From 217c3cd1e029b0e28707a23325a624584989bc5d Mon Sep 17 00:00:00 2001
From: tgaspe <theodorogtc@gmail.com>
Date: Tue, 30 Jul 2024 10:40:14 -0300
Subject: [PATCH 01/13] Initial Commit

---
 src/bedtools/bedtools_bamtofastq/config.vsh.yaml | 0
 src/bedtools/bedtools_bamtofastq/script.sh       | 2 ++
 src/bedtools/bedtools_bamtofastq/test.sh         | 0
 3 files changed, 2 insertions(+)
 create mode 100644 src/bedtools/bedtools_bamtofastq/config.vsh.yaml
 create mode 100644 src/bedtools/bedtools_bamtofastq/script.sh
 create mode 100644 src/bedtools/bedtools_bamtofastq/test.sh

diff --git a/src/bedtools/bedtools_bamtofastq/config.vsh.yaml b/src/bedtools/bedtools_bamtofastq/config.vsh.yaml
new file mode 100644
index 00000000..e69de29b
diff --git a/src/bedtools/bedtools_bamtofastq/script.sh b/src/bedtools/bedtools_bamtofastq/script.sh
new file mode 100644
index 00000000..139597f9
--- /dev/null
+++ b/src/bedtools/bedtools_bamtofastq/script.sh
@@ -0,0 +1,2 @@
+
+
diff --git a/src/bedtools/bedtools_bamtofastq/test.sh b/src/bedtools/bedtools_bamtofastq/test.sh
new file mode 100644
index 00000000..e69de29b

From 1afd6d1cbe62b0e8d73cc484fd52b97663926a63 Mon Sep 17 00:00:00 2001
From: tgaspe <theodorogtc@gmail.com>
Date: Tue, 30 Jul 2024 10:57:11 -0300
Subject: [PATCH 02/13] update

---
 .../bedtools_bamtofastq/config.vsh.yaml       | 63 +++++++++++++++++++
 src/bedtools/bedtools_bamtofastq/help.txt     | 23 +++++++
 2 files changed, 86 insertions(+)
 create mode 100644 src/bedtools/bedtools_bamtofastq/help.txt

diff --git a/src/bedtools/bedtools_bamtofastq/config.vsh.yaml b/src/bedtools/bedtools_bamtofastq/config.vsh.yaml
index e69de29b..a18980c5 100644
--- a/src/bedtools/bedtools_bamtofastq/config.vsh.yaml
+++ b/src/bedtools/bedtools_bamtofastq/config.vsh.yaml
@@ -0,0 +1,63 @@
+name: bedtools_bamtofastq
+namespace: bedtools
+description: Conversion tool for extracting FASTQ records from sequence alignments in BAM format.
+keywords: [BAM, FASTQ]
+links:
+  documentation: https://bedtools.readthedocs.io/en/latest/content/tools/bamtofastq.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
+        alternatives: -i
+        type: file
+        description: Input BAM file to be converted to FASTQ.
+        required: true
+      
+    
+  - name: Outputs
+    arguments:
+      - name: --output
+        alternatives: -o
+        type: file
+        direction: output
+        description: Output FASTQ file to be written.
+
+  - name: Options
+    arguments:
+      - name: 
+        type: 
+        description: 
+      
+      
+      
+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
\ No newline at end of file
diff --git a/src/bedtools/bedtools_bamtofastq/help.txt b/src/bedtools/bedtools_bamtofastq/help.txt
new file mode 100644
index 00000000..d03b85d1
--- /dev/null
+++ b/src/bedtools/bedtools_bamtofastq/help.txt
@@ -0,0 +1,23 @@
+```bash
+bedtools bamtofastq
+```
+
+Tool:    bedtools bamtofastq (aka bamToFastq)
+Version: v2.27.1
+Summary: Convert BAM alignments to FASTQ files. 
+
+Usage:   bamToFastq [OPTIONS] -i <BAM> -fq <FQ> 
+
+Options:
+	-fq2	FASTQ for second end.  Used if BAM contains paired-end data.
+		BAM should be sorted by query name is creating paired FASTQ.
+
+	-tags	Create FASTQ based on the mate info
+		in the BAM R2 and Q2 tags.
+
+Tips: 
+	If you want to create a single, interleaved FASTQ file 
+	for paired-end data, you can just write both to /dev/stdout:
+
+	bedtools bamtofastq -i x.bam -fq /dev/stdout -fq2 /dev/stdout > x.ilv.fq
+

From 996ec6ec2cd79f64660bd525089a581cd78e2361 Mon Sep 17 00:00:00 2001
From: tgaspe <theodorogtc@gmail.com>
Date: Tue, 30 Jul 2024 15:13:52 -0300
Subject: [PATCH 03/13] update

---
 src/bedtools/bedtools_bamtofastq/config.vsh.yaml  |  12 ++++++++++++
 .../bedtools_bamtofastq/test_data/example.bam     | Bin 0 -> 144 bytes
 .../bedtools_bamtofastq/test_data/example.sam     |   6 ++++++
 3 files changed, 18 insertions(+)
 create mode 100644 src/bedtools/bedtools_bamtofastq/test_data/example.bam
 create mode 100644 src/bedtools/bedtools_bamtofastq/test_data/example.sam

diff --git a/src/bedtools/bedtools_bamtofastq/config.vsh.yaml b/src/bedtools/bedtools_bamtofastq/config.vsh.yaml
index a18980c5..3d04b606 100644
--- a/src/bedtools/bedtools_bamtofastq/config.vsh.yaml
+++ b/src/bedtools/bedtools_bamtofastq/config.vsh.yaml
@@ -22,6 +22,18 @@ argument_groups:
         type: file
         description: Input BAM file to be converted to FASTQ.
         required: true
+
+      # - name: --fq
+      #   alternatives: -fq
+      #   type: file
+      #   description: 
+      #   required: true
+
+      # - name: --fq2
+      #   alternatives: -fq2
+      #   type: file
+      #   description: 
+      #   required: true
       
     
   - name: Outputs
diff --git a/src/bedtools/bedtools_bamtofastq/test_data/example.bam b/src/bedtools/bedtools_bamtofastq/test_data/example.bam
new file mode 100644
index 0000000000000000000000000000000000000000..804269f74cdf196e6d3b5ff9ee9d4f7d4a96a983
GIT binary patch
literal 144
zcmb2|=3rp}f&Xj_PR>jW#SFzoUsAuMBqS7kD0s;8d9%?K;|Dz7wric$KBuqc>HDyV
zgYOB?x6NMXG>o2n`MBB0XyXPGQ)5FTr%47)9uksKQnRHZiwqfglUb7{h_P);zW!r@
ejB?v4&7U<4zY1@5<pZsfN3&C!ff?)s5CH%??Jv#%

literal 0
HcmV?d00001

diff --git a/src/bedtools/bedtools_bamtofastq/test_data/example.sam b/src/bedtools/bedtools_bamtofastq/test_data/example.sam
new file mode 100644
index 00000000..e0e59e05
--- /dev/null
+++ b/src/bedtools/bedtools_bamtofastq/test_data/example.sam
@@ -0,0 +1,6 @@
+@HD VN:1.0  SO:unsorted
+@SQ	SN:chr1	LN:248956422
+@SQ	SN:chr2	LN:242193529
+read1	0	chr1	100	60	50M	*	0	0	GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAAGGTACGCGTAC	*  
+read2	0	chr1	150	60	50M	*	0	0	TTTCAAAGCAGTATCGATCAAATAGTAAAGGTACGCGTACGAGTGGAA	*  
+read3	0	chr2	200	60	50M	*	0	0	GGTTCAAAGCAGTATCGATCAAATAGTAAAGGTACGCGTACGAGTGGG	*  

From 3676351fb66a5b7c2c7089807dac8e2444228e43 Mon Sep 17 00:00:00 2001
From: tgaspe <theodorogtc@gmail.com>
Date: Tue, 30 Jul 2024 15:50:08 -0300
Subject: [PATCH 04/13] Config file and Script.sh

---
 output.bam                                    |   0
 .../bedtools_bamtofastq/config.vsh.yaml       |  44 ++++++++----------
 src/bedtools/bedtools_bamtofastq/script.sh    |  13 ++++++
 src/bedtools/bedtools_bamtofastq/test.sh      |   5 ++
 .../bedtools_bamtofastq/test_data/example.bam | Bin 144 -> 268 bytes
 .../bedtools_bamtofastq/test_data/example.fq  |  12 +++++
 .../bedtools_bamtofastq/test_data/example.sam |   8 ++--
 7 files changed, 53 insertions(+), 29 deletions(-)
 create mode 100644 output.bam
 create mode 100644 src/bedtools/bedtools_bamtofastq/test_data/example.fq

diff --git a/output.bam b/output.bam
new file mode 100644
index 00000000..e69de29b
diff --git a/src/bedtools/bedtools_bamtofastq/config.vsh.yaml b/src/bedtools/bedtools_bamtofastq/config.vsh.yaml
index 3d04b606..d0e27a4b 100644
--- a/src/bedtools/bedtools_bamtofastq/config.vsh.yaml
+++ b/src/bedtools/bedtools_bamtofastq/config.vsh.yaml
@@ -1,7 +1,7 @@
 name: bedtools_bamtofastq
 namespace: bedtools
 description: Conversion tool for extracting FASTQ records from sequence alignments in BAM format.
-keywords: [BAM, FASTQ]
+keywords: [Conversion ,BAM, FASTQ]
 links:
   documentation: https://bedtools.readthedocs.io/en/latest/content/tools/bamtofastq.html
   repository: https://github.com/arq5x/bedtools2
@@ -22,36 +22,30 @@ argument_groups:
         type: file
         description: Input BAM file to be converted to FASTQ.
         required: true
-
-      # - name: --fq
-      #   alternatives: -fq
-      #   type: file
-      #   description: 
-      #   required: true
-
-      # - name: --fq2
-      #   alternatives: -fq2
-      #   type: file
-      #   description: 
-      #   required: true
-      
     
   - name: Outputs
     arguments:
-      - name: --output
-        alternatives: -o
-        type: file
+      - name: --output_fq
+        alternatives: -fq
         direction: output
-        description: Output FASTQ file to be written.
-
+        type: file
+        description: Output FASTQ file.
+        required: true
+         
   - name: Options
     arguments:
-      - name: 
-        type: 
-        description: 
-      
-      
-      
+      - name: --output_fq2
+        alternatives: -fq2
+        type: file
+        description: |
+          FASTQ for second end.  Used if BAM contains paired-end data.
+          BAM should be sorted by query name is creating paired FASTQ.
+
+      - name: --tags
+        type: boolean_true
+        description: |
+          Create FASTQ based on the mate info in the BAM R2 and Q2 tags.
+
 resources:
   - type: bash_script
     path: script.sh
diff --git a/src/bedtools/bedtools_bamtofastq/script.sh b/src/bedtools/bedtools_bamtofastq/script.sh
index 139597f9..d48e12aa 100644
--- a/src/bedtools/bedtools_bamtofastq/script.sh
+++ b/src/bedtools/bedtools_bamtofastq/script.sh
@@ -1,2 +1,15 @@
+#!/bin/bash
 
+## VIASH START
+## VIASH END
+
+# Unset parameters
+[[ "$par_tags" == "false" ]] && unset par_tags
+
+# Execute bedtools bamtofastq with the provided arguments
+bedtools bamtofastq \
+    ${par_tags:+-tags} \
+    -i "$par_input" \
+    -fq "$par_output_fq"
+    ${par_output_fq2:+-fq2 "$par_output_fq2"}
 
diff --git a/src/bedtools/bedtools_bamtofastq/test.sh b/src/bedtools/bedtools_bamtofastq/test.sh
index e69de29b..83dc00cd 100644
--- a/src/bedtools/bedtools_bamtofastq/test.sh
+++ b/src/bedtools/bedtools_bamtofastq/test.sh
@@ -0,0 +1,5 @@
+#!/bin/bash
+
+#viash ns build -q bedtools_bamtofastq --setup cb
+
+
diff --git a/src/bedtools/bedtools_bamtofastq/test_data/example.bam b/src/bedtools/bedtools_bamtofastq/test_data/example.bam
index 804269f74cdf196e6d3b5ff9ee9d4f7d4a96a983..5454b2f4d2414f57b95110195ac6daf707c6a8a0 100644
GIT binary patch
delta 158
zcmbQh*uykImMM^9qP#E5(mbu+i3K9{)ePE64Gk#@X`4TaB(Yp#bND0A<xu3hvQx8-
zhvy6rPoJ!=o}6!!QkR^NmQYtyuUwOooRgoN(|=DESLQVB6U!d6<e0MEesyV~#tW58
zH=f*3(NMgk@#4~oMVD46U3&Csz6%3G=J8i^k{B5n<hwao7(n1Z8-tTG6N5AZGbfl2
FA^<f(G$8;0

delta 23
fcmeBSn!q?gmgynSM0sD9UxhcjCKiZHV&nk;VVMX&

diff --git a/src/bedtools/bedtools_bamtofastq/test_data/example.fq b/src/bedtools/bedtools_bamtofastq/test_data/example.fq
new file mode 100644
index 00000000..00f3c33c
--- /dev/null
+++ b/src/bedtools/bedtools_bamtofastq/test_data/example.fq
@@ -0,0 +1,12 @@
+@read1
+GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAAGGTACGCGTAC
++
+                                                
+@read1
+GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAAGGTACGCGTAC
++
+                                                
+@read3
+GGTTCAAAGCAGTATCGATCAAATAGTAAAGGTACGCGTACGAGTGGG
++
+                                                
diff --git a/src/bedtools/bedtools_bamtofastq/test_data/example.sam b/src/bedtools/bedtools_bamtofastq/test_data/example.sam
index e0e59e05..3e573ca9 100644
--- a/src/bedtools/bedtools_bamtofastq/test_data/example.sam
+++ b/src/bedtools/bedtools_bamtofastq/test_data/example.sam
@@ -1,6 +1,6 @@
-@HD VN:1.0  SO:unsorted
+@HD VN:1.0	SO:unsorted
 @SQ	SN:chr1	LN:248956422
 @SQ	SN:chr2	LN:242193529
-read1	0	chr1	100	60	50M	*	0	0	GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAAGGTACGCGTAC	*  
-read2	0	chr1	150	60	50M	*	0	0	TTTCAAAGCAGTATCGATCAAATAGTAAAGGTACGCGTACGAGTGGAA	*  
-read3	0	chr2	200	60	50M	*	0	0	GGTTCAAAGCAGTATCGATCAAATAGTAAAGGTACGCGTACGAGTGGG	*  
+read1	0	chr1	100	60	48M	*	0	0	GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAAGGTACGCGTAC	*
+read1	0	chr1	100	60	48M	*	0	0	GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAAGGTACGCGTAC	*
+read3	0	chr2	200	60	48M	*	0	0	GGTTCAAAGCAGTATCGATCAAATAGTAAAGGTACGCGTACGAGTGGG	*

From 8430eb5e833a10d8cc0e4f17649b435569d3b62a Mon Sep 17 00:00:00 2001
From: tgaspe <theodorogtc@gmail.com>
Date: Tue, 30 Jul 2024 15:57:08 -0300
Subject: [PATCH 05/13] Test Script

---
 .../bedtools_bamtofastq/config.vsh.yaml       |  8 +--
 src/bedtools/bedtools_bamtofastq/test.sh      | 53 ++++++++++++++++++-
 2 files changed, 56 insertions(+), 5 deletions(-)

diff --git a/src/bedtools/bedtools_bamtofastq/config.vsh.yaml b/src/bedtools/bedtools_bamtofastq/config.vsh.yaml
index d0e27a4b..e15d4460 100644
--- a/src/bedtools/bedtools_bamtofastq/config.vsh.yaml
+++ b/src/bedtools/bedtools_bamtofastq/config.vsh.yaml
@@ -31,16 +31,16 @@ argument_groups:
         type: file
         description: Output FASTQ file.
         required: true
-         
-  - name: Options
-    arguments:
+        
       - name: --output_fq2
         alternatives: -fq2
         type: file
         description: |
           FASTQ for second end.  Used if BAM contains paired-end data.
           BAM should be sorted by query name is creating paired FASTQ.
-
+         
+  - name: Options
+    arguments:
       - name: --tags
         type: boolean_true
         description: |
diff --git a/src/bedtools/bedtools_bamtofastq/test.sh b/src/bedtools/bedtools_bamtofastq/test.sh
index 83dc00cd..5bb5b345 100644
--- a/src/bedtools/bedtools_bamtofastq/test.sh
+++ b/src/bedtools/bedtools_bamtofastq/test.sh
@@ -1,5 +1,56 @@
 #!/bin/bash
 
-#viash ns build -q bedtools_bamtofastq --setup cb
+# viash ns build -q bedtools_bamtofastq --setup cb
 
+# exit on error
+set -e
 
+## VIASH START
+meta_executable="target/executable/bedtools/bedtools_sort/bedtools_bamtofastq"
+meta_resources_dir="src/bedtools/bedtools_bamtofastq"
+## 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" "$1" \
+    || (echo "Files are not identical!" && exit 1)
+}
+#############################################
+
+# Create directories for tests
+echo "Creating Test Data..."
+mkdir -p test_data
+
+# Create and populate example files
+
+# Create expected output files
+
+
+# Test 1: 
+mkdir test1
+cd test1
+
+echo "> Run bedtools bamtofastq on BAM file"
+"$meta_executable" \
+  --input "example.bam" \
+  --output_fq "output.fastq"
+
+# checks
+assert_file_exists "output.fastq"
+assert_file_not_empty "output.fastq"
+assert_identical_content "output.fastq" "../test_data/expected.fastq"
+echo "- test1 succeeded -"
+
+cd ..
+
+# Test 2:

From 800e86a695f30a9dbe9d90b1e43d193d46bd790e Mon Sep 17 00:00:00 2001
From: tgaspe <theodorogtc@gmail.com>
Date: Tue, 30 Jul 2024 16:32:31 -0300
Subject: [PATCH 06/13] adding test

---
 src/bedtools/bedtools_bamtofastq/test.sh | 77 ++++++++++++++++++++----
 1 file changed, 66 insertions(+), 11 deletions(-)

diff --git a/src/bedtools/bedtools_bamtofastq/test.sh b/src/bedtools/bedtools_bamtofastq/test.sh
index 5bb5b345..6a2cd85f 100644
--- a/src/bedtools/bedtools_bamtofastq/test.sh
+++ b/src/bedtools/bedtools_bamtofastq/test.sh
@@ -5,10 +5,7 @@
 # exit on error
 set -e
 
-## VIASH START
-meta_executable="target/executable/bedtools/bedtools_sort/bedtools_bamtofastq"
-meta_resources_dir="src/bedtools/bedtools_bamtofastq"
-## VIASH END
+test_data="$meta_resources_dir/test_data"
 
 #############################################
 # helper functions
@@ -27,14 +24,29 @@ assert_identical_content() {
 }
 #############################################
 
-# Create directories for tests
-echo "Creating Test Data..."
-mkdir -p test_data
-
-# Create and populate example files
+mkdir -p data
 
 # Create expected output files
+cat << EOF > data/expected.fastq
+@read1
+GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAAGGTACGCGTAC
++
+                        
+@read1
+GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAAGGTACGCGTAC
++
+                        
+@read3
+GGTTCAAAGCAGTATCGATCAAATAGTAAAGGTACGCGTACGAGTGGG
++
+                        
+EOF
+
+# cat << EOF > data/expected_tags.fastq
+# EOF
 
+# cat << EOF > data/expected_fq2.fastq
+# EOF
 
 # Test 1: 
 mkdir test1
@@ -42,15 +54,58 @@ cd test1
 
 echo "> Run bedtools bamtofastq on BAM file"
 "$meta_executable" \
-  --input "example.bam" \
+  --input "$test_data/example.bam" \
   --output_fq "output.fastq"
 
 # checks
 assert_file_exists "output.fastq"
 assert_file_not_empty "output.fastq"
-assert_identical_content "output.fastq" "../test_data/expected.fastq"
+assert_identical_content "output.fastq" "../data/expected.fastq"
 echo "- test1 succeeded -"
 
 cd ..
 
 # Test 2:
+# mkdir test2
+# cd test2
+
+# echo "> Run bedtools bamtofastq on BAM file with tags"
+# "$meta_executable" \
+#   --input "$test_data/example.bam" \
+#   --output_fq "output.fastq" \
+#   --tags
+
+# # checks
+# assert_file_exists "output.fastq"
+# assert_file_not_empty "output.fastq"
+# assert_identical_content "output.fastq" "../data/expected.fastq"
+# echo "- test2 succeeded -"
+
+# cd ..
+
+# # Test 3:
+# mkdir test3
+# cd test3
+
+# echo "> Run bedtools bamtofastq on BAM file with tags and output_fq2"
+# "$meta_executable" \
+#   --input "$test_data/example.bam" \
+#   --output_fq "output1.fastq" \
+#   --output_fq2 "output2.fastq" \
+#   --tags
+
+# # checks
+# assert_file_exists "output1.fastq"
+# assert_file_not_empty "output1.fastq"
+# assert_identical_content "output1.fastq" "../data/expected.fastq"
+# assert_file_exists "output2.fastq"
+# assert_file_not_empty "output2.fastq"
+# assert_identical_content "output2.fastq" "../data/expected.fastq"
+# echo "- test3 succeeded -"
+
+# cd ..
+
+echo "All tests succeeded"
+exit 0
+
+

From 7ecac3fa6286f9dad0a6aa78f89863bab6a55114 Mon Sep 17 00:00:00 2001
From: tgaspe <theodorogtc@gmail.com>
Date: Tue, 30 Jul 2024 17:33:03 -0300
Subject: [PATCH 07/13] working on testing

---
 .../bedtools_bamtofastq/config.vsh.yaml       |   3 +-
 src/bedtools/bedtools_bamtofastq/test.sh      | 105 +++++++-----------
 .../bedtools_bamtofastq/test_data/example.bam | Bin 268 -> 346 bytes
 .../bedtools_bamtofastq/test_data/example.fq  |  12 --
 .../bedtools_bamtofastq/test_data/example.sam |   7 +-
 .../test_data/expected.fastq                  |   8 ++
 .../test_data/expected_fq2.fastq              |   0
 .../test_data/expected_tags.fastq             |   0
 .../bedtools_bamtofastq/test_data/script.sh   |  30 +++++
 9 files changed, 83 insertions(+), 82 deletions(-)
 delete mode 100644 src/bedtools/bedtools_bamtofastq/test_data/example.fq
 create mode 100644 src/bedtools/bedtools_bamtofastq/test_data/expected.fastq
 create mode 100644 src/bedtools/bedtools_bamtofastq/test_data/expected_fq2.fastq
 create mode 100644 src/bedtools/bedtools_bamtofastq/test_data/expected_tags.fastq
 create mode 100755 src/bedtools/bedtools_bamtofastq/test_data/script.sh

diff --git a/src/bedtools/bedtools_bamtofastq/config.vsh.yaml b/src/bedtools/bedtools_bamtofastq/config.vsh.yaml
index e15d4460..125ce6bd 100644
--- a/src/bedtools/bedtools_bamtofastq/config.vsh.yaml
+++ b/src/bedtools/bedtools_bamtofastq/config.vsh.yaml
@@ -31,7 +31,7 @@ argument_groups:
         type: file
         description: Output FASTQ file.
         required: true
-        
+
       - name: --output_fq2
         alternatives: -fq2
         type: file
@@ -53,6 +53,7 @@ resources:
 test_resources:
   - type: bash_script
     path: test.sh
+  - path: test_data
 
 engines:
   - type: docker
diff --git a/src/bedtools/bedtools_bamtofastq/test.sh b/src/bedtools/bedtools_bamtofastq/test.sh
index 6a2cd85f..1e860663 100644
--- a/src/bedtools/bedtools_bamtofastq/test.sh
+++ b/src/bedtools/bedtools_bamtofastq/test.sh
@@ -24,31 +24,7 @@ assert_identical_content() {
 }
 #############################################
 
-mkdir -p data
-
-# Create expected output files
-cat << EOF > data/expected.fastq
-@read1
-GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAAGGTACGCGTAC
-+
-                        
-@read1
-GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAAGGTACGCGTAC
-+
-                        
-@read3
-GGTTCAAAGCAGTATCGATCAAATAGTAAAGGTACGCGTACGAGTGGG
-+
-                        
-EOF
-
-# cat << EOF > data/expected_tags.fastq
-# EOF
-
-# cat << EOF > data/expected_fq2.fastq
-# EOF
-
-# Test 1: 
+# Test 1: normal conversion 
 mkdir test1
 cd test1
 
@@ -60,50 +36,49 @@ echo "> Run bedtools bamtofastq on BAM file"
 # checks
 assert_file_exists "output.fastq"
 assert_file_not_empty "output.fastq"
-assert_identical_content "output.fastq" "../data/expected.fastq"
+assert_identical_content "output.fastq" "$test_data/expected.fastq"
 echo "- test1 succeeded -"
 
 cd ..
 
-# Test 2:
-# mkdir test2
-# cd test2
-
-# echo "> Run bedtools bamtofastq on BAM file with tags"
-# "$meta_executable" \
-#   --input "$test_data/example.bam" \
-#   --output_fq "output.fastq" \
-#   --tags
-
-# # checks
-# assert_file_exists "output.fastq"
-# assert_file_not_empty "output.fastq"
-# assert_identical_content "output.fastq" "../data/expected.fastq"
-# echo "- test2 succeeded -"
-
-# cd ..
-
-# # Test 3:
-# mkdir test3
-# cd test3
-
-# echo "> Run bedtools bamtofastq on BAM file with tags and output_fq2"
-# "$meta_executable" \
-#   --input "$test_data/example.bam" \
-#   --output_fq "output1.fastq" \
-#   --output_fq2 "output2.fastq" \
-#   --tags
-
-# # checks
-# assert_file_exists "output1.fastq"
-# assert_file_not_empty "output1.fastq"
-# assert_identical_content "output1.fastq" "../data/expected.fastq"
-# assert_file_exists "output2.fastq"
-# assert_file_not_empty "output2.fastq"
-# assert_identical_content "output2.fastq" "../data/expected.fastq"
-# echo "- test3 succeeded -"
-
-# cd ..
+# Test 2: with tags
+mkdir test2
+cd test2
+
+echo "> Run bedtools bamtofastq on BAM file with tags"
+"$meta_executable" \
+  --input "$test_data/example.bam" \
+  --output_fq "output.fastq" \
+  --tags
+
+# checks
+assert_file_exists "output.fastq"
+assert_file_not_empty "output.fastq"
+assert_identical_content "output.fastq" "../data/expected.fastq"
+echo "- test2 succeeded -"
+
+cd ..
+
+# Test 3: with option fq2
+mkdir test3
+cd test3
+
+echo "> Run bedtools bamtofastq on BAM file with output_fq2"
+"$meta_executable" \
+  --input "$test_data/example.bam" \
+  --output_fq "output1.fastq" \
+  --output_fq2 "output2.fastq" 
+
+# checks
+assert_file_exists "output1.fastq"
+assert_file_not_empty "output1.fastq"
+assert_identical_content "output1.fastq" "../data/expected.fastq"
+assert_file_exists "output2.fastq"
+assert_file_not_empty "output2.fastq"
+assert_identical_content "output2.fastq" "../data/expected.fastq"
+echo "- test3 succeeded -"
+
+cd ..
 
 echo "All tests succeeded"
 exit 0
diff --git a/src/bedtools/bedtools_bamtofastq/test_data/example.bam b/src/bedtools/bedtools_bamtofastq/test_data/example.bam
index 5454b2f4d2414f57b95110195ac6daf707c6a8a0..9c7ddef66218ed98e55bb989c9796511663b944f 100644
GIT binary patch
delta 208
zcmV;>05AWH0@?zQ9RlGDksnP2`f=Hck#H1$$pCx600GHB%x2>$#0X>=K*gp4aS9L@
zr6#5rGB7YRFgSL!xOg-PiYR(Ws7NRZHhKt(cnCRp2>mA!`1v|B__{=y8ZZPIMTNLK
zyN5VBySs;kI6AsJg4r+;I1^4X1R6zok^~qYBl!p7$H{O%g8V%P=pv9Gjlh2Fz~VnR
zM-Lal|0DvS9~psuG&FEGwgh?8-7zF2#N8d_O=m}-N1Z`F4RHnvgSa6e9#E75Zvp_Z
KY=(i$k?kLE5KwIZ

delta 130
zcmV-|0Db@30*nHX9Rg7ZksnP2rEV&Xk#H1gdjKn9fPiEmX0!1WVg%9#K>QyHKypQ?
zi7AE*49pA+jvXy79!-KGiXIXw5{iP29)cnsLQWn+|49Tz17<78rsD)`H3r-2(xE8m
kB+}UA*d!<+(kSTCsG`!SBGTgWpF{uvX~*iEVv{=oAF-n{+5i9m

diff --git a/src/bedtools/bedtools_bamtofastq/test_data/example.fq b/src/bedtools/bedtools_bamtofastq/test_data/example.fq
deleted file mode 100644
index 00f3c33c..00000000
--- a/src/bedtools/bedtools_bamtofastq/test_data/example.fq
+++ /dev/null
@@ -1,12 +0,0 @@
-@read1
-GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAAGGTACGCGTAC
-+
-                                                
-@read1
-GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAAGGTACGCGTAC
-+
-                                                
-@read3
-GGTTCAAAGCAGTATCGATCAAATAGTAAAGGTACGCGTACGAGTGGG
-+
-                                                
diff --git a/src/bedtools/bedtools_bamtofastq/test_data/example.sam b/src/bedtools/bedtools_bamtofastq/test_data/example.sam
index 3e573ca9..0be4fa10 100644
--- a/src/bedtools/bedtools_bamtofastq/test_data/example.sam
+++ b/src/bedtools/bedtools_bamtofastq/test_data/example.sam
@@ -1,6 +1,5 @@
-@HD VN:1.0	SO:unsorted
+@HD	VN:1.0	SO:unsorted
 @SQ	SN:chr1	LN:248956422
 @SQ	SN:chr2	LN:242193529
-read1	0	chr1	100	60	48M	*	0	0	GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAAGGTACGCGTAC	*
-read1	0	chr1	100	60	48M	*	0	0	GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAAGGTACGCGTAC	*
-read3	0	chr2	200	60	48M	*	0	0	GGTTCAAAGCAGTATCGATCAAATAGTAAAGGTACGCGTACGAGTGGG	*
+read1	99	chr1	100	60	48M	=	150	100	GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAAGGTACGCGTAC	*	NM:i:0	MD:Z:50	R2:Z:TGCGTACGGTTAAGAGTACGCGTACGGTACGCGTACGCGTACGCGT	Q2:Z:IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+read2	147	chr1	150	60	48M	=	100	-100	TTTCAAAGCAGTATCGATCAAATAGTAAAGGTACGCGTACGAGTGGAA	*	NM:i:1	MD:Z:10G39	R2:Z:GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAAGGTACGCGT	Q2:Z:IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
diff --git a/src/bedtools/bedtools_bamtofastq/test_data/expected.fastq b/src/bedtools/bedtools_bamtofastq/test_data/expected.fastq
new file mode 100644
index 00000000..a601e74a
--- /dev/null
+++ b/src/bedtools/bedtools_bamtofastq/test_data/expected.fastq
@@ -0,0 +1,8 @@
+@read1
+GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAAGGTACGCGTAC
++
+                                                
+@read2
+TTCCACTCGTACGCGTACCTTTACTATTTGATCGATACTGCTTTGAAA
++
+                                                
diff --git a/src/bedtools/bedtools_bamtofastq/test_data/expected_fq2.fastq b/src/bedtools/bedtools_bamtofastq/test_data/expected_fq2.fastq
new file mode 100644
index 00000000..e69de29b
diff --git a/src/bedtools/bedtools_bamtofastq/test_data/expected_tags.fastq b/src/bedtools/bedtools_bamtofastq/test_data/expected_tags.fastq
new file mode 100644
index 00000000..e69de29b
diff --git a/src/bedtools/bedtools_bamtofastq/test_data/script.sh b/src/bedtools/bedtools_bamtofastq/test_data/script.sh
new file mode 100755
index 00000000..52a8026e
--- /dev/null
+++ b/src/bedtools/bedtools_bamtofastq/test_data/script.sh
@@ -0,0 +1,30 @@
+#!/bin/bash
+
+# NOTE: you need to have docker running for this script to work.
+
+# create sam file
+printf "@HD\tVN:1.0\tSO:unsorted\n" > example.sam
+printf "@SQ\tSN:chr1\tLN:248956422\n" >> example.sam
+printf "@SQ\tSN:chr2\tLN:242193529\n" >> example.sam
+printf "read1\t99\tchr1\t100\t60\t48M\t=\t150\t100\tGATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAAGGTACGCGTAC\t*\tNM:i:0\tMD:Z:50\tR2:Z:TGCGTACGGTTAAGAGTACGCGTACGGTACGCGTACGCGTACGCGT\tQ2:Z:IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n" >> example.sam
+printf "read2\t147\tchr1\t150\t60\t48M\t=\t100\t-100\tTTTCAAAGCAGTATCGATCAAATAGTAAAGGTACGCGTACGAGTGGAA\t*\tNM:i:1\tMD:Z:10G39\tR2:Z:GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAAGGTACGCGT\tQ2:Z:IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n" >> example.sam
+
+# create bam file
+# docker run -it -v `pwd`:/host biocontainers/samtools:v1.9-4-deb_cv1 bash
+# cd /host
+# samtools view -b example.sam > example.bam
+# exit
+
+# # create fastq files
+# docker run -it -v `pwd`:/host biocontainers/bedtools:v2.27.1dfsg-4-deb_cv1 bash
+# cd /host
+
+# # expected.fastq
+# bedtools bamtofastq -i example.bam -fq expected.fastq
+
+# # expected_tags.fastq
+#bedtools bamtofastq -i example.bam -fq expected.fastq -tags
+
+# # expected_fq2.fastq
+
+# exit
\ No newline at end of file

From 1da77d50de1822efb9a98143a55e97b4b3181a22 Mon Sep 17 00:00:00 2001
From: tgaspe <theodorogtc@gmail.com>
Date: Wed, 31 Jul 2024 11:59:19 -0300
Subject: [PATCH 08/13] Fixing Bugs

---
 .../bedtools_bamtofastq/config.vsh.yaml       |   3 +-
 src/bedtools/bedtools_bamtofastq/help.txt     |   4 ++-
 src/bedtools/bedtools_bamtofastq/test.sh      |   8 ++----
 .../bedtools_bamtofastq/test_data/example.bam | Bin 346 -> 334 bytes
 .../bedtools_bamtofastq/test_data/example.sam |   8 ++----
 .../test_data/expected.fastq                  |  20 +++++++++----
 .../test_data/expected_1.fastq                |   4 +++
 .../test_data/expected_2.fastq                |   4 +++
 .../test_data/expected_fq2.fastq              |   0
 .../test_data/expected_tags.fastq             |  16 +++++++++++
 .../bedtools_bamtofastq/test_data/script.sh   |  27 ++++--------------
 11 files changed, 54 insertions(+), 40 deletions(-)
 create mode 100644 src/bedtools/bedtools_bamtofastq/test_data/expected_1.fastq
 create mode 100644 src/bedtools/bedtools_bamtofastq/test_data/expected_2.fastq
 delete mode 100644 src/bedtools/bedtools_bamtofastq/test_data/expected_fq2.fastq

diff --git a/src/bedtools/bedtools_bamtofastq/config.vsh.yaml b/src/bedtools/bedtools_bamtofastq/config.vsh.yaml
index 125ce6bd..aba65081 100644
--- a/src/bedtools/bedtools_bamtofastq/config.vsh.yaml
+++ b/src/bedtools/bedtools_bamtofastq/config.vsh.yaml
@@ -31,10 +31,11 @@ argument_groups:
         type: file
         description: Output FASTQ file.
         required: true
-
+      
       - name: --output_fq2
         alternatives: -fq2
         type: file
+        direction: output
         description: |
           FASTQ for second end.  Used if BAM contains paired-end data.
           BAM should be sorted by query name is creating paired FASTQ.
diff --git a/src/bedtools/bedtools_bamtofastq/help.txt b/src/bedtools/bedtools_bamtofastq/help.txt
index d03b85d1..ed2b7468 100644
--- a/src/bedtools/bedtools_bamtofastq/help.txt
+++ b/src/bedtools/bedtools_bamtofastq/help.txt
@@ -3,7 +3,7 @@ bedtools bamtofastq
 ```
 
 Tool:    bedtools bamtofastq (aka bamToFastq)
-Version: v2.27.1
+Version: v2.30.0
 Summary: Convert BAM alignments to FASTQ files. 
 
 Usage:   bamToFastq [OPTIONS] -i <BAM> -fq <FQ> 
@@ -21,3 +21,5 @@ Tips:
 
 	bedtools bamtofastq -i x.bam -fq /dev/stdout -fq2 /dev/stdout > x.ilv.fq
 
+	Also, the samtools fastq command has more fucntionality and is a useful alternative.
+
diff --git a/src/bedtools/bedtools_bamtofastq/test.sh b/src/bedtools/bedtools_bamtofastq/test.sh
index 1e860663..cb618992 100644
--- a/src/bedtools/bedtools_bamtofastq/test.sh
+++ b/src/bedtools/bedtools_bamtofastq/test.sh
@@ -1,7 +1,5 @@
 #!/bin/bash
 
-# viash ns build -q bedtools_bamtofastq --setup cb
-
 # exit on error
 set -e
 
@@ -54,7 +52,7 @@ echo "> Run bedtools bamtofastq on BAM file with tags"
 # checks
 assert_file_exists "output.fastq"
 assert_file_not_empty "output.fastq"
-assert_identical_content "output.fastq" "../data/expected.fastq"
+assert_identical_content "output.fastq" "$test_data/expected.fastq"
 echo "- test2 succeeded -"
 
 cd ..
@@ -72,10 +70,10 @@ echo "> Run bedtools bamtofastq on BAM file with output_fq2"
 # checks
 assert_file_exists "output1.fastq"
 assert_file_not_empty "output1.fastq"
-assert_identical_content "output1.fastq" "../data/expected.fastq"
+assert_identical_content "output1.fastq" "$test_data/expected_1.fastq"
 assert_file_exists "output2.fastq"
 assert_file_not_empty "output2.fastq"
-assert_identical_content "output2.fastq" "../data/expected.fastq"
+assert_identical_content "output2.fastq" "$test_data/expected_2.fastq"
 echo "- test3 succeeded -"
 
 cd ..
diff --git a/src/bedtools/bedtools_bamtofastq/test_data/example.bam b/src/bedtools/bedtools_bamtofastq/test_data/example.bam
index 9c7ddef66218ed98e55bb989c9796511663b944f..ffc075ab83a83a98ed1edbf88b26cc27ad8946c6 100644
GIT binary patch
delta 298
zcmV+_0oDH60?q<bABzYC000000RIL6LPG)oQ~+~w^kvjwU|?_v4&)5>vr5h=GO{u>
zH?lM~GqW_-1+y#+4GlSc{HzR33@x}Afodgz7?(nZE>;Ex0MD-^nN^W-6Mx(Qy^z0Z
z0znXm=bDgqjw`lZNnpyePm%otxfGWaDl9f4YAJ}FojXjirQmD$YQBQ!iXyf)e(*KF
zslGYFm2LL@>$fam2J_o?C;)cZ<z}*8Oy}_Z20%zvPdp-eRS7doqNJlo)d+G`_NcsE
z4W_89QlzPS0byuHf31T->q|aOHq@>NeFq_L;XnK1p!MT^UBmGq?i#$m2Vb7BI(6M+
wFdNIFlNKw&5xrH7wv<dFB4d11kts1X`ool{QB>8vfG2{_9@*ND;*&c8AA&7{ng9R*

literal 346
zcmb2|=3rp}f&Xj_PR>jW#SFzoUsAuMBqS7kD0s;8d9%?K;|Dz7wric$KBuqc>HDyV
zgYOB?x6NMXG>o2n`MBB0XyXPGQ)5FTr%47)9uksKQnRHZiwqfglUb7{h_P);zW!r@
zjB?v4&7U<4zY1@5<pZsfN3-)JL-hd$#*+?b(jIFb;Yg8mIJ%6fkV`;(soF9LBLf3t
z1B<dPJ1R^#yELjiR(NP|nN@LgRd85Va{N^n{PEMu_{T1nnNkKUlCG^gtarCtSnb~3
z-eO_3%ev{NfuM!3pAn0cYvm*s2|4AT?2nG0EU<6-W6S<RX@Y$3fx0&b9@)F|iy!>2
z!n8nMva!y@q`-U|OXcOehAJvY?#e##O?O}5KG)HXw~&pid55BcT)-5jd?tpCIc<%n
P88Lk#&A<!}Ob`J8Yo~ZW

diff --git a/src/bedtools/bedtools_bamtofastq/test_data/example.sam b/src/bedtools/bedtools_bamtofastq/test_data/example.sam
index 0be4fa10..4afb0aef 100644
--- a/src/bedtools/bedtools_bamtofastq/test_data/example.sam
+++ b/src/bedtools/bedtools_bamtofastq/test_data/example.sam
@@ -1,5 +1,3 @@
-@HD	VN:1.0	SO:unsorted
-@SQ	SN:chr1	LN:248956422
-@SQ	SN:chr2	LN:242193529
-read1	99	chr1	100	60	48M	=	150	100	GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAAGGTACGCGTAC	*	NM:i:0	MD:Z:50	R2:Z:TGCGTACGGTTAAGAGTACGCGTACGGTACGCGTACGCGTACGCGT	Q2:Z:IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
-read2	147	chr1	150	60	48M	=	100	-100	TTTCAAAGCAGTATCGATCAAATAGTAAAGGTACGCGTACGAGTGGAA	*	NM:i:1	MD:Z:10G39	R2:Z:GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAAGGTACGCGT	Q2:Z:IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@SQ	SN:chr2:172936693-172938111	LN:1418
+my_read	99	chr2:172936693-172938111	129	60	100M	=	429	400	CTAACTAGCCTGGGAAAAAAGGATAGTGTCTCTCTGTTCTTTCATAGGAAATGTTGAATCAGACCCCTACTGGGAAAAGAAATTTAATGCATATCTCACT	*	XT:A:U	NM:i:0	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:100
+my_read	147	chr2:172936693-172938111	429	60	100M	=	129	-400	TCGAGCTCTGCATTCATGGCTGTGTCTAAAGGGCATGTCAGCCTTTGATTCTCTCTGAGAGGTAATTATCCTTTTCCTGTCACGGAACAACAAATGATAG	*	XT:A:U	NM:i:0	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:100
diff --git a/src/bedtools/bedtools_bamtofastq/test_data/expected.fastq b/src/bedtools/bedtools_bamtofastq/test_data/expected.fastq
index a601e74a..358331d4 100644
--- a/src/bedtools/bedtools_bamtofastq/test_data/expected.fastq
+++ b/src/bedtools/bedtools_bamtofastq/test_data/expected.fastq
@@ -1,8 +1,16 @@
-@read1
-GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAAGGTACGCGTAC
+@my_read
+CTAACTAGCCTGGGAAAAAAGGATAGTGTCTCTCTGTTCTTTCATAGGAAATGTTGAATCAGACCCCTACTGGGAAAAGAAATTTAATGCATATCTCACT
 +
-                                                
-@read2
-TTCCACTCGTACGCGTACCTTTACTATTTGATCGATACTGCTTTGAAA
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+@my_read
+CTAACTAGCCTGGGAAAAAAGGATAGTGTCTCTCTGTTCTTTCATAGGAAATGTTGAATCAGACCCCTACTGGGAAAAGAAATTTAATGCATATCTCACT
 +
-                                                
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+@my_read
+CTATCATTTGTTGTTCCGTGACAGGAAAAGGATAATTACCTCTCAGAGAGAATCAAAGGCTGACATGCCCTTTAGACACAGCCATGAATGCAGAGCTCGA
++
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+@my_read
+CTATCATTTGTTGTTCCGTGACAGGAAAAGGATAATTACCTCTCAGAGAGAATCAAAGGCTGACATGCCCTTTAGACACAGCCATGAATGCAGAGCTCGA
++
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
diff --git a/src/bedtools/bedtools_bamtofastq/test_data/expected_1.fastq b/src/bedtools/bedtools_bamtofastq/test_data/expected_1.fastq
new file mode 100644
index 00000000..c5dfe571
--- /dev/null
+++ b/src/bedtools/bedtools_bamtofastq/test_data/expected_1.fastq
@@ -0,0 +1,4 @@
+@my_read/1
+CTAACTAGCCTGGGAAAAAAGGATAGTGTCTCTCTGTTCTTTCATAGGAAATGTTGAATCAGACCCCTACTGGGAAAAGAAATTTAATGCATATCTCACT
++
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
diff --git a/src/bedtools/bedtools_bamtofastq/test_data/expected_2.fastq b/src/bedtools/bedtools_bamtofastq/test_data/expected_2.fastq
new file mode 100644
index 00000000..50d1bd62
--- /dev/null
+++ b/src/bedtools/bedtools_bamtofastq/test_data/expected_2.fastq
@@ -0,0 +1,4 @@
+@my_read/2
+CTATCATTTGTTGTTCCGTGACAGGAAAAGGATAATTACCTCTCAGAGAGAATCAAAGGCTGACATGCCCTTTAGACACAGCCATGAATGCAGAGCTCGA
++
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
diff --git a/src/bedtools/bedtools_bamtofastq/test_data/expected_fq2.fastq b/src/bedtools/bedtools_bamtofastq/test_data/expected_fq2.fastq
deleted file mode 100644
index e69de29b..00000000
diff --git a/src/bedtools/bedtools_bamtofastq/test_data/expected_tags.fastq b/src/bedtools/bedtools_bamtofastq/test_data/expected_tags.fastq
index e69de29b..358331d4 100644
--- a/src/bedtools/bedtools_bamtofastq/test_data/expected_tags.fastq
+++ b/src/bedtools/bedtools_bamtofastq/test_data/expected_tags.fastq
@@ -0,0 +1,16 @@
+@my_read
+CTAACTAGCCTGGGAAAAAAGGATAGTGTCTCTCTGTTCTTTCATAGGAAATGTTGAATCAGACCCCTACTGGGAAAAGAAATTTAATGCATATCTCACT
++
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+@my_read
+CTAACTAGCCTGGGAAAAAAGGATAGTGTCTCTCTGTTCTTTCATAGGAAATGTTGAATCAGACCCCTACTGGGAAAAGAAATTTAATGCATATCTCACT
++
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+@my_read
+CTATCATTTGTTGTTCCGTGACAGGAAAAGGATAATTACCTCTCAGAGAGAATCAAAGGCTGACATGCCCTTTAGACACAGCCATGAATGCAGAGCTCGA
++
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+@my_read
+CTATCATTTGTTGTTCCGTGACAGGAAAAGGATAATTACCTCTCAGAGAGAATCAAAGGCTGACATGCCCTTTAGACACAGCCATGAATGCAGAGCTCGA
++
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
diff --git a/src/bedtools/bedtools_bamtofastq/test_data/script.sh b/src/bedtools/bedtools_bamtofastq/test_data/script.sh
index 52a8026e..df595510 100755
--- a/src/bedtools/bedtools_bamtofastq/test_data/script.sh
+++ b/src/bedtools/bedtools_bamtofastq/test_data/script.sh
@@ -1,30 +1,13 @@
 #!/bin/bash
 
-# NOTE: you need to have docker running for this script to work.
-
 # create sam file
-printf "@HD\tVN:1.0\tSO:unsorted\n" > example.sam
-printf "@SQ\tSN:chr1\tLN:248956422\n" >> example.sam
-printf "@SQ\tSN:chr2\tLN:242193529\n" >> example.sam
-printf "read1\t99\tchr1\t100\t60\t48M\t=\t150\t100\tGATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAAGGTACGCGTAC\t*\tNM:i:0\tMD:Z:50\tR2:Z:TGCGTACGGTTAAGAGTACGCGTACGGTACGCGTACGCGTACGCGT\tQ2:Z:IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n" >> example.sam
-printf "read2\t147\tchr1\t150\t60\t48M\t=\t100\t-100\tTTTCAAAGCAGTATCGATCAAATAGTAAAGGTACGCGTACGAGTGGAA\t*\tNM:i:1\tMD:Z:10G39\tR2:Z:GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAAGGTACGCGT\tQ2:Z:IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n" >> example.sam
+printf "@SQ\tSN:chr2:172936693-172938111\tLN:1418\n" > example.sam
+printf "my_read\t99\tchr2:172936693-172938111\t129\t60\t100M\t=\t429\t400\tCTAACTAGCCTGGGAAAAAAGGATAGTGTCTCTCTGTTCTTTCATAGGAAATGTTGAATCAGACCCCTACTGGGAAAAGAAATTTAATGCATATCTCACT\t*\tXT:A:U\tNM:i:0\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:100\n" >> example.sam
+printf "my_read\t147\tchr2:172936693-172938111\t429\t60\t100M\t=\t129\t-400\tTCGAGCTCTGCATTCATGGCTGTGTCTAAAGGGCATGTCAGCCTTTGATTCTCTCTGAGAGGTAATTATCCTTTTCCTGTCACGGAACAACAAATGATAG\t*\tXT:A:U\tNM:i:0\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:100\n" >> example.sam
 
 # create bam file
-# docker run -it -v `pwd`:/host biocontainers/samtools:v1.9-4-deb_cv1 bash
-# cd /host
 # samtools view -b example.sam > example.bam
-# exit
-
-# # create fastq files
-# docker run -it -v `pwd`:/host biocontainers/bedtools:v2.27.1dfsg-4-deb_cv1 bash
-# cd /host
 
-# # expected.fastq
+# create fastq files
 # bedtools bamtofastq -i example.bam -fq expected.fastq
-
-# # expected_tags.fastq
-#bedtools bamtofastq -i example.bam -fq expected.fastq -tags
-
-# # expected_fq2.fastq
-
-# exit
\ No newline at end of file
+# bedtools bamtofastq -i example.bam -fq expected_1.fastq -fq2 expected_2.fastq

From 3977543a7a4ecadd42aa4d7b0ec1ea45d30fa22d Mon Sep 17 00:00:00 2001
From: tgaspe <theodorogtc@gmail.com>
Date: Wed, 31 Jul 2024 14:30:15 -0300
Subject: [PATCH 09/13] Working version

---
 src/bedtools/bedtools_bamtofastq/script.sh       |  3 ++-
 .../test_data/expected_tags.fastq                | 16 ----------------
 2 files changed, 2 insertions(+), 17 deletions(-)
 delete mode 100644 src/bedtools/bedtools_bamtofastq/test_data/expected_tags.fastq

diff --git a/src/bedtools/bedtools_bamtofastq/script.sh b/src/bedtools/bedtools_bamtofastq/script.sh
index d48e12aa..4d00d77b 100644
--- a/src/bedtools/bedtools_bamtofastq/script.sh
+++ b/src/bedtools/bedtools_bamtofastq/script.sh
@@ -9,7 +9,8 @@
 # Execute bedtools bamtofastq with the provided arguments
 bedtools bamtofastq \
     ${par_tags:+-tags} \
+    ${par_output_fq2:+-fq2 "$par_output_fq2"} \
     -i "$par_input" \
     -fq "$par_output_fq"
-    ${par_output_fq2:+-fq2 "$par_output_fq2"}
+    
 
diff --git a/src/bedtools/bedtools_bamtofastq/test_data/expected_tags.fastq b/src/bedtools/bedtools_bamtofastq/test_data/expected_tags.fastq
deleted file mode 100644
index 358331d4..00000000
--- a/src/bedtools/bedtools_bamtofastq/test_data/expected_tags.fastq
+++ /dev/null
@@ -1,16 +0,0 @@
-@my_read
-CTAACTAGCCTGGGAAAAAAGGATAGTGTCTCTCTGTTCTTTCATAGGAAATGTTGAATCAGACCCCTACTGGGAAAAGAAATTTAATGCATATCTCACT
-+
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-@my_read
-CTAACTAGCCTGGGAAAAAAGGATAGTGTCTCTCTGTTCTTTCATAGGAAATGTTGAATCAGACCCCTACTGGGAAAAGAAATTTAATGCATATCTCACT
-+
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-@my_read
-CTATCATTTGTTGTTCCGTGACAGGAAAAGGATAATTACCTCTCAGAGAGAATCAAAGGCTGACATGCCCTTTAGACACAGCCATGAATGCAGAGCTCGA
-+
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-@my_read
-CTATCATTTGTTGTTCCGTGACAGGAAAAGGATAATTACCTCTCAGAGAGAATCAAAGGCTGACATGCCCTTTAGACACAGCCATGAATGCAGAGCTCGA
-+
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

From d0700ad1579543ee12fd64920089b78c88a3fffc Mon Sep 17 00:00:00 2001
From: tgaspe <theodorogtc@gmail.com>
Date: Wed, 31 Jul 2024 14:35:08 -0300
Subject: [PATCH 10/13] Update CHANGELOG.md

---
 CHANGELOG.md | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c4575cb9..4a2d99a5 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -21,6 +21,11 @@
 
 * `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).
+    - `bedtools/bedtools_sort`: Sorts a feature file (bed/gff/vcf) by chromosome and other criteria (PR #98).
+    - `bedtools/bedtools_bamtofastq`: Convert BAM alignments to FASTQ files (PR #101).
+
 ## MINOR CHANGES
 
 * `busco` components: update BUSCO to `5.7.1` (PR #72).

From d3cb54af176cf78198c9d125f9195042a2baebdf Mon Sep 17 00:00:00 2001
From: tgaspe <theodorogtc@gmail.com>
Date: Sat, 10 Aug 2024 18:33:14 +0200
Subject: [PATCH 11/13] Required Changes

---
 output.bam                                       |  0
 src/bedtools/bedtools_bamtofastq/config.vsh.yaml | 11 ++++++-----
 src/bedtools/bedtools_bamtofastq/script.sh       |  4 ++--
 src/bedtools/bedtools_bamtofastq/test.sh         |  8 ++++----
 4 files changed, 12 insertions(+), 11 deletions(-)
 delete mode 100644 output.bam

diff --git a/output.bam b/output.bam
deleted file mode 100644
index e69de29b..00000000
diff --git a/src/bedtools/bedtools_bamtofastq/config.vsh.yaml b/src/bedtools/bedtools_bamtofastq/config.vsh.yaml
index aba65081..ea767976 100644
--- a/src/bedtools/bedtools_bamtofastq/config.vsh.yaml
+++ b/src/bedtools/bedtools_bamtofastq/config.vsh.yaml
@@ -1,13 +1,14 @@
 name: bedtools_bamtofastq
 namespace: bedtools
-description: Conversion tool for extracting FASTQ records from sequence alignments in BAM format.
+description: | 
+  Conversion tool for extracting FASTQ records from sequence alignments in BAM format.
 keywords: [Conversion ,BAM, FASTQ]
 links:
   documentation: https://bedtools.readthedocs.io/en/latest/content/tools/bamtofastq.html
   repository: https://github.com/arq5x/bedtools2
 references:
   doi: 10.1093/bioinformatics/btq033
-license: GPL-2.0, MIT
+license: MIT
 requirements:
   commands: [bedtools]
 authors:
@@ -25,19 +26,19 @@ argument_groups:
     
   - name: Outputs
     arguments:
-      - name: --output_fq
+      - name: --fastq
         alternatives: -fq
         direction: output
         type: file
         description: Output FASTQ file.
         required: true
       
-      - name: --output_fq2
+      - name: --fastq2
         alternatives: -fq2
         type: file
         direction: output
         description: |
-          FASTQ for second end.  Used if BAM contains paired-end data.
+          FASTQ for second end. Used if BAM contains paired-end data.
           BAM should be sorted by query name is creating paired FASTQ.
          
   - name: Options
diff --git a/src/bedtools/bedtools_bamtofastq/script.sh b/src/bedtools/bedtools_bamtofastq/script.sh
index 4d00d77b..bbd9fd65 100644
--- a/src/bedtools/bedtools_bamtofastq/script.sh
+++ b/src/bedtools/bedtools_bamtofastq/script.sh
@@ -9,8 +9,8 @@
 # Execute bedtools bamtofastq with the provided arguments
 bedtools bamtofastq \
     ${par_tags:+-tags} \
-    ${par_output_fq2:+-fq2 "$par_output_fq2"} \
+    ${par_fastq2:+-fq2 "$par_fastq2"} \
     -i "$par_input" \
-    -fq "$par_output_fq"
+    -fq "$par_fastq"
     
 
diff --git a/src/bedtools/bedtools_bamtofastq/test.sh b/src/bedtools/bedtools_bamtofastq/test.sh
index cb618992..bc209b2b 100644
--- a/src/bedtools/bedtools_bamtofastq/test.sh
+++ b/src/bedtools/bedtools_bamtofastq/test.sh
@@ -29,7 +29,7 @@ cd test1
 echo "> Run bedtools bamtofastq on BAM file"
 "$meta_executable" \
   --input "$test_data/example.bam" \
-  --output_fq "output.fastq"
+  --fastq "output.fastq"
 
 # checks
 assert_file_exists "output.fastq"
@@ -46,7 +46,7 @@ cd test2
 echo "> Run bedtools bamtofastq on BAM file with tags"
 "$meta_executable" \
   --input "$test_data/example.bam" \
-  --output_fq "output.fastq" \
+  --fastq "output.fastq" \
   --tags
 
 # checks
@@ -64,8 +64,8 @@ cd test3
 echo "> Run bedtools bamtofastq on BAM file with output_fq2"
 "$meta_executable" \
   --input "$test_data/example.bam" \
-  --output_fq "output1.fastq" \
-  --output_fq2 "output2.fastq" 
+  --fastq "output1.fastq" \
+  --fastq2 "output2.fastq" 
 
 # checks
 assert_file_exists "output1.fastq"

From d3f04227867caaf502bd2826137903b6b2bdc818 Mon Sep 17 00:00:00 2001
From: tgaspe <theodorogtc@gmail.com>
Date: Mon, 12 Aug 2024 20:56:46 +0200
Subject: [PATCH 12/13] Adding exit on error

---
 src/bedtools/bedtools_bamtofastq/script.sh | 3 +++
 src/bedtools/bedtools_bamtofastq/test.sh   | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/bedtools/bedtools_bamtofastq/script.sh b/src/bedtools/bedtools_bamtofastq/script.sh
index bbd9fd65..4b32f2d7 100644
--- a/src/bedtools/bedtools_bamtofastq/script.sh
+++ b/src/bedtools/bedtools_bamtofastq/script.sh
@@ -3,6 +3,9 @@
 ## VIASH START
 ## VIASH END
 
+# Exit on error
+set -eo pipefail
+
 # Unset parameters
 [[ "$par_tags" == "false" ]] && unset par_tags
 
diff --git a/src/bedtools/bedtools_bamtofastq/test.sh b/src/bedtools/bedtools_bamtofastq/test.sh
index bc209b2b..6d913d85 100644
--- a/src/bedtools/bedtools_bamtofastq/test.sh
+++ b/src/bedtools/bedtools_bamtofastq/test.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 # exit on error
-set -e
+set -eo pipefail
 
 test_data="$meta_resources_dir/test_data"
 

From d33ba6d27ce554df4f9b561a946b8d941ca6a750 Mon Sep 17 00:00:00 2001
From: tgaspe <theodorogtc@gmail.com>
Date: Mon, 12 Aug 2024 21:26:02 +0200
Subject: [PATCH 13/13] adding more links

---
 src/bedtools/bedtools_bamtofastq/config.vsh.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/bedtools/bedtools_bamtofastq/config.vsh.yaml b/src/bedtools/bedtools_bamtofastq/config.vsh.yaml
index ea767976..cd30cb71 100644
--- a/src/bedtools/bedtools_bamtofastq/config.vsh.yaml
+++ b/src/bedtools/bedtools_bamtofastq/config.vsh.yaml
@@ -6,6 +6,8 @@ keywords: [Conversion ,BAM, FASTQ]
 links:
   documentation: https://bedtools.readthedocs.io/en/latest/content/tools/bamtofastq.html
   repository: https://github.com/arq5x/bedtools2
+  homepage: https://bedtools.readthedocs.io/en/latest/#
+  issue_tracker: https://github.com/arq5x/bedtools2/issues
 references:
   doi: 10.1093/bioinformatics/btq033
 license: MIT