the number of overlaps with B.
+		- Reports 0 for A entries that have no overlap with B.
+		- Overlaps restricted by -f, -F, -r, and -s.
+
+	-C	For each entry in A, separately report the number of
+		- overlaps with each B file on a distinct line.
+		- Reports 0 for A entries that have no overlap with B.
+		- Overlaps restricted by -f, -F, -r, and -s.
+
+	-v	Only report those entries in A that have _no overlaps_ with B.
+		- Similar to "grep -v" (an homage).
+
+	-ubam	Write uncompressed BAM output. Default writes compressed BAM.
+
+	-s	Require same strandedness.  That is, only report hits in B
+		that overlap A on the _same_ strand.
+		- By default, overlaps are reported without respect to strand.
+
+	-S	Require different strandedness.  That is, only report hits in B
+		that overlap A on the _opposite_ strand.
+		- By default, overlaps are reported without respect to strand.
+
+	-f	Minimum overlap required as a fraction of A.
+		- Default is 1E-9 (i.e., 1bp).
+		- FLOAT (e.g. 0.50)
+
+	-F	Minimum overlap required as a fraction of B.
+		- Default is 1E-9 (i.e., 1bp).
+		- FLOAT (e.g. 0.50)
+
+	-r	Require that the fraction overlap be reciprocal for A AND B.
+		- In other words, if -f is 0.90 and -r is used, this requires
+		  that B overlap 90% of A and A _also_ overlaps 90% of B.
+
+	-e	Require that the minimum fraction be satisfied for A OR B.
+		- In other words, if -e is used with -f 0.90 and -F 0.10 this requires
+		  that either 90% of A is covered OR 10% of  B is covered.
+		  Without -e, both fractions would have to be satisfied.
+
+	-split	Treat "split" BAM or BED12 entries as distinct BED intervals.
+
+	-g	Provide a genome file to enforce consistent chromosome sort order
+		across input files. Only applies when used with -sorted option.
+
+	-nonamecheck	For sorted data, don't throw an error if the file has different naming conventions
+			for the same chromosome. ex. "chr1" vs "chr01".
+
+	-sorted	Use the "chromsweep" algorithm for sorted (-k1,1 -k2,2n) input.
+
+	-names	When using multiple databases, provide an alias for each that
+		will appear instead of a fileId when also printing the DB record.
+
+	-filenames	When using multiple databases, show each complete filename
+			instead of a fileId when also printing the DB record.
+
+	-sortout	When using multiple databases, sort the output DB hits
+			for each record.
+
+	-bed	If using BAM input, write output as BED.
+
+	-header	Print the header from the A file prior to results.
+
+	-nobuf	Disable buffered output. Using this option will cause each line
+		of output to be printed as it is generated, rather than saved
+		in a buffer. This will make printing large output files 
+		noticeably slower, but can be useful in conjunction with
+		other software tools and scripts that need to process one
+		line of bedtools output at a time.
+
+	-iobuf	Specify amount of memory to use for input buffer.
+		Takes an integer argument. Optional suffixes K/M/G supported.
+		Note: currently has no effect with compressed files.
+
+Notes: 
+	(1) When a BAM file is used for the A file, the alignment is retained if overlaps exist,
+	and excluded if an overlap cannot be found.  If multiple overlaps exist, they are not
+	reported, as we are only testing for one or more overlaps.
+
+
+
+
+***** ERROR: No input file given. Exiting. *****
diff --git a/src/bedtools/bedtools_intersect/script.sh b/src/bedtools/bedtools_intersect/script.sh
new file mode 100644
index 00000000..2141859d
--- /dev/null
+++ b/src/bedtools/bedtools_intersect/script.sh
@@ -0,0 +1,61 @@
+#!/bin/bash
+
+## 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
+
+# Create input array 
+IFS=";" read -ra input <<< $par_input_b
+
+bedtools intersect \
+    ${par_write_a:+-wa} \
+    ${par_write_b:+-wb} \
+    ${par_left_outer_join:+-loj} \
+    ${par_write_overlap:+-wo} \
+    ${par_write_overlap_plus:+-wao} \
+    ${par_report_A_if_no_overlap:+-u} \
+    ${par_number_of_overlaps_A:+-c} \
+    ${par_report_no_overlaps_A:+-v} \
+    ${par_uncompressed_bam:+-ubam} \
+    ${par_same_strand:+-s} \
+    ${par_opposite_strand:+-S} \
+    ${par_min_overlap_A:+-f "$par_min_overlap_A"} \
+    ${par_min_overlap_B:+-F "$par_min_overlap_B"} \
+    ${par_reciprocal_overlap:+-r} \
+    ${par_either_overlap:+-e} \
+    ${par_split:+-split} \
+    ${par_genome:+-g "$par_genome"} \
+    ${par_nonamecheck:+-nonamecheck} \
+    ${par_sorted:+-sorted} \
+    ${par_names:+-names "$par_names"} \
+    ${par_filenames:+-filenames} \
+    ${par_sortout:+-sortout} \
+    ${par_bed:+-bed} \
+    ${par_header:+-header} \
+    ${par_no_buffer_output:+-nobuf} \
+    ${par_io_buffer_size:+-iobuf "$par_io_buffer_size"} \
+    -a "$par_input_a" \
+    ${par_input_b:+ -b ${input[*]}} \
+    > "$par_output"
+    
\ No newline at end of file
diff --git a/src/bedtools/bedtools_intersect/test.sh b/src/bedtools/bedtools_intersect/test.sh
new file mode 100644
index 00000000..b9405a59
--- /dev/null
+++ b/src/bedtools/bedtools_intersect/test.sh
@@ -0,0 +1,340 @@
+#!/bin/bash
+
+# exit on error
+set -e
+
+## VIASH START
+meta_executable="target/executable/bedtools/bedtools_intersect/bedtools_intersect"
+meta_resources_dir="src/bedtools/bedtools_intersect"
+## VIASH END
+
+#############################################
+# helper functions
+assert_file_exists() {
+  [ -f "$1" ] || { echo "File '$1' does not exist" && exit 1; }
+}
+assert_file_not_empty() {
+  [ -s "$1" ] || { echo "File '$1' is empty but shouldn't be" && exit 1; }
+}
+assert_file_contains() {
+  grep -q "$2" "$1" || { echo "File '$1' does not contain '$2'" && exit 1; }
+}
+assert_identical_content() {
+  diff -a "$2" "$1" \
+    || (echo "Files are not identical!" && exit 1)
+}
+#############################################
+
+# Create directories for tests
+echo "Creating Test Data..."
+mkdir -p test_data
+
+# Create and populate featuresA.bed
+printf "chr1\t100\t200\nchr1\t150\t250\nchr1\t300\t400\n" > "test_data/featuresA.bed"
+
+# Create and populate featuresB.bed
+printf "chr1\t180\t280\nchr1\t290\t390\nchr1\t500\t600\n" > "test_data/featuresB.bed"
+
+# Create and populate featuresC.bed
+printf "chr1\t120\t220\nchr1\t250\t350\nchr1\t500\t580\n" > "test_data/featuresC.bed"
+
+# Create and populate examples gff files
+# example1.gff
+printf "##gff-version 3\n" > "test_data/example1.gff"
+printf "chr1\t.\tgene\t1000\t2000\t.\t+\t.\tID=gene1;Name=Gene1\n" >> "test_data/example1.gff"
+printf "chr1\t.\tmRNA\t1000\t2000\t.\t+\t.\tID=transcript1;Parent=gene1\n" >> "test_data/example1.gff"
+printf "chr1\t.\texon\t1000\t1200\t.\t+\t.\tID=exon1;Parent=transcript1\n" >> "test_data/example1.gff"
+printf "chr1\t.\texon\t1500\t1700\t.\t+\t.\tID=exon2;Parent=transcript1\n" >> "test_data/example1.gff"
+printf "chr1\t.\tCDS\t1000\t1200\t.\t+\t0\tID=cds1;Parent=transcript1\n" >> "test_data/example1.gff"
+printf "chr1\t.\tCDS\t1500\t1700\t.\t+\t2\tID=cds2;Parent=transcript1\n" >> "test_data/example1.gff"
+# example2.gff
+printf "##gff-version 3\n" > "test_data/example2.gff"
+printf "chr1\t.\tgene\t1200\t1800\t.\t-\t.\tID=gene2;Name=Gene2\n" >> "test_data/example2.gff"
+printf "chr1\t.\tmRNA\t1400\t2000\t.\t-\t.\tID=transcript2;Parent=gene2\n" >> "test_data/example2.gff"
+printf "chr1\t.\texon\t1400\t2000\t.\t-\t.\tID=exon3;Parent=transcript2\n" >> "test_data/example2.gff"
+printf "chr1\t.\texon\t1600\t2000\t.\t-\t.\tID=exon4;Parent=transcript2\n" >> "test_data/example2.gff"
+printf "chr1\t.\tCDS\t3000\t3200\t.\t-\t1\tID=cds3;Parent=transcript2\n" >> "test_data/example2.gff"
+printf "chr1\t.\tCDS\t3500\t3700\t.\t-\t0\tID=cds4;Parent=transcript2\n" >> "test_data/example2.gff"
+
+# Create and populate expected output files for different tests
+printf "chr1\t180\t200\nchr1\t180\t250\nchr1\t300\t390\n" > "test_data/expected_default.bed"
+printf "chr1\t100\t200\nchr1\t150\t250\nchr1\t300\t400\n" > "test_data/expected_wa.bed"
+printf "chr1\t180\t200\tchr1\t180\t280\nchr1\t180\t250\tchr1\t180\t280\nchr1\t300\t390\tchr1\t290\t390\n" > "test_data/expected_wb.bed"
+printf "chr1\t100\t200\tchr1\t180\t280\nchr1\t150\t250\tchr1\t180\t280\nchr1\t300\t400\tchr1\t290\t390\n" > "test_data/expected_loj.bed"
+printf "chr1\t100\t200\tchr1\t180\t280\t20\nchr1\t150\t250\tchr1\t180\t280\t70\nchr1\t300\t400\tchr1\t290\t390\t90\n" > "test_data/expected_wo.bed"
+printf "chr1\t100\t200\nchr1\t150\t250\nchr1\t300\t400\n" > "test_data/expected_u.bed"
+printf "chr1\t100\t200\t1\nchr1\t150\t250\t1\nchr1\t300\t400\t1\n" > "test_data/expected_c.bed"
+printf "chr1\t180\t250\nchr1\t300\t390\n" > "test_data/expected_f50.bed"
+printf "chr1\t180\t250\nchr1\t300\t390\n" > "test_data/expected_f30.bed"
+printf "chr1\t180\t200\nchr1\t180\t250\nchr1\t300\t390\n" > "test_data/expected_f10.bed"
+printf "chr1\t180\t200\nchr1\t180\t250\nchr1\t300\t390\n" > "test_data/expected_r.bed"
+printf "chr1\t180\t200\nchr1\t120\t200\nchr1\t180\t250\nchr1\t150\t220\nchr1\t300\t390\nchr1\t300\t350\n" > "test_data/expected_multiple.bed"
+# expected gff file
+printf "chr1\t.\tgene\t1200\t1800\t.\t+\t.\tID=gene1;Name=Gene1\n" >> "test_data/expected.gff"
+printf "chr1\t.\tgene\t1400\t2000\t.\t+\t.\tID=gene1;Name=Gene1\n" >> "test_data/expected.gff"
+printf "chr1\t.\tgene\t1400\t2000\t.\t+\t.\tID=gene1;Name=Gene1\n" >> "test_data/expected.gff"
+printf "chr1\t.\tgene\t1600\t2000\t.\t+\t.\tID=gene1;Name=Gene1\n" >> "test_data/expected.gff"
+printf "chr1\t.\tmRNA\t1200\t1800\t.\t+\t.\tID=transcript1;Parent=gene1\n" >> "test_data/expected.gff"
+printf "chr1\t.\tmRNA\t1400\t2000\t.\t+\t.\tID=transcript1;Parent=gene1\n" >> "test_data/expected.gff"
+printf "chr1\t.\tmRNA\t1400\t2000\t.\t+\t.\tID=transcript1;Parent=gene1\n" >> "test_data/expected.gff"
+printf "chr1\t.\tmRNA\t1600\t2000\t.\t+\t.\tID=transcript1;Parent=gene1\n" >> "test_data/expected.gff"
+printf "chr1\t.\texon\t1200\t1200\t.\t+\t.\tID=exon1;Parent=transcript1\n" >> "test_data/expected.gff"
+printf "chr1\t.\texon\t1500\t1700\t.\t+\t.\tID=exon2;Parent=transcript1\n" >> "test_data/expected.gff"
+printf "chr1\t.\texon\t1500\t1700\t.\t+\t.\tID=exon2;Parent=transcript1\n" >> "test_data/expected.gff"
+printf "chr1\t.\texon\t1500\t1700\t.\t+\t.\tID=exon2;Parent=transcript1\n" >> "test_data/expected.gff"
+printf "chr1\t.\texon\t1600\t1700\t.\t+\t.\tID=exon2;Parent=transcript1\n" >> "test_data/expected.gff"
+printf "chr1\t.\tCDS\t1200\t1200\t.\t+\t0\tID=cds1;Parent=transcript1\n" >> "test_data/expected.gff"
+printf "chr1\t.\tCDS\t1500\t1700\t.\t+\t2\tID=cds2;Parent=transcript1\n" >> "test_data/expected.gff"
+printf "chr1\t.\tCDS\t1500\t1700\t.\t+\t2\tID=cds2;Parent=transcript1\n" >> "test_data/expected.gff"
+printf "chr1\t.\tCDS\t1500\t1700\t.\t+\t2\tID=cds2;Parent=transcript1\n" >> "test_data/expected.gff"
+printf "chr1\t.\tCDS\t1600\t1700\t.\t+\t2\tID=cds2;Parent=transcript1\n" >> "test_data/expected.gff"
+
+# Test 1: Default intersect
+mkdir test1
+cd test1
+
+echo "> Run bedtools_intersect on BED files with default intersect"
+"$meta_executable" \
+  --input_a "../test_data/featuresA.bed" \
+  --input_b "../test_data/featuresB.bed" \
+  --output "output.bed"
+
+# checks
+assert_file_exists "output.bed"
+assert_file_not_empty "output.bed"
+assert_identical_content "output.bed" "../test_data/expected_default.bed"
+echo "- test1 succeeded -"
+
+cd ..
+
+# Test 2: Write A option
+mkdir test2
+cd test2
+
+echo "> Run bedtools_intersect on BED files with -wa option"
+"$meta_executable" \
+  --input_a "../test_data/featuresA.bed" \
+  --input_b "../test_data/featuresB.bed" \
+  --output "output.bed" \
+  --write_a
+
+# checks
+assert_file_exists "output.bed"
+assert_file_not_empty "output.bed"
+assert_identical_content "output.bed" "../test_data/expected_wa.bed"
+echo "- test2 succeeded -"
+
+cd ..
+
+# Test 3: -wb option
+mkdir test3
+cd test3
+
+echo "> Run bedtools_intersect on BED files with -wb option"
+"$meta_executable" \
+  --input_a "../test_data/featuresA.bed" \
+  --input_b "../test_data/featuresB.bed" \
+  --output "output.bed" \
+  --write_b 
+
+# checks
+assert_file_exists "output.bed"
+assert_file_not_empty "output.bed"
+assert_identical_content "output.bed" "../test_data/expected_wb.bed"
+echo "- test3 succeeded -"
+
+cd ..
+
+# Test 4: -loj option
+mkdir test4
+cd test4
+
+echo "> Run bedtools_intersect on BED files with -loj option"
+"$meta_executable" \
+  --input_a "../test_data/featuresA.bed" \
+  --input_b "../test_data/featuresB.bed" \
+  --output "output.bed" \
+  --left_outer_join
+
+# checks
+assert_file_exists "output.bed"
+assert_file_not_empty "output.bed"
+assert_identical_content "output.bed" "../test_data/expected_loj.bed"
+echo "- test4 succeeded -"
+
+cd ..
+
+# Test 5: -wo option
+mkdir test5
+cd test5
+
+echo "> Run bedtools_intersect on BED files with -wo option"
+"$meta_executable" \
+  --input_a "../test_data/featuresA.bed" \
+  --input_b "../test_data/featuresB.bed" \
+  --output "output.bed" \
+  --write_overlap 
+  
+
+# checks
+assert_file_exists "output.bed"
+assert_file_not_empty "output.bed"
+assert_identical_content "output.bed" "../test_data/expected_wo.bed"
+echo "- test5 succeeded -"
+
+cd ..
+
+# Test 6: -u option
+mkdir test6
+cd test6
+
+echo "> Run bedtools_intersect on BED files with -u option"
+"$meta_executable" \
+  --input_a "../test_data/featuresA.bed" \
+  --input_b "../test_data/featuresB.bed" \
+  --output "output.bed" \
+  --report_A_if_no_overlap true
+
+# checks
+assert_file_exists "output.bed"
+assert_file_not_empty "output.bed"
+assert_identical_content "output.bed" "../test_data/expected_u.bed"
+echo "- test6 succeeded -"
+
+cd ..
+
+# Test 7: -c option
+mkdir test7
+cd test7
+
+echo "> Run bedtools_intersect on BED files with -c option"
+"$meta_executable" \
+  --input_a "../test_data/featuresA.bed" \
+  --input_b "../test_data/featuresB.bed" \
+  --output "output.bed" \
+  --number_of_overlaps_A true
+
+# checks
+assert_file_exists "output.bed"
+assert_file_not_empty "output.bed"
+assert_identical_content "output.bed" "../test_data/expected_c.bed"
+echo "- test7 succeeded -"
+
+cd ..
+
+# Test 8: -f 0.50 option
+mkdir test8
+cd test8
+
+echo "> Run bedtools_intersect on BED files with -f 0.50 option"
+"$meta_executable" \
+  --input_a "../test_data/featuresA.bed" \
+  --input_b "../test_data/featuresB.bed" \
+  --output "output.bed" \
+  --min_overlap_A 0.50
+
+# checks
+assert_file_exists "output.bed"
+assert_file_not_empty "output.bed"
+assert_identical_content "output.bed" "../test_data/expected_f50.bed"
+echo "- test8 succeeded -"
+
+cd ..
+
+# Test 9: -f 0.30 option
+mkdir test9
+cd test9
+
+echo "> Run bedtools_intersect on BED files with -f 0.30 option"
+"$meta_executable" \
+  --input_a "../test_data/featuresA.bed" \
+  --input_b "../test_data/featuresB.bed" \
+  --output "output.bed" \
+  --min_overlap_A 0.30
+
+# checks
+assert_file_exists "output.bed"
+assert_file_not_empty "output.bed"
+assert_identical_content "output.bed" "../test_data/expected_f30.bed"
+echo "- test9 succeeded -"
+
+cd ..
+
+# Test 10: -f 0.10 option
+mkdir test10
+cd test10
+
+echo "> Run bedtools_intersect on BED files with -f 0.10 option"
+"$meta_executable" \
+  --input_a "../test_data/featuresA.bed" \
+  --input_b "../test_data/featuresB.bed" \
+  --output "output.bed" \
+  --min_overlap_A 0.10
+
+# checks
+assert_file_exists "output.bed"
+assert_file_not_empty "output.bed"
+assert_identical_content "output.bed" "../test_data/expected_f10.bed"
+echo "- test10 succeeded -"
+
+cd ..
+
+# Test 11: -r option
+mkdir test11
+cd test11
+
+echo "> Run bedtools_intersect on BED files with -r option"
+"$meta_executable" \
+  --input_a "../test_data/featuresA.bed" \
+  --input_b "../test_data/featuresB.bed" \
+  --output "output.bed" \
+  --reciprocal_overlap true
+
+# checks
+assert_file_exists "output.bed"
+assert_file_not_empty "output.bed"
+assert_identical_content "output.bed" "../test_data/expected_r.bed"
+echo "- test11 succeeded -"
+
+cd ..
+
+
+# Test 12: Multiple files
+mkdir test12
+cd test12
+
+echo "> Run bedtools_intersect on multiple BED files"
+"$meta_executable" \
+  --input_a "../test_data/featuresA.bed" \
+  --input_b "../test_data/featuresB.bed" \
+  --input_b "../test_data/featuresC.bed" \
+  --output "output.bed"
+
+# checks
+assert_file_exists "output.bed"
+assert_file_not_empty "output.bed"
+assert_identical_content "output.bed" "../test_data/expected_multiple.bed"
+echo "- test12 succeeded -"
+
+cd ..
+
+# Test 13: VCF file format
+mkdir test13
+cd test13
+
+echo "> Run bedtools_intersect on GFF files"
+"$meta_executable" \
+  --input_a "../test_data/example1.gff" \
+  --input_b "../test_data/example2.gff" \
+  --output "output.bed"
+
+# checks
+assert_file_exists "output.bed"
+assert_file_not_empty "output.bed"
+assert_identical_content "output.bed" "../test_data/expected.gff"
+echo "- test13 succeeded -"
+
+cd ..
+
+echo "---- All tests succeeded! ----"
+exit 0