From b39835ecae7986dfb89bc195eefd386abe479cb6 Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Tue, 6 Aug 2024 16:25:33 +0200
Subject: [PATCH 01/12] add help

---
 .../agat_sp_alignment_output_style/help.txt   | 67 +++++++++++++++++++
 1 file changed, 67 insertions(+)
 create mode 100644 src/agat/agat_sp_alignment_output_style/help.txt

diff --git a/src/agat/agat_sp_alignment_output_style/help.txt b/src/agat/agat_sp_alignment_output_style/help.txt
new file mode 100644
index 00000000..ea2ca8c0
--- /dev/null
+++ b/src/agat/agat_sp_alignment_output_style/help.txt
@@ -0,0 +1,67 @@
+```sh
+agat_sp_alignment_output_style.pl --help
+```
+
+ ------------------------------------------------------------------------------
+|   Another GFF Analysis Toolkit (AGAT) - Version: v1.4.0                      |
+|   https://github.com/NBISweden/AGAT                                          |
+|   National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se         |
+ ------------------------------------------------------------------------------
+
+
+Name:
+    agat_sp_alignment_output_style.pl
+
+Description:
+    The script takes a normal gtf/gff annotation format file and convert it
+    to gff3 alignment format. It means it add a structure of match /
+    match_part as relationship between the different features.
+
+Usage:
+        agat_sp_alignment_output_style.pl -g infile.gff [ -o outfile ]
+        agat_sp_alignment_output_style.pl --help
+
+Options:
+    -g, --gff or -ref
+            Input GTF/GFF file.
+
+    -v      Verbose option to see the warning messages when parsing the gff
+            file.
+
+    -o or --output
+            Output GFF file. If no output file is specified, the output will
+            be written to STDOUT.
+
+    -c or --config
+            String - Input agat config file. By default AGAT takes as input
+            agat_config.yaml file from the working directory if any,
+            otherwise it takes the orignal agat_config.yaml shipped with
+            AGAT. To get the agat_config.yaml locally type: "agat config
+            --expose". The --config option gives you the possibility to use
+            your own AGAT config file (located elsewhere or named
+            differently).
+
+    -h or --help
+            Display this helpful text.
+
+Feedback:
+  Did you find a bug?:
+    Do not hesitate to report bugs to help us keep track of the bugs and
+    their resolution. Please use the GitHub issue tracking system available
+    at this address:
+
+                https://github.com/NBISweden/AGAT/issues
+
+     Ensure that the bug was not already reported by searching under Issues.
+     If you're unable to find an (open) issue addressing the problem, open a new one.
+     Try as much as possible to include in the issue when relevant:
+     - a clear description,
+     - as much relevant information as possible,
+     - the command used,
+     - a data sample,
+     - an explanation of the expected behaviour that is not occurring.
+
+  Do you want to contribute?:
+    You are very welcome, visit this address for the Contributing
+    guidelines:
+    https://github.com/NBISweden/AGAT/blob/master/CONTRIBUTING.md
\ No newline at end of file

From a3344e97168ce9f0afbfd2a3901724eaa809e7fa Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Tue, 6 Aug 2024 16:29:17 +0200
Subject: [PATCH 02/12] add config

---
 .../config.vsh.yaml                           | 69 +++++++++++++++++++
 1 file changed, 69 insertions(+)
 create mode 100644 src/agat/agat_sp_alignment_output_style/config.vsh.yaml

diff --git a/src/agat/agat_sp_alignment_output_style/config.vsh.yaml b/src/agat/agat_sp_alignment_output_style/config.vsh.yaml
new file mode 100644
index 00000000..29e07bc3
--- /dev/null
+++ b/src/agat/agat_sp_alignment_output_style/config.vsh.yaml
@@ -0,0 +1,69 @@
+name: agat_sp_alignment_output_style
+namespace: agat
+description: |
+  The script takes a normal gtf/gff annotation format file and convert it
+  to gff3 alignment format. It means it add a structure of match /
+  match_part as relationship between the different features.
+keywords: [gene annotations, GFF conversion]
+links:
+  homepage: https://github.com/NBISweden/AGAT
+  documentation: https://agat.readthedocs.io/en/latest/tools/agat_sp_alignment_output_style.html
+  issue_tracker: https://github.com/NBISweden/AGAT/issues
+  repository: https://github.com/NBISweden/AGAT
+references: 
+  doi: 10.5281/zenodo.3552717
+license: GPL-3.0
+authors:
+  - __merge__: /src/_authors/leila_paquay.yaml
+    roles: [ author, maintainer ]
+argument_groups:
+  - name: Inputs
+    arguments:
+      - name: --gff
+        alternatives: [-g, -ref]
+        description: Input GTF/GFF file.
+        type: file
+        required: true
+        direction: input
+        example: input.gff
+  - name: Outputs
+    arguments:
+      - name: --output
+        alternatives: [-o]
+        description: Output GFF file.
+        type: file
+        direction: output
+        required: true
+        example: output.gff
+  - name: Arguments
+    arguments:
+      - name: --verbose
+        alternatives: [-v]
+        description: Verbose option to see the warning messages when parsing the gff file.
+        type: boolean_true
+        required: false
+      - name: --config
+        alternatives: [-c]
+        description: |
+          Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: `agat config --expose`. The `--config` option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).
+        type: file
+        required: false
+        example: custom_agat_config.yaml
+resources:
+  - type: bash_script
+    path: script.sh
+test_resources:
+  - type: bash_script
+    path: test.sh
+  - type: file
+    path: test_data
+engines:
+  - type: docker
+    image: quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0
+    setup:
+      - type: docker
+        run: |
+          agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.txt
+runners:
+  - type: executable
+  - type: nextflow
\ No newline at end of file

From 70ba7ad2de2da2980d88ce04f361dd1a2863e128 Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Tue, 6 Aug 2024 17:52:15 +0200
Subject: [PATCH 03/12] add run script

---
 src/agat/agat_sp_alignment_output_style/script.sh | 14 ++++++++++++++
 1 file changed, 14 insertions(+)
 create mode 100644 src/agat/agat_sp_alignment_output_style/script.sh

diff --git a/src/agat/agat_sp_alignment_output_style/script.sh b/src/agat/agat_sp_alignment_output_style/script.sh
new file mode 100644
index 00000000..e56324c2
--- /dev/null
+++ b/src/agat/agat_sp_alignment_output_style/script.sh
@@ -0,0 +1,14 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+# unset flags
+[[ "$par_verbose" == "false" ]] && unset par_verbose
+
+# run agat_sp_alignment_output_style.pl
+agat_sp_alignment_output_style.pl \
+  --gff "$par_gff" \
+  --output "$par_output" \
+  ${par_verbose:+--verbose} \
+  ${par_config:+--config "${par_config}"}

From 106f03daf921287f229ceb6e49e056dd017fd3a1 Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Tue, 6 Aug 2024 17:55:03 +0200
Subject: [PATCH 04/12] add test data & expected output + script to fetch them

---
 .../test_data/0.gff                           | 36 +++++++++++++++++++
 .../agat_sp_alignment_output_style_1.gff      | 16 +++++++++
 .../test_data/script.sh                       | 10 ++++++
 3 files changed, 62 insertions(+)
 create mode 100644 src/agat/agat_sp_alignment_output_style/test_data/0.gff
 create mode 100644 src/agat/agat_sp_alignment_output_style/test_data/agat_sp_alignment_output_style_1.gff
 create mode 100755 src/agat/agat_sp_alignment_output_style/test_data/script.sh

diff --git a/src/agat/agat_sp_alignment_output_style/test_data/0.gff b/src/agat/agat_sp_alignment_output_style/test_data/0.gff
new file mode 100644
index 00000000..fafe86ed
--- /dev/null
+++ b/src/agat/agat_sp_alignment_output_style/test_data/0.gff
@@ -0,0 +1,36 @@
+##gff-version 3
+scaffold625	maker	gene	337818	343277	.	+	.	ID=CLUHARG00000005458;Name=TUBB3_2
+scaffold625	maker	mRNA	337818	343277	.	+	.	ID=CLUHART00000008717;Parent=CLUHARG00000005458
+scaffold625	maker	exon	337818	337971	.	+	.	ID=CLUHART00000008717:exon:1404;Parent=CLUHART00000008717
+scaffold625	maker	exon	340733	340841	.	+	.	ID=CLUHART00000008717:exon:1405;Parent=CLUHART00000008717
+scaffold625	maker	exon	341518	341628	.	+	.	ID=CLUHART00000008717:exon:1406;Parent=CLUHART00000008717
+scaffold625	maker	exon	341964	343277	.	+	.	ID=CLUHART00000008717:exon:1407;Parent=CLUHART00000008717
+scaffold625	maker	CDS	337915	337971	.	+	0	ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
+scaffold625	maker	CDS	340733	340841	.	+	0	ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
+scaffold625	maker	CDS	341518	341628	.	+	2	ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
+scaffold625	maker	CDS	341964	343033	.	+	2	ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
+scaffold625	maker	five_prime_UTR	337818	337914	.	+	.	ID=CLUHART00000008717:five_prime_utr;Parent=CLUHART00000008717
+scaffold625	maker	three_prime_UTR	343034	343277	.	+	.	ID=CLUHART00000008717:three_prime_utr;Parent=CLUHART00000008717
+scaffold789	maker	gene	558184	564780	.	+	.	ID=CLUHARG00000003852;Name=PF11_0240
+scaffold789	maker	mRNA	558184	564780	.	+	.	ID=CLUHART00000006146;Parent=CLUHARG00000003852
+scaffold789	maker	exon	558184	560123	.	+	.	ID=CLUHART00000006146:exon:995;Parent=CLUHART00000006146
+scaffold789	maker	exon	561401	561519	.	+	.	ID=CLUHART00000006146:exon:996;Parent=CLUHART00000006146
+scaffold789	maker	exon	564171	564235	.	+	.	ID=CLUHART00000006146:exon:997;Parent=CLUHART00000006146
+scaffold789	maker	exon	564372	564780	.	+	.	ID=CLUHART00000006146:exon:998;Parent=CLUHART00000006146
+scaffold789	maker	CDS	558191	560123	.	+	0	ID=CLUHART00000006146:cds;Parent=CLUHART00000006146
+scaffold789	maker	CDS	561401	561519	.	+	2	ID=CLUHART00000006146:cds;Parent=CLUHART00000006146
+scaffold789	maker	CDS	564171	564235	.	+	0	ID=CLUHART00000006146:cds;Parent=CLUHART00000006146
+scaffold789	maker	CDS	564372	564588	.	+	1	ID=CLUHART00000006146:cds;Parent=CLUHART00000006146
+scaffold789	maker	five_prime_UTR	558184	558190	.	+	.	ID=CLUHART00000006146:five_prime_utr;Parent=CLUHART00000006146
+scaffold789	maker	three_prime_UTR	564589	564780	.	+	.	ID=CLUHART00000006146:three_prime_utr;Parent=CLUHART00000006146
+scaffold789	maker	mRNA	558184	564780	.	+	.	ID=CLUHART00000006147;Parent=CLUHARG00000003852
+scaffold789	maker	exon	558184	560123	.	+	.	ID=CLUHART00000006147:exon:997;Parent=CLUHART00000006147
+scaffold789	maker	exon	561401	561519	.	+	.	ID=CLUHART00000006147:exon:998;Parent=CLUHART00000006147
+scaffold789	maker	exon	562057	562121	.	+	.	ID=CLUHART00000006147:exon:999;Parent=CLUHART00000006147
+scaffold789	maker	exon	564372	564780	.	+	.	ID=CLUHART00000006147:exon:1000;Parent=CLUHART00000006147
+scaffold789	maker	CDS	558191	560123	.	+	0	ID=CLUHART00000006147:cds;Parent=CLUHART00000006147
+scaffold789	maker	CDS	561401	561519	.	+	2	ID=CLUHART00000006147:cds;Parent=CLUHART00000006147
+scaffold789	maker	CDS	562057	562121	.	+	0	ID=CLUHART00000006147:cds;Parent=CLUHART00000006147
+scaffold789	maker	CDS	564372	564588	.	+	1	ID=CLUHART00000006147:cds;Parent=CLUHART00000006147
+scaffold789	maker	five_prime_UTR	558184	558190	.	+	.	ID=CLUHART00000006147:five_prime_utr;Parent=CLUHART00000006147
+scaffold789	maker	three_prime_UTR	564589	564780	.	+	.	ID=CLUHART00000006147:three_prime_utr;Parent=CLUHART00000006147
diff --git a/src/agat/agat_sp_alignment_output_style/test_data/agat_sp_alignment_output_style_1.gff b/src/agat/agat_sp_alignment_output_style/test_data/agat_sp_alignment_output_style_1.gff
new file mode 100644
index 00000000..d530177c
--- /dev/null
+++ b/src/agat/agat_sp_alignment_output_style/test_data/agat_sp_alignment_output_style_1.gff
@@ -0,0 +1,16 @@
+##gff-version 3
+scaffold625	maker	match	337818	343277	.	+	.	ID=CLUHART00000008717
+scaffold625	maker	match_part	337818	337971	.	+	.	ID=CLUHART00000008717:exon:1404;Parent=CLUHART00000008717;Target=CLUHART00000008717 1 154 +
+scaffold625	maker	match_part	340733	340841	.	+	.	ID=CLUHART00000008717:exon:1405;Parent=CLUHART00000008717;Target=CLUHART00000008717 155 263 +
+scaffold625	maker	match_part	341518	341628	.	+	.	ID=CLUHART00000008717:exon:1406;Parent=CLUHART00000008717;Target=CLUHART00000008717 264 374 +
+scaffold625	maker	match_part	341964	343277	.	+	.	ID=CLUHART00000008717:exon:1407;Parent=CLUHART00000008717;Target=CLUHART00000008717 375 1688 +
+scaffold789	maker	match	558184	564780	.	+	.	ID=CLUHART00000006146
+scaffold789	maker	match_part	558184	560123	.	+	.	ID=CLUHART00000006146:exon:995;Parent=CLUHART00000006146;Target=CLUHART00000006146 1 1940 +
+scaffold789	maker	match_part	561401	561519	.	+	.	ID=CLUHART00000006146:exon:996;Parent=CLUHART00000006146;Target=CLUHART00000006146 1941 2059 +
+scaffold789	maker	match_part	564171	564235	.	+	.	ID=CLUHART00000006146:exon:997;Parent=CLUHART00000006146;Target=CLUHART00000006146 2060 2124 +
+scaffold789	maker	match_part	564372	564780	.	+	.	ID=CLUHART00000006146:exon:998;Parent=CLUHART00000006146;Target=CLUHART00000006146 2125 2533 +
+scaffold789	maker	match	558184	564780	.	+	.	ID=CLUHART00000006147
+scaffold789	maker	match_part	558184	560123	.	+	.	ID=CLUHART00000006147:exon:997;Parent=CLUHART00000006147;Target=CLUHART00000006147 1 1940 +
+scaffold789	maker	match_part	561401	561519	.	+	.	ID=CLUHART00000006147:exon:998;Parent=CLUHART00000006147;Target=CLUHART00000006147 1941 2059 +
+scaffold789	maker	match_part	562057	562121	.	+	.	ID=CLUHART00000006147:exon:999;Parent=CLUHART00000006147;Target=CLUHART00000006147 2060 2124 +
+scaffold789	maker	match_part	564372	564780	.	+	.	ID=CLUHART00000006147:exon:1000;Parent=CLUHART00000006147;Target=CLUHART00000006147 2125 2533 +
diff --git a/src/agat/agat_sp_alignment_output_style/test_data/script.sh b/src/agat/agat_sp_alignment_output_style/test_data/script.sh
new file mode 100755
index 00000000..34bb3bf9
--- /dev/null
+++ b/src/agat/agat_sp_alignment_output_style/test_data/script.sh
@@ -0,0 +1,10 @@
+#!/bin/bash
+
+# clone repo
+if [ ! -d /tmp/agat_source ]; then
+  git clone --depth 1 --single-branch --branch master https://github.com/NBISweden/AGAT /tmp/agat_source
+fi
+
+# copy test data
+cp -r /tmp/agat_source/t/scripts_output/in/0.gff src/agat/agat_sp_alignment_output_style/test_data
+cp -r /tmp/agat_source/t/scripts_output/out/agat_sp_alignment_output_style_1.gff src/agat/agat_sp_alignment_output_style/test_data
\ No newline at end of file

From bbafe2394f90a9cad5c48108ab5117582c0cc8fb Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Tue, 6 Aug 2024 17:57:29 +0200
Subject: [PATCH 05/12] config: remove required argument for boolean_true

---
 src/agat/agat_sp_alignment_output_style/config.vsh.yaml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/agat/agat_sp_alignment_output_style/config.vsh.yaml b/src/agat/agat_sp_alignment_output_style/config.vsh.yaml
index 29e07bc3..0e397bdd 100644
--- a/src/agat/agat_sp_alignment_output_style/config.vsh.yaml
+++ b/src/agat/agat_sp_alignment_output_style/config.vsh.yaml
@@ -41,7 +41,6 @@ argument_groups:
         alternatives: [-v]
         description: Verbose option to see the warning messages when parsing the gff file.
         type: boolean_true
-        required: false
       - name: --config
         alternatives: [-c]
         description: |

From 4544fe71d4e4d4c8a843195a4c4ba23e3a661a25 Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Tue, 6 Aug 2024 17:57:59 +0200
Subject: [PATCH 06/12] add test

---
 .../agat_sp_alignment_output_style/test.sh    | 28 +++++++++++++++++++
 1 file changed, 28 insertions(+)
 create mode 100644 src/agat/agat_sp_alignment_output_style/test.sh

diff --git a/src/agat/agat_sp_alignment_output_style/test.sh b/src/agat/agat_sp_alignment_output_style/test.sh
new file mode 100644
index 00000000..80605209
--- /dev/null
+++ b/src/agat/agat_sp_alignment_output_style/test.sh
@@ -0,0 +1,28 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+test_dir="${meta_resources_dir}/test_data"
+out_dir="${meta_resources_dir}/out_data"
+
+echo "> Run $meta_name with test data"
+"$meta_executable" \
+  --gff "$test_dir/0.gff" \
+  --output "$out_dir/output.gff" 
+
+echo ">> Checking output"
+[ ! -f "$out_dir/output.gff" ] && echo "Output file output.gff does not exist" && exit 1
+
+echo ">> Check if output is empty"
+[ ! -s "$out_dir/output.gff" ] && echo "Output file output.gff is empty" && exit 1
+
+echo ">> Check if output matches expected output"
+diff "$out_dir/output.gff" "$test_dir/agat_sp_alignment_output_style_1.gff
+.gff"
+if [ $? -ne 0 ]; then
+  echo "Output file output.gff does not match expected output"
+  exit 1
+fi
+
+echo "> Test successful"
\ No newline at end of file

From b66cf653805b774ee5a21974501d84632646989c Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Tue, 6 Aug 2024 18:01:07 +0200
Subject: [PATCH 07/12] update changelog

---
 CHANGELOG.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9dd2389c..ae4a1c35 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -22,7 +22,8 @@
 * `agat`:
   - `agat_convert_sp_gff2gtf`: convert any GTF/GFF file into a proper GTF file (PR #76).
   - `/agat_convert_bed2gff`: convert bed file to gff format (PR #97).
-
+  - `agat_sp_alignment_output_style`: takes a normal gtf/gff annotation format file and convert it to gff3 alignment format (PR #124).
+  
 * `bedtools`:
   - `bedtools/bedtools_intersect`: Allows one to screen for overlaps between two sets of genomic features (PR #94).
   - `bedtools/bedtools_sort`: Sorts a feature file (bed/gff/vcf) by chromosome and other criteria (PR #98).

From af0d1d3f3c052d241b194ba1c7ff0dc06b2bb563 Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Tue, 6 Aug 2024 18:10:26 +0200
Subject: [PATCH 08/12] run script: replace -`-verbose` by `-v`

---
 src/agat/agat_sp_alignment_output_style/script.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/agat/agat_sp_alignment_output_style/script.sh b/src/agat/agat_sp_alignment_output_style/script.sh
index e56324c2..2bc05bf5 100644
--- a/src/agat/agat_sp_alignment_output_style/script.sh
+++ b/src/agat/agat_sp_alignment_output_style/script.sh
@@ -10,5 +10,5 @@
 agat_sp_alignment_output_style.pl \
   --gff "$par_gff" \
   --output "$par_output" \
-  ${par_verbose:+--verbose} \
+  ${par_verbose:+-v} \
   ${par_config:+--config "${par_config}"}

From be9357f8783a6ce0af61eb45ab481c1a20ea1487 Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Mon, 19 Aug 2024 16:42:49 +0200
Subject: [PATCH 09/12] add set -eo pipefail to sccript and test files

---
 src/agat/agat_sp_alignment_output_style/script.sh | 2 ++
 src/agat/agat_sp_alignment_output_style/test.sh   | 2 ++
 2 files changed, 4 insertions(+)

diff --git a/src/agat/agat_sp_alignment_output_style/script.sh b/src/agat/agat_sp_alignment_output_style/script.sh
index 2bc05bf5..6acc4d5e 100644
--- a/src/agat/agat_sp_alignment_output_style/script.sh
+++ b/src/agat/agat_sp_alignment_output_style/script.sh
@@ -1,5 +1,7 @@
 #!/bin/bash
 
+set -eo pipefail
+
 ## VIASH START
 ## VIASH END
 
diff --git a/src/agat/agat_sp_alignment_output_style/test.sh b/src/agat/agat_sp_alignment_output_style/test.sh
index 80605209..23ad13a0 100644
--- a/src/agat/agat_sp_alignment_output_style/test.sh
+++ b/src/agat/agat_sp_alignment_output_style/test.sh
@@ -1,5 +1,7 @@
 #!/bin/bash
 
+set -eo pipefail
+
 ## VIASH START
 ## VIASH END
 

From 0d9c5f1d14c4884417ce285261d88a4c1793ff84 Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Mon, 19 Aug 2024 16:43:23 +0200
Subject: [PATCH 10/12] create temporary directory and clean up on exit

---
 src/agat/agat_sp_alignment_output_style/test.sh | 16 +++++++++++-----
 1 file changed, 11 insertions(+), 5 deletions(-)

diff --git a/src/agat/agat_sp_alignment_output_style/test.sh b/src/agat/agat_sp_alignment_output_style/test.sh
index 23ad13a0..e488646b 100644
--- a/src/agat/agat_sp_alignment_output_style/test.sh
+++ b/src/agat/agat_sp_alignment_output_style/test.sh
@@ -6,21 +6,27 @@ set -eo pipefail
 ## VIASH END
 
 test_dir="${meta_resources_dir}/test_data"
-out_dir="${meta_resources_dir}/out_data"
+
+# create temporary directory and clean up on exit
+TMPDIR=$(mktemp -d "$meta_temp_dir/$meta_functionality_name-XXXXXX")
+function clean_up {
+ [[ -d "$TMPDIR" ]] && rm -rf "$TMPDIR"
+}
+trap clean_up EXIT
 
 echo "> Run $meta_name with test data"
 "$meta_executable" \
   --gff "$test_dir/0.gff" \
-  --output "$out_dir/output.gff" 
+  --output "$TMPDIR/output.gff" 
 
 echo ">> Checking output"
-[ ! -f "$out_dir/output.gff" ] && echo "Output file output.gff does not exist" && exit 1
+[ ! -f "$TMPDIR/output.gff" ] && echo "Output file output.gff does not exist" && exit 1
 
 echo ">> Check if output is empty"
-[ ! -s "$out_dir/output.gff" ] && echo "Output file output.gff is empty" && exit 1
+[ ! -s "$TMPDIR/output.gff" ] && echo "Output file output.gff is empty" && exit 1
 
 echo ">> Check if output matches expected output"
-diff "$out_dir/output.gff" "$test_dir/agat_sp_alignment_output_style_1.gff
+diff "$TMPDIR/output.gff" "$test_dir/agat_sp_alignment_output_style_1.gff
 .gff"
 if [ $? -ne 0 ]; then
   echo "Output file output.gff does not match expected output"

From 19cd3e1f9ddde70e1fdcda2e869d17af4b1b1a76 Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Mon, 19 Aug 2024 16:45:33 +0200
Subject: [PATCH 11/12] update config: add requirements, update --config
 description

---
 src/agat/agat_sp_alignment_output_style/config.vsh.yaml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/agat/agat_sp_alignment_output_style/config.vsh.yaml b/src/agat/agat_sp_alignment_output_style/config.vsh.yaml
index 0e397bdd..296887b0 100644
--- a/src/agat/agat_sp_alignment_output_style/config.vsh.yaml
+++ b/src/agat/agat_sp_alignment_output_style/config.vsh.yaml
@@ -13,6 +13,8 @@ links:
 references: 
   doi: 10.5281/zenodo.3552717
 license: GPL-3.0
+requirements:
+  - commands: [agat]
 authors:
   - __merge__: /src/_authors/leila_paquay.yaml
     roles: [ author, maintainer ]
@@ -44,7 +46,7 @@ argument_groups:
       - name: --config
         alternatives: [-c]
         description: |
-          Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: `agat config --expose`. The `--config` option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).
+          AGAT config file. By default AGAT takes the original agat_config.yaml shipped with AGAT. The `--config` option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).
         type: file
         required: false
         example: custom_agat_config.yaml

From 562e86ae3e2b5c5004c84c5b99dce101bb3feff2 Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Mon, 19 Aug 2024 16:47:51 +0200
Subject: [PATCH 12/12] fix bug in test

---
 src/agat/agat_sp_alignment_output_style/test.sh | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/agat/agat_sp_alignment_output_style/test.sh b/src/agat/agat_sp_alignment_output_style/test.sh
index e488646b..7e6ecea5 100644
--- a/src/agat/agat_sp_alignment_output_style/test.sh
+++ b/src/agat/agat_sp_alignment_output_style/test.sh
@@ -26,8 +26,7 @@ echo ">> Check if output is empty"
 [ ! -s "$TMPDIR/output.gff" ] && echo "Output file output.gff is empty" && exit 1
 
 echo ">> Check if output matches expected output"
-diff "$TMPDIR/output.gff" "$test_dir/agat_sp_alignment_output_style_1.gff
-.gff"
+diff "$TMPDIR/output.gff" "$test_dir/agat_sp_alignment_output_style_1.gff"
 if [ $? -ne 0 ]; then
   echo "Output file output.gff does not match expected output"
   exit 1