From adda847757640210b2d197ddf844b7c65f91b9a7 Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Wed, 7 Aug 2024 16:29:44 +0200
Subject: [PATCH 01/13] add help

---
 .../agat_sp_complement_annotations/help.txt   | 91 +++++++++++++++++++
 1 file changed, 91 insertions(+)
 create mode 100644 src/agat/agat_sp_complement_annotations/help.txt

diff --git a/src/agat/agat_sp_complement_annotations/help.txt b/src/agat/agat_sp_complement_annotations/help.txt
new file mode 100644
index 00000000..5db5e40a
--- /dev/null
+++ b/src/agat/agat_sp_complement_annotations/help.txt
@@ -0,0 +1,91 @@
+```sh
+agat_sp_complement_annotations.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_complement_annotations.pl
+
+Description:
+    The script allows to complement a reference annotation with other
+    annotations. A l1 feature from the addfile.gff that does not overlap a
+    l1 feature from the reference annotation will be added. A l1 feature
+    from the addfile.gff without a CDS that overlaps a l1 feature with a CDS
+    from the reference annotation will be added. A l1 feature from the
+    addfile.gff with a CDS that overlaps a l1 feature without a CDS from the
+    reference annotation will be added. A l1 feature from the addfile.gff
+    with a CDS that overlaps a l1 feature with a CDS from the reference
+    annotation will be added only if the CDSs don't overlap. A l1 feature
+    from the addfile.gff without a CDS that overlaps a l1 feature without a
+    CDS from the reference annotation will be added only if none of the l3
+    features overlap. /!\ It is sufficiant that only one isoform is
+    overlapping to prevent the whole gene (l1 feature) from the addfile.gff
+    to be added in the output.
+
+Usage:
+        agat_sp_complement_annotations.pl --ref annotation_ref.gff --add addfile1.gff --add addfile2.gff --out outFile
+        agat_sp_complement_annotations.pl --help
+
+Options:
+    --ref, -r or -i
+            Input GTF/GFF file used as reference.
+
+    --add or -a
+            Annotation(s) file you would like to use to complement the
+            reference annotation. You can specify as much file you want like
+            so: -a addfile1 -a addfile2 -a addfile3 /!\ The order you
+            provide these files matter. Once the reference file has been
+            complemented by file1, this new annotation becomes the new
+            reference that will be complemented by file2 etc. /!\ The result
+            with -a addfile1 -a addfile2 will differ to the result from -a
+            addfile2 -a addfile1. So, be aware of what you want if you use
+            several addfiles.
+
+    --size_min or -s
+            Option to keep the non-overlping gene only if the CDS size (in
+            nucleotide) is over the minimum size defined. Default = 0 that
+            means all of them are kept.
+
+    --out, --output, --outfile or -o
+            Output gff3 containing the reference annotation with all the
+            non-overlapping newly added genes from addfiles.gff.
+
+    -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).
+
+    --help or -h
+            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

From 19a921114cbb2cc80fefbde87db96d671062e9f0 Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Wed, 7 Aug 2024 16:37:50 +0200
Subject: [PATCH 02/13] add config

---
 .../config.vsh.yaml                           | 128 ++++++++++++++++++
 1 file changed, 128 insertions(+)
 create mode 100644 src/agat/agat_sp_complement_annotations/config.vsh.yaml

diff --git a/src/agat/agat_sp_complement_annotations/config.vsh.yaml b/src/agat/agat_sp_complement_annotations/config.vsh.yaml
new file mode 100644
index 00000000..c46f2e55
--- /dev/null
+++ b/src/agat/agat_sp_complement_annotations/config.vsh.yaml
@@ -0,0 +1,128 @@
+name: agat_sp_complement_annotations
+namespace: agat
+description: |
+    The script allows to complement a reference annotation with other
+    annotations. 
+    
+      * A l1 feature from the addfile.gff that does not overlap a l1 feature from the reference annotation will be added. 
+      * A l1 feature from the addfile.gff without a CDS that overlaps a l1 feature with a CDS from the reference annotation will be added. 
+      * A l1 feature from the addfile.gff with a CDS that overlaps a l1 feature without a CDS from the reference annotation will be added. 
+      * A l1 feature from the addfile.gff with a CDS that overlaps a l1 feature with a CDS from the reference annotation will be added only if the CDSs don't overlap. 
+      * A l1 feature from the addfile.gff without a CDS that overlaps a l1 feature without a CDS from the reference annotation will be added only if none of the l3 features overlap. 
+      
+      /!\ It is sufficient that only one isoform is overlapping to prevent the whole gene (l1 feature) from the addfile.gff to be added in the output.
+keywords: [gene annotations]
+links:
+  homepage: https://github.com/NBISweden/AGAT
+  documentation: https://agat.readthedocs.io/en/latest/tools/agat_sp_complement_annotations.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 ]
+name: agat_sp_complement_annotations
+namespace: agat
+description: |
+    The script allows to complement a reference annotation with other
+    annotations. 
+    
+      * A l1 feature from the addfile.gff that does not overlap a l1 feature from the reference annotation will be added. 
+      * A l1 feature from the addfile.gff without a CDS that overlaps a l1 feature with a CDS from the reference annotation will be added. 
+      * A l1 feature from the addfile.gff with a CDS that overlaps a l1 feature without a CDS from the reference annotation will be added. 
+      * A l1 feature from the addfile.gff with a CDS that overlaps a l1 feature with a CDS from the reference annotation will be added only if the CDSs don't overlap. 
+      * A l1 feature from the addfile.gff without a CDS that overlaps a l1 feature without a CDS from the reference annotation will be added only if none of the l3 features overlap. 
+      
+      /!\ It is sufficient that only one isoform is overlapping to prevent the whole gene (l1 feature) from the addfile.gff to be added in the output.
+keywords: [gene annotations]
+links:
+  homepage: https://github.com/NBISweden/AGAT
+  documentation: https://agat.readthedocs.io/en/latest/tools/agat_sp_complement_annotations.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: --ref
+        alternatives: [-r, -i]
+        description: Input GTF/GFF file used as reference.
+        type: file
+        required: true
+        direction: input
+        example: reference.gff
+      - name: --add
+        alternatives: [-a]
+        description: |
+          Annotation(s) file you would like to use to complement the
+          reference annotation. You can specify as much file you want like
+          so: -a addfile1 -a addfile2 -a addfile3 /!\ The order you
+          provide these files matter. Once the reference file has been
+          complemented by file1, this new annotation becomes the new
+          reference that will be complemented by file2 etc. /!\ The result
+          with -a addfile1 -a addfile2 will differ to the result from -a
+          addfile2 -a addfile1. So, be aware of what you want if you use
+          several addfiles.
+        type: file
+        required: true
+        direction: input
+        multiple: true
+        example: addfile1.gff
+  - name: Outputs
+    arguments:       
+      - name: --output
+        alternatives: [-o, --out, --outfile]
+        description: Output gff3 containing the reference annotation with all the non-overlapping newly added genes from addfiles.gff.
+        type: file
+        direction: output
+        required: true
+        example: output.gff
+  - name: Arguments
+    arguments:
+      - name: --size_min
+        alternatives: [-s]
+        description: |
+          Option to keep the non-overlapping gene only if the CDS size (in
+          nucleotide) is over the minimum size defined. Default = 0 that
+          means all of them are kept.
+        type: integer
+        required: false
+        example: 100
+      - 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 original 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_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 0dbc6236eb76f2869832e01a747e0caef394f87f Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Wed, 7 Aug 2024 16:49:58 +0200
Subject: [PATCH 03/13] add run script

---
 .../agat_sp_complement_annotations/script.sh  | 25 +++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 src/agat/agat_sp_complement_annotations/script.sh

diff --git a/src/agat/agat_sp_complement_annotations/script.sh b/src/agat/agat_sp_complement_annotations/script.sh
new file mode 100644
index 00000000..9d06756a
--- /dev/null
+++ b/src/agat/agat_sp_complement_annotations/script.sh
@@ -0,0 +1,25 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+# unset flags
+[[ "$par_verbose" == "false" ]] && unset par_verbose
+
+# Convert a list of file names to multiple -gff arguments
+input_files=""
+IFS=";" read -ra file_names <<< "$par_gff"
+for file in "${file_names[@]}"; do
+    input_files+="--gff $file "
+done
+unset IFS
+
+
+# run agat_sp_complement_annotations.pl
+agat_sp_complement_annotations.pl \
+  --ref "$par_ref" \
+  $input_files \
+  -o "$par_output" \
+  ${par_size_min:+--size_min "${par_size_min}"} \
+  ${par_config:+--config "${par_config}"} \
+  ${par_verbose:+--verbose}

From 8d1b485b8b8aaa9973112ab96ed0d116f1a51f68 Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Wed, 7 Aug 2024 16:57:25 +0200
Subject: [PATCH 04/13] add test data 7 expected output + script to fetch them

---
 .../test_data/25_test.gff                     | 32 +++++++++++
 .../test_data/9_test.gff                      | 20 +++++++
 .../agat_sp_complement_annotations_1.gff      | 56 +++++++++++++++++++
 .../agat_sp_complement_annotations_2.gff      |  7 +++
 .../agat_sp_complement_annotations_add.gff    |  6 ++
 .../agat_sp_complement_annotations_ref.gff    |  6 ++
 .../test_data/script.sh                       | 14 +++++
 7 files changed, 141 insertions(+)
 create mode 100644 src/agat/agat_sp_complement_annotations/test_data/25_test.gff
 create mode 100644 src/agat/agat_sp_complement_annotations/test_data/9_test.gff
 create mode 100644 src/agat/agat_sp_complement_annotations/test_data/agat_sp_complement_annotations_1.gff
 create mode 100644 src/agat/agat_sp_complement_annotations/test_data/agat_sp_complement_annotations_2.gff
 create mode 100644 src/agat/agat_sp_complement_annotations/test_data/agat_sp_complement_annotations_add.gff
 create mode 100644 src/agat/agat_sp_complement_annotations/test_data/agat_sp_complement_annotations_ref.gff
 create mode 100755 src/agat/agat_sp_complement_annotations/test_data/script.sh

diff --git a/src/agat/agat_sp_complement_annotations/test_data/25_test.gff b/src/agat/agat_sp_complement_annotations/test_data/25_test.gff
new file mode 100644
index 00000000..906b8e81
--- /dev/null
+++ b/src/agat/agat_sp_complement_annotations/test_data/25_test.gff
@@ -0,0 +1,32 @@
+# gffread all_merged.stringtie.gtf -E -F -o -
+# gffread v0.9.9
+##gff-version 3
+scaffold1	StringTie	transcript	2551	2965	1000.00	.	.	ID=MSTRG.1.1;geneID=MSTRG.1
+scaffold1	StringTie	exon	2551	2965	1000.00	.	.	Parent=MSTRG.1.1;cov=68.607231
+scaffold1	StringTie	transcript	8147	13353	1000.00	-	.	ID=MSTRG.6.1;geneID=MSTRG.6
+scaffold1	StringTie	exon	8147	8981	1000.00	-	.	Parent=MSTRG.6.1;cov=529.868042
+scaffold1	StringTie	exon	9082	9171	1000.00	-	.	Parent=MSTRG.6.1;cov=451.066681
+scaffold1	StringTie	exon	9328	9433	1000.00	-	.	Parent=MSTRG.6.1;cov=548.889893
+scaffold1	StringTie	exon	9682	9875	1000.00	-	.	Parent=MSTRG.6.1;cov=416.032471
+scaffold1	StringTie	exon	10018	10228	1000.00	-	.	Parent=MSTRG.6.1;cov=268.398773
+scaffold1	StringTie	exon	10436	10511	1000.00	-	.	Parent=MSTRG.6.1;cov=263.012329
+scaffold1	StringTie	exon	10665	10744	1000.00	-	.	Parent=MSTRG.6.1;cov=262.177094
+scaffold1	StringTie	exon	10901	10996	1000.00	-	.	Parent=MSTRG.6.1;cov=285.484375
+scaffold1	StringTie	exon	11277	11348	1000.00	-	.	Parent=MSTRG.6.1;cov=272.513885
+scaffold1	StringTie	exon	11521	11718	1000.00	-	.	Parent=MSTRG.6.1;cov=323.955170
+scaffold1	StringTie	exon	11802	12004	1000.00	-	.	Parent=MSTRG.6.1;cov=258.021729
+scaffold1	StringTie	exon	12106	13353	1000.00	-	.	Parent=MSTRG.6.1;cov=192.039612
+scaffold1	StringTie	transcript	21499	23178	1000.00	.	.	ID=MSTRG.7.1;geneID=MSTRG.7
+scaffold1	StringTie	exon	21499	23178	1000.00	.	.	Parent=MSTRG.7.1;cov=207.398804
+scaffold1	StringTie	transcript	44218	47964	1000.00	-	.	ID=MSTRG.11.1;geneID=MSTRG.11
+scaffold1	StringTie	exon	44218	45365	1000.00	-	.	Parent=MSTRG.11.1;cov=3001.629883
+scaffold1	StringTie	exon	47660	47706	1000.00	-	.	Parent=MSTRG.11.1;cov=4399.870117
+scaffold1	StringTie	exon	47827	47964	1000.00	-	.	Parent=MSTRG.11.1;cov=2103.559082
+scaffold1	StringTie	transcript	44218	47964	1000.00	-	.	ID=MSTRG.11.2;geneID=MSTRG.11
+scaffold1	StringTie	exon	44218	45365	1000.00	-	.	Parent=MSTRG.11.2;cov=487.085846
+scaffold1	StringTie	exon	47660	47718	1000.00	-	.	Parent=MSTRG.11.2;cov=557.812744
+scaffold1	StringTie	exon	47824	47964	1000.00	-	.	Parent=MSTRG.11.2;cov=242.265823
+scaffold1	StringTie	transcript	44427	47958	1000.00	-	.	ID=MSTRG.11.3;geneID=MSTRG.11
+scaffold1	StringTie	exon	44427	45365	1000.00	-	.	Parent=MSTRG.11.3;cov=2892.249023
+scaffold1	StringTie	exon	47660	47723	1000.00	-	.	Parent=MSTRG.11.3;cov=2083.479492
+scaffold1	StringTie	exon	47827	47958	1000.00	-	.	Parent=MSTRG.11.3;cov=734.545044
diff --git a/src/agat/agat_sp_complement_annotations/test_data/9_test.gff b/src/agat/agat_sp_complement_annotations/test_data/9_test.gff
new file mode 100644
index 00000000..0e82a0ca
--- /dev/null
+++ b/src/agat/agat_sp_complement_annotations/test_data/9_test.gff
@@ -0,0 +1,20 @@
+##gff-version 3
+#!gff-spec-version 1.14
+#!source-version NCBI C++ formatter 0.2
+##Type DNA NC_003070.9
+NC_003070.9	RefSeq	source	1	30427671	.	+	.	organism=Arabidopsis thaliana;mol_type=genomic DNA;db_xref=taxon:3702;chromosome=1;ecotype=Columbia
+NC_003070.9	RefSeq	gene	3631	5899	.	+	.	ID=NC_003070.9:NAC001;locus_tag=AT1G01010;
+NC_003070.9	RefSeq	exon	3631	3913	.	+	.	ID=NM_099983.2;Parent=NC_003070.9:NAC001;gbkey=mRNA;locus_tag=AT1G01010;
+NC_003070.9	RefSeq	exon	3996	4276	.	+	.	ID=NM_099983.2;Parent=NC_003070.9:NAC001;gbkey=mRNA;locus_tag=AT1G01010;
+NC_003070.9	RefSeq	exon	4486	4605	.	+	.	ID=NM_099983.2;Parent=NC_003070.9:NAC001;gbkey=mRNA;locus_tag=AT1G01010;
+NC_003070.9	RefSeq	exon	4706	5095	.	+	.	ID=NM_099983.2;Parent=NC_003070.9:NAC001;gbkey=mRNA;locus_tag=AT1G01010;
+NC_003070.9	RefSeq	exon	5174	5326	.	+	.	ID=NM_099983.2;Parent=NC_003070.9:NAC001;gbkey=mRNA;locus_tag=AT1G01010;
+NC_003070.9	RefSeq	exon	5439	5899	.	+	.	ID=NM_099983.2;Parent=NC_003070.9:NAC001;gbkey=mRNA;locus_tag=AT1G01010;
+NC_003070.9	RefSeq	CDS	3760	3913	.	+	0	ID=NM_099983.2;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010;
+NC_003070.9	RefSeq	CDS	3996	4276	.	+	2	ID=NM_099983.2;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010;
+NC_003070.9	RefSeq	CDS	4486	4605	.	+	0	ID=NM_099983.2;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010;
+NC_003070.9	RefSeq	CDS	4706	5095	.	+	0	ID=NM_099983.2;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010;
+NC_003070.9	RefSeq	CDS	5174	5326	.	+	0	ID=NM_099983.2;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010;
+NC_003070.9	RefSeq	CDS	5439	5627	.	+	0	ID=NM_099983.2;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010;
+NC_003070.9	RefSeq	start_codon	3760	3762	.	+	0	ID=NM_099983.2;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010;
+NC_003070.9	RefSeq	stop_codon	5628	5630	.	+	0	ID=NM_099983.2;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010;
diff --git a/src/agat/agat_sp_complement_annotations/test_data/agat_sp_complement_annotations_1.gff b/src/agat/agat_sp_complement_annotations/test_data/agat_sp_complement_annotations_1.gff
new file mode 100644
index 00000000..486495da
--- /dev/null
+++ b/src/agat/agat_sp_complement_annotations/test_data/agat_sp_complement_annotations_1.gff
@@ -0,0 +1,56 @@
+##gff-version 3
+# gffread all_merged.stringtie.gtf -E -F -o -
+# gffread v0.9.9
+NC_003070.9	RefSeq	gene	3631	5899	.	+	.	ID=IDmodified-gene-1;locus_tag=AT1G01010
+NC_003070.9	AGAT	mRNA	3631	5899	.	+	.	ID=NC_003070.9:NAC001;Parent=IDmodified-gene-1;locus_tag=AT1G01010
+NC_003070.9	RefSeq	exon	3631	3913	.	+	.	ID=NM_099983.2;Parent=NC_003070.9:NAC001;gbkey=mRNA;locus_tag=AT1G01010
+NC_003070.9	RefSeq	exon	3996	4276	.	+	.	ID=IDmodified-exon-1;Parent=NC_003070.9:NAC001;gbkey=mRNA;locus_tag=AT1G01010
+NC_003070.9	RefSeq	exon	4486	4605	.	+	.	ID=IDmodified-exon-2;Parent=NC_003070.9:NAC001;gbkey=mRNA;locus_tag=AT1G01010
+NC_003070.9	RefSeq	exon	4706	5095	.	+	.	ID=IDmodified-exon-3;Parent=NC_003070.9:NAC001;gbkey=mRNA;locus_tag=AT1G01010
+NC_003070.9	RefSeq	exon	5174	5326	.	+	.	ID=IDmodified-exon-4;Parent=NC_003070.9:NAC001;gbkey=mRNA;locus_tag=AT1G01010
+NC_003070.9	RefSeq	exon	5439	5899	.	+	.	ID=IDmodified-exon-5;Parent=NC_003070.9:NAC001;gbkey=mRNA;locus_tag=AT1G01010
+NC_003070.9	RefSeq	CDS	3760	3913	.	+	0	ID=agat-cds-1;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010
+NC_003070.9	RefSeq	CDS	3996	4276	.	+	2	ID=IDmodified-cds-1;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010
+NC_003070.9	RefSeq	CDS	4486	4605	.	+	0	ID=IDmodified-cds-2;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010
+NC_003070.9	RefSeq	CDS	4706	5095	.	+	0	ID=IDmodified-cds-3;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010
+NC_003070.9	RefSeq	CDS	5174	5326	.	+	0	ID=IDmodified-cds-4;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010
+NC_003070.9	RefSeq	CDS	5439	5630	.	+	0	ID=IDmodified-cds-5;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010
+NC_003070.9	AGAT	five_prime_UTR	3631	3759	.	+	.	ID=agat-five_prime_utr-1;Parent=NC_003070.9:NAC001;gbkey=mRNA;locus_tag=AT1G01010
+NC_003070.9	RefSeq	start_codon	3760	3762	.	+	0	ID=agat-start_codon-1;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010
+NC_003070.9	RefSeq	stop_codon	5628	5630	.	+	0	ID=agat-stop_codon-1;Parent=NC_003070.9:NAC001;locus_tag=AT1G01010
+NC_003070.9	AGAT	three_prime_UTR	5631	5899	.	+	.	ID=agat-three_prime_utr-1;Parent=NC_003070.9:NAC001;gbkey=mRNA;locus_tag=AT1G01010
+scaffold1	AGAT	gene	2551	2965	.	.	.	ID=agat-gene-1;geneID=MSTRG.1
+scaffold1	StringTie	transcript	2551	2965	1000.00	.	.	ID=MSTRG.1.1;Parent=agat-gene-1;geneID=MSTRG.1
+scaffold1	StringTie	exon	2551	2965	1000.00	.	.	ID=agat-exon-1;Parent=MSTRG.1.1;cov=68.607231
+scaffold1	AGAT	gene	8147	13353	.	-	.	ID=agat-gene-2;geneID=MSTRG.6
+scaffold1	StringTie	transcript	8147	13353	1000.00	-	.	ID=MSTRG.6.1;Parent=agat-gene-2;geneID=MSTRG.6
+scaffold1	StringTie	exon	8147	8981	1000.00	-	.	ID=agat-exon-2;Parent=MSTRG.6.1;cov=529.868042
+scaffold1	StringTie	exon	9082	9171	1000.00	-	.	ID=agat-exon-3;Parent=MSTRG.6.1;cov=451.066681
+scaffold1	StringTie	exon	9328	9433	1000.00	-	.	ID=agat-exon-4;Parent=MSTRG.6.1;cov=548.889893
+scaffold1	StringTie	exon	9682	9875	1000.00	-	.	ID=agat-exon-5;Parent=MSTRG.6.1;cov=416.032471
+scaffold1	StringTie	exon	10018	10228	1000.00	-	.	ID=agat-exon-6;Parent=MSTRG.6.1;cov=268.398773
+scaffold1	StringTie	exon	10436	10511	1000.00	-	.	ID=agat-exon-7;Parent=MSTRG.6.1;cov=263.012329
+scaffold1	StringTie	exon	10665	10744	1000.00	-	.	ID=agat-exon-8;Parent=MSTRG.6.1;cov=262.177094
+scaffold1	StringTie	exon	10901	10996	1000.00	-	.	ID=agat-exon-9;Parent=MSTRG.6.1;cov=285.484375
+scaffold1	StringTie	exon	11277	11348	1000.00	-	.	ID=agat-exon-10;Parent=MSTRG.6.1;cov=272.513885
+scaffold1	StringTie	exon	11521	11718	1000.00	-	.	ID=agat-exon-11;Parent=MSTRG.6.1;cov=323.955170
+scaffold1	StringTie	exon	11802	12004	1000.00	-	.	ID=agat-exon-12;Parent=MSTRG.6.1;cov=258.021729
+scaffold1	StringTie	exon	12106	13353	1000.00	-	.	ID=agat-exon-13;Parent=MSTRG.6.1;cov=192.039612
+scaffold1	AGAT	gene	21499	23178	.	.	.	ID=agat-gene-3;geneID=MSTRG.7
+scaffold1	StringTie	transcript	21499	23178	1000.00	.	.	ID=MSTRG.7.1;Parent=agat-gene-3;geneID=MSTRG.7
+scaffold1	StringTie	exon	21499	23178	1000.00	.	.	ID=agat-exon-14;Parent=MSTRG.7.1;cov=207.398804
+scaffold1	AGAT	gene	44218	47964	.	-	.	ID=agat-gene-4;geneID=MSTRG.11
+scaffold1	StringTie	transcript	44218	47964	1000.00	-	.	ID=MSTRG.11.1;Parent=agat-gene-4;geneID=MSTRG.11
+scaffold1	StringTie	exon	44218	45365	1000.00	-	.	ID=agat-exon-15;Parent=MSTRG.11.1;cov=3001.629883
+scaffold1	StringTie	exon	47660	47706	1000.00	-	.	ID=agat-exon-16;Parent=MSTRG.11.1;cov=4399.870117
+scaffold1	StringTie	exon	47827	47964	1000.00	-	.	ID=agat-exon-17;Parent=MSTRG.11.1;cov=2103.559082
+scaffold1	AGAT	gene	44218	47964	.	-	.	ID=agat-gene-5;geneID=MSTRG.11
+scaffold1	StringTie	transcript	44218	47964	1000.00	-	.	ID=MSTRG.11.2;Parent=agat-gene-5;geneID=MSTRG.11
+scaffold1	StringTie	exon	44218	45365	1000.00	-	.	ID=agat-exon-18;Parent=MSTRG.11.2;cov=487.085846
+scaffold1	StringTie	exon	47660	47718	1000.00	-	.	ID=agat-exon-19;Parent=MSTRG.11.2;cov=557.812744
+scaffold1	StringTie	exon	47824	47964	1000.00	-	.	ID=agat-exon-20;Parent=MSTRG.11.2;cov=242.265823
+scaffold1	AGAT	gene	44427	47958	.	-	.	ID=agat-gene-6;geneID=MSTRG.11
+scaffold1	StringTie	transcript	44427	47958	1000.00	-	.	ID=MSTRG.11.3;Parent=agat-gene-6;geneID=MSTRG.11
+scaffold1	StringTie	exon	44427	45365	1000.00	-	.	ID=agat-exon-21;Parent=MSTRG.11.3;cov=2892.249023
+scaffold1	StringTie	exon	47660	47723	1000.00	-	.	ID=agat-exon-22;Parent=MSTRG.11.3;cov=2083.479492
+scaffold1	StringTie	exon	47827	47958	1000.00	-	.	ID=agat-exon-23;Parent=MSTRG.11.3;cov=734.545044
diff --git a/src/agat/agat_sp_complement_annotations/test_data/agat_sp_complement_annotations_2.gff b/src/agat/agat_sp_complement_annotations/test_data/agat_sp_complement_annotations_2.gff
new file mode 100644
index 00000000..784a39c9
--- /dev/null
+++ b/src/agat/agat_sp_complement_annotations/test_data/agat_sp_complement_annotations_2.gff
@@ -0,0 +1,7 @@
+##gff-version 3
+Chr1	Helixer	gene	41064	54753	.	+	.	ID=Chr1_000001
+Chr1	Helixer	mRNA	41064	54753	.	+	.	ID=Chr1_000001.1;Parent=Chr1_000001
+Chr1	Helixer	exon	41064	54753	.	+	.	ID=Chr1_000001.1.exon.1;Parent=Chr1_000001.1
+Chr1	Helixer	CDS	41311	54435	.	+	0	ID=Chr1_000001.1.CDS.1;Parent=Chr1_000001.1
+Chr1	Helixer	five_prime_UTR	41064	41310	.	+	.	ID=Chr1_000001.1.five_prime_UTR.1;Parent=Chr1_000001.1
+Chr1	Helixer	three_prime_UTR	54436	54753	.	+	.	ID=Chr1_000001.1.three_prime_UTR.1;Parent=Chr1_000001.1
diff --git a/src/agat/agat_sp_complement_annotations/test_data/agat_sp_complement_annotations_add.gff b/src/agat/agat_sp_complement_annotations/test_data/agat_sp_complement_annotations_add.gff
new file mode 100644
index 00000000..fb03df17
--- /dev/null
+++ b/src/agat/agat_sp_complement_annotations/test_data/agat_sp_complement_annotations_add.gff
@@ -0,0 +1,6 @@
+Chr1	Liftoff	gene	41075	54676	.	+	.	ID=gene-gene1
+Chr1	Liftoff	mRNA	41075	54676	.	+	.	ID=rna-transcript1;Parent=gene-gene1
+Chr1	Liftoff	exon	41075	54676	.	+	.	ID=exon-transcript1-1;Parent=rna-transcript1
+Chr1	Liftoff	CDS	41311	54435	.	+	0	ID=cds-codingsequence-1.1;Parent=rna-transcript1
+Chr1	Liftoff	five_prime_UTR	41075	41310	.	+	.	ID=nbis-five_prime_utr-19342;Parent=rna-transcript1
+Chr1	Liftoff	three_prime_UTR	54436	54676	.	+	.	ID=nbis-three_prime_utr-18368;Parent=rna-transcript1
diff --git a/src/agat/agat_sp_complement_annotations/test_data/agat_sp_complement_annotations_ref.gff b/src/agat/agat_sp_complement_annotations/test_data/agat_sp_complement_annotations_ref.gff
new file mode 100644
index 00000000..a3791da2
--- /dev/null
+++ b/src/agat/agat_sp_complement_annotations/test_data/agat_sp_complement_annotations_ref.gff
@@ -0,0 +1,6 @@
+Chr1	Helixer	gene	41064	54753	.	+	.	ID=Chr1_000001
+Chr1	Helixer	mRNA	41064	54753	.	+	.	ID=Chr1_000001.1;Parent=Chr1_000001
+Chr1	Helixer	exon	41064	54753	.	+	.	ID=Chr1_000001.1.exon.1;Parent=Chr1_000001.1
+Chr1	Helixer	five_prime_UTR	41064	41310	.	+	.	ID=Chr1_000001.1.five_prime_UTR.1;Parent=Chr1_000001.1
+Chr1	Helixer	CDS	41311	54435	.	+	0	ID=Chr1_000001.1.CDS.1;Parent=Chr1_000001.1
+Chr1	Helixer	three_prime_UTR	54436	54753	.	+	.	ID=Chr1_000001.1.three_prime_UTR.1;Parent=Chr1_000001.1
diff --git a/src/agat/agat_sp_complement_annotations/test_data/script.sh b/src/agat/agat_sp_complement_annotations/test_data/script.sh
new file mode 100755
index 00000000..139540f9
--- /dev/null
+++ b/src/agat/agat_sp_complement_annotations/test_data/script.sh
@@ -0,0 +1,14 @@
+#!/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/gff_syntax/in/25_test.gff src/agat/agat_sp_complement_annotations/test_data
+cp -r /tmp/agat_source/t/gff_syntax/in/9_test.gff src/agat/agat_sp_complement_annotations/test_data
+cp -r /tmp/agat_source/t/scripts_output/in/agat_sp_complement_annotations/agat_sp_complement_annotations_ref.gff src/agat/agat_sp_complement_annotations/test_data
+cp -r /tmp/agat_source/t/scripts_output/in/agat_sp_complement_annotations/agat_sp_complement_annotations_add.gff src/agat/agat_sp_complement_annotations/test_data
+cp -r /tmp/agat_source/t/scripts_output/out/agat_sp_complement_annotations_1.gff src/agat/agat_sp_complement_annotations/test_data
+cp -r /tmp/agat_source/t/scripts_output/out/agat_sp_complement_annotations_2.gff src/agat/agat_sp_complement_annotations/test_data
\ No newline at end of file

From 89aff1ac222f163ad01006a7ccdfce1e7afbf4c3 Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Wed, 7 Aug 2024 17:06:49 +0200
Subject: [PATCH 05/13] run script: handle multiple input

---
 src/agat/agat_sp_complement_annotations/script.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/agat/agat_sp_complement_annotations/script.sh b/src/agat/agat_sp_complement_annotations/script.sh
index 9d06756a..2673fc56 100644
--- a/src/agat/agat_sp_complement_annotations/script.sh
+++ b/src/agat/agat_sp_complement_annotations/script.sh
@@ -8,9 +8,9 @@
 
 # Convert a list of file names to multiple -gff arguments
 input_files=""
-IFS=";" read -ra file_names <<< "$par_gff"
+IFS=";" read -ra file_names <<< "$par_add"
 for file in "${file_names[@]}"; do
-    input_files+="--gff $file "
+    input_files+="--add $file "
 done
 unset IFS
 

From 400d84d6b6692363ba3d2b490616fa0fc080b11c Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Wed, 7 Aug 2024 17:06:56 +0200
Subject: [PATCH 06/13] add test

---
 .../agat_sp_complement_annotations/test.sh    | 48 +++++++++++++++++++
 1 file changed, 48 insertions(+)
 create mode 100644 src/agat/agat_sp_complement_annotations/test.sh

diff --git a/src/agat/agat_sp_complement_annotations/test.sh b/src/agat/agat_sp_complement_annotations/test.sh
new file mode 100644
index 00000000..cf5446f3
--- /dev/null
+++ b/src/agat/agat_sp_complement_annotations/test.sh
@@ -0,0 +1,48 @@
+#!/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" \
+  --ref "$test_dir/25_test.gff" \
+  --add "$test_dir/9_test.gff";"$test_dir/9_test.gff" \
+  --output "$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_complement_annotations_1.gff"
+if [ $? -ne 0 ]; then
+  echo "Output file output.gff does not match expected output"
+  exit 1
+fi
+
+rm -rf "$out_dir/output.gff"
+
+echo "> Run $meta_name with test data"
+"$meta_executable" \
+  --ref "$test_dir/agat_sp_complement_annotations_ref.gff" \
+  --add "$test_dir/agat_sp_complement_annotations_add.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_complement_annotations_2.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 49ef55f121e0ecd9c1dd3da9284ed01366a2c43a Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Wed, 7 Aug 2024 17:10:06 +0200
Subject: [PATCH 07/13] update changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9dd2389c..f4ef7b48 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -22,6 +22,7 @@
 * `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_complement_annotations`: complement a reference annotation with other annotations (PR #129).
 
 * `bedtools`:
   - `bedtools/bedtools_intersect`: Allows one to screen for overlaps between two sets of genomic features (PR #94).

From 5c1b098def9b4a3cfbdfc1e4e6028b25581fb7f5 Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Wed, 7 Aug 2024 17:15:08 +0200
Subject: [PATCH 08/13] cleanup

---
 .../config.vsh.yaml                           | 28 +------------------
 .../agat_sp_complement_annotations/script.sh  |  2 +-
 .../agat_sp_complement_annotations/test.sh    |  2 +-
 3 files changed, 3 insertions(+), 29 deletions(-)

diff --git a/src/agat/agat_sp_complement_annotations/config.vsh.yaml b/src/agat/agat_sp_complement_annotations/config.vsh.yaml
index c46f2e55..65d4fe7e 100644
--- a/src/agat/agat_sp_complement_annotations/config.vsh.yaml
+++ b/src/agat/agat_sp_complement_annotations/config.vsh.yaml
@@ -1,33 +1,7 @@
 name: agat_sp_complement_annotations
 namespace: agat
 description: |
-    The script allows to complement a reference annotation with other
-    annotations. 
-    
-      * A l1 feature from the addfile.gff that does not overlap a l1 feature from the reference annotation will be added. 
-      * A l1 feature from the addfile.gff without a CDS that overlaps a l1 feature with a CDS from the reference annotation will be added. 
-      * A l1 feature from the addfile.gff with a CDS that overlaps a l1 feature without a CDS from the reference annotation will be added. 
-      * A l1 feature from the addfile.gff with a CDS that overlaps a l1 feature with a CDS from the reference annotation will be added only if the CDSs don't overlap. 
-      * A l1 feature from the addfile.gff without a CDS that overlaps a l1 feature without a CDS from the reference annotation will be added only if none of the l3 features overlap. 
-      
-      /!\ It is sufficient that only one isoform is overlapping to prevent the whole gene (l1 feature) from the addfile.gff to be added in the output.
-keywords: [gene annotations]
-links:
-  homepage: https://github.com/NBISweden/AGAT
-  documentation: https://agat.readthedocs.io/en/latest/tools/agat_sp_complement_annotations.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 ]
-name: agat_sp_complement_annotations
-namespace: agat
-description: |
-    The script allows to complement a reference annotation with other
-    annotations. 
+    The script allows to complement a reference annotation with other annotations. 
     
       * A l1 feature from the addfile.gff that does not overlap a l1 feature from the reference annotation will be added. 
       * A l1 feature from the addfile.gff without a CDS that overlaps a l1 feature with a CDS from the reference annotation will be added. 
diff --git a/src/agat/agat_sp_complement_annotations/script.sh b/src/agat/agat_sp_complement_annotations/script.sh
index 2673fc56..578447a1 100644
--- a/src/agat/agat_sp_complement_annotations/script.sh
+++ b/src/agat/agat_sp_complement_annotations/script.sh
@@ -6,7 +6,7 @@
 # unset flags
 [[ "$par_verbose" == "false" ]] && unset par_verbose
 
-# Convert a list of file names to multiple -gff arguments
+# Convert a list of file names to multiple --add arguments
 input_files=""
 IFS=";" read -ra file_names <<< "$par_add"
 for file in "${file_names[@]}"; do
diff --git a/src/agat/agat_sp_complement_annotations/test.sh b/src/agat/agat_sp_complement_annotations/test.sh
index cf5446f3..4d28b924 100644
--- a/src/agat/agat_sp_complement_annotations/test.sh
+++ b/src/agat/agat_sp_complement_annotations/test.sh
@@ -9,7 +9,7 @@ out_dir="${meta_resources_dir}/out_data"
 echo "> Run $meta_name with test data"
 "$meta_executable" \
   --ref "$test_dir/25_test.gff" \
-  --add "$test_dir/9_test.gff";"$test_dir/9_test.gff" \
+  --add "$test_dir/9_test.gff" \
   --output "$out_dir/output.gff" 
 
 echo ">> Checking output"

From 05a9292f1d1deba5d7381028592c89b1ab9c1ba4 Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Mon, 19 Aug 2024 17:16:19 +0200
Subject: [PATCH 09/13] cleanup changelog

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index ddfe5419..b3eeea96 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -25,7 +25,7 @@
   - `agat/agat_convert_embl2gff`: convert an EMBL file into GFF format (PR #99).
   - `agat/agat_convert_sp_gff2tsv`: convert gtf/gff file into tabulated file (PR #102).
   - `agat/agat_convert_sp_gxf2gxf`: fixes and/or standardizes any GTF/GFF file into full sorted GTF/GFF file (PR #103).
-  - `agat_sp_complement_annotations`: complement a reference annotation with other annotations (PR #129).
+  - `agat/agat_sp_complement_annotations`: complement a reference annotation with other annotations (PR #129).
 
 * `bedtools`:
   - `bedtools/bedtools_intersect`: Allows one to screen for overlaps between two sets of genomic features (PR #94).

From 0ad50eb154f4204db9aab2dab2ce73bfcceeae01 Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Mon, 19 Aug 2024 17:17:02 +0200
Subject: [PATCH 10/13] add set -eo pipefail to test and script files

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

diff --git a/src/agat/agat_sp_complement_annotations/script.sh b/src/agat/agat_sp_complement_annotations/script.sh
index 578447a1..969a1329 100644
--- a/src/agat/agat_sp_complement_annotations/script.sh
+++ b/src/agat/agat_sp_complement_annotations/script.sh
@@ -1,5 +1,7 @@
 #!/bin/bash
 
+set -eo pipefail
+
 ## VIASH START
 ## VIASH END
 
diff --git a/src/agat/agat_sp_complement_annotations/test.sh b/src/agat/agat_sp_complement_annotations/test.sh
index 4d28b924..cd23bf2b 100644
--- a/src/agat/agat_sp_complement_annotations/test.sh
+++ b/src/agat/agat_sp_complement_annotations/test.sh
@@ -1,5 +1,7 @@
 #!/bin/bash
 
+set -eo pipefail
+
 ## VIASH START
 ## VIASH END
 

From e78d4cfc2cd99b40bee591d026ea9f064ef08743 Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Mon, 19 Aug 2024 17:20:34 +0200
Subject: [PATCH 11/13] update config: add keywords, add requirements, update
 --config description

---
 .../config.vsh.yaml                           | 25 +++++++------------
 1 file changed, 9 insertions(+), 16 deletions(-)

diff --git a/src/agat/agat_sp_complement_annotations/config.vsh.yaml b/src/agat/agat_sp_complement_annotations/config.vsh.yaml
index 65d4fe7e..aff815f7 100644
--- a/src/agat/agat_sp_complement_annotations/config.vsh.yaml
+++ b/src/agat/agat_sp_complement_annotations/config.vsh.yaml
@@ -9,8 +9,8 @@ description: |
       * A l1 feature from the addfile.gff with a CDS that overlaps a l1 feature with a CDS from the reference annotation will be added only if the CDSs don't overlap. 
       * A l1 feature from the addfile.gff without a CDS that overlaps a l1 feature without a CDS from the reference annotation will be added only if none of the l3 features overlap. 
       
-      /!\ It is sufficient that only one isoform is overlapping to prevent the whole gene (l1 feature) from the addfile.gff to be added in the output.
-keywords: [gene annotations]
+      ! It is sufficient that only one isoform is overlapping to prevent the whole gene (l1 feature) from the addfile.gff to be added in the output.
+keywords: [gene annotations, GFF]
 links:
   homepage: https://github.com/NBISweden/AGAT
   documentation: https://agat.readthedocs.io/en/latest/tools/agat_sp_complement_annotations.html
@@ -19,6 +19,8 @@ links:
 references: 
   doi: 10.5281/zenodo.3552717
 license: GPL-3.0
+requirements:
+  - commands: [agat]
 authors:
   - __merge__: /src/_authors/leila_paquay.yaml
     roles: [ author, maintainer ]
@@ -36,14 +38,11 @@ argument_groups:
         alternatives: [-a]
         description: |
           Annotation(s) file you would like to use to complement the
-          reference annotation. You can specify as much file you want like
-          so: -a addfile1 -a addfile2 -a addfile3 /!\ The order you
-          provide these files matter. Once the reference file has been
+          reference annotation. You can specify as much file you want like.
+          The order you provide these files matter. Once the reference file has been
           complemented by file1, this new annotation becomes the new
-          reference that will be complemented by file2 etc. /!\ The result
-          with -a addfile1 -a addfile2 will differ to the result from -a
-          addfile2 -a addfile1. So, be aware of what you want if you use
-          several addfiles.
+          reference that will be complemented by file2 etc. 
+          So, be aware of what you want if you use several addfiles.
         type: file
         required: true
         direction: input
@@ -72,13 +71,7 @@ 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 original 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_config.yaml

From 3827b0cd4835754a9925d59e281cf2895d43dcf0 Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Mon, 19 Aug 2024 17:20:47 +0200
Subject: [PATCH 12/13]  create temporary directory and clean up on exit

---
 .../agat_sp_complement_annotations/test.sh    | 26 ++++++++++++-------
 1 file changed, 16 insertions(+), 10 deletions(-)

diff --git a/src/agat/agat_sp_complement_annotations/test.sh b/src/agat/agat_sp_complement_annotations/test.sh
index cd23bf2b..14e03713 100644
--- a/src/agat/agat_sp_complement_annotations/test.sh
+++ b/src/agat/agat_sp_complement_annotations/test.sh
@@ -6,43 +6,49 @@ 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" \
   --ref "$test_dir/25_test.gff" \
   --add "$test_dir/9_test.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_complement_annotations_1.gff"
+diff "$TMPDIR/output.gff" "$test_dir/agat_sp_complement_annotations_1.gff"
 if [ $? -ne 0 ]; then
   echo "Output file output.gff does not match expected output"
   exit 1
 fi
 
-rm -rf "$out_dir/output.gff"
+rm -rf "$TMPDIR/output.gff"
 
 echo "> Run $meta_name with test data"
 "$meta_executable" \
   --ref "$test_dir/agat_sp_complement_annotations_ref.gff" \
   --add "$test_dir/agat_sp_complement_annotations_add.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_complement_annotations_2.gff"
+diff "$TMPDIR/output.gff" "$test_dir/agat_sp_complement_annotations_2.gff"
 if [ $? -ne 0 ]; then
   echo "Output file output.gff does not match expected output"
   exit 1

From bf10c753a951aba6388e0c1c919cd7d6ba4dca1c Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Mon, 19 Aug 2024 17:21:25 +0200
Subject: [PATCH 13/13] remove UNSET IFS

---
 src/agat/agat_sp_complement_annotations/script.sh | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/agat/agat_sp_complement_annotations/script.sh b/src/agat/agat_sp_complement_annotations/script.sh
index 969a1329..36a668a8 100644
--- a/src/agat/agat_sp_complement_annotations/script.sh
+++ b/src/agat/agat_sp_complement_annotations/script.sh
@@ -14,8 +14,6 @@ IFS=";" read -ra file_names <<< "$par_add"
 for file in "${file_names[@]}"; do
     input_files+="--add $file "
 done
-unset IFS
-
 
 # run agat_sp_complement_annotations.pl
 agat_sp_complement_annotations.pl \