diff --git a/CHANGELOG.md b/CHANGELOG.md
index c8d0a08b..151b7a41 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -43,10 +43,14 @@
     - `samtools/samtools_index`: Index SAM/BAM/CRAM files (PR #35).
     - `samtools/samtools_sort`: Sort SAM/BAM/CRAM files (PR #36).
     - `samtools/samtools_stats`: Reports alignment summary statistics for a BAM file (PR #39).
-    - `samtools/samtools_stats`: Indexes FASTA files to enable random access to fasta and fastq files (PR #41).
+    - `samtools/samtools_faidx`: Indexes FASTA files to enable random access to fasta and fastq files (PR #41).
+    - `samtools/samtools_collate`: Shuffles and groups reads in SAM/BAM/CRAM files together by their names (PR #42).
+    - `samtools/samtools_view`: Views and converts SAM/BAM/CRAM files (PR #48).
+    - `samtools/samtools_fastq`: Converts a SAM/BAM/CRAM file to FASTQ (PR #52).
 
 * `falco`: A C++ drop-in replacement of FastQC to assess the quality of sequence read data (PR #43).
 
+
 ## MAJOR CHANGES
 
 ## MINOR CHANGES
@@ -55,6 +59,10 @@
 
 * Update to Viash 0.8.5 (PR #25).
 
+* Update to Viash 0.9.0-RC3 (PR #51).
+
 ## DOCUMENTATION
 
 ## BUG FIXES
+
+* Add escaping character before leading hashtag in the description field of the config file (PR #50).
\ No newline at end of file
diff --git a/README.md b/README.md
index 1639481f..ecf807ca 100644
--- a/README.md
+++ b/README.md
@@ -26,34 +26,25 @@ We encourage contributions from the community. To contribute:
 
 ## Contribution Guidelines
 
-- **Documentation of Functionality**: The purpose and functionality of
-  each component should be adequately described.
-- **Documentation of Inputs and Outputs**: All input and output
-  arguments should have a description and example (with extension).
-- **Docker Image**: A Docker image (with optional additional
-  dependencies) should be provided.
-- **Write unit tests**: A unit test with possibly test resources needs
-  to be provided.
-- **Provide test resources**: If the unit test requires test resources,
-  these should be provided in the `test_resources` section of the
-  component.
-- **Versioning**: If the component uses custom software (not installed
-  via Apt, Apk, Yum, Pip, Conda, or R), a Bash script `version.sh` needs
-  to be provided that outputs the version of the software.
-- **File format specifications**: If a component returns a directory or
-  data structure such as AnnData or MuData, a specification of the file
-  format should be provided.
+The contribution guidelines describes which steps you should follow to
+contribute a component to this repository.
+
+1.  Find a component to contribute
+2.  Add config template
+3.  Fill in the metadata
+4.  Find a suitable container
+5.  Create help file
+6.  Create or fetch test data
+7.  Add arguments for the input files
+8.  Add arguments for the output files
+9.  Add arguments for the other arguments
+10. Add a Docker engine
+11. Write a runner script
+12. Create test script
+13. Create a `/var/software_versions.txt` file
 
 See the [CONTRIBUTING](CONTRIBUTING.md) file for more details.
 
-## Repository Structure
-
-…
-
-## Installation and Usage
-
-…
-
 ## Support and Community
 
 For support, questions, or to join our community:
diff --git a/README.qmd b/README.qmd
index f7e5139b..656cdac7 100644
--- a/README.qmd
+++ b/README.qmd
@@ -21,29 +21,24 @@ We encourage contributions from the community. To contribute:
 
 ## Contribution Guidelines
 
+The contribution guidelines describes which steps you should follow to contribute a component to this repository.
+
 ```{r echo=FALSE}
 lines <- readr::read_lines("CONTRIBUTING.md")
 
-index_start <- grep("^## ", lines)
+index_start <- grep("^### Step [0-9]*:", lines)
+
 index_end <- c(index_start[-1] - 1, length(lines))
 
-name <- gsub("^## ", "", lines[index_start])
-description <- lines[index_start + 2]
+name <- gsub("^### Step [0-9]*: *", "", lines[index_start])
 
 knitr::asis_output(
-  paste(paste0(" * **", name, "**: ", description, "\n"), collapse = "")
+  paste(paste0(" 1. ", name, "\n"), collapse = "")
 )
 ```
 
 See the [CONTRIBUTING](CONTRIBUTING.md) file for more details.
 
-## Repository Structure
-
-...
-
-## Installation and Usage
-
-...
 
 ## Support and Community
 
diff --git a/_viash.yaml b/_viash.yaml
index a72a1ab7..397a8d69 100644
--- a/_viash.yaml
+++ b/_viash.yaml
@@ -7,4 +7,7 @@ links:
   issue_tracker: https://github.com/viash-hub/biobase/issues
   repository: https://github.com/viash-hub/biobase
 
-viash_version: 0.9.0-RC2
\ No newline at end of file
+viash_version: 0.9.0-RC3
+
+config_mods: |
+  .requirements.commands := ['ps']
diff --git a/src/bcl_convert/config.vsh.yaml b/src/bcl_convert/config.vsh.yaml
index 7a9bce24..d0cedfa7 100644
--- a/src/bcl_convert/config.vsh.yaml
+++ b/src/bcl_convert/config.vsh.yaml
@@ -50,20 +50,20 @@ argument_groups:
         example: true
       - name: --bcl_num_parallel_tiles
         type: integer
-        description: "# of tiles to process in parallel (default 1)"
+        description: "\\# of tiles to process in parallel (default 1)"
         example: 1
       - name: --bcl_num_conversion_threads
         type: integer
-        description: "# of threads for conversion (per tile, default # cpu threads)"
+        description: "\\# of threads for conversion (per tile, default # cpu threads)"
         example: 1
       - name: --bcl_num_compression_threads
         type: integer
-        description: "# of threads for fastq.gz output compression (per tile, default # cpu threads, or HW+12)"
+        description: "\\# of threads for fastq.gz output compression (per tile, default # cpu threads, or HW+12)"
         example: 1
       - name: --bcl_num_decompression_threads
         type: integer
         description:
-          "# of threads for bcl/cbcl input decompression (per tile, default half # cpu threads, or HW+8).
+          "\\# of threads for bcl/cbcl input decompression (per tile, default half # cpu threads, or HW+8).
           Only applies when preloading files"
         example: 1
 
@@ -79,7 +79,7 @@ argument_groups:
         example: true
       - name: --num_unknown_barcodes_reported
         type: integer
-        description: "# of Top Unknown Barcodes to output (1000 by default)"
+        description: "\\# of Top Unknown Barcodes to output (1000 by default)"
         example: 1000
       - name: --bcl_validate_sample_sheet_only
         type: boolean
diff --git a/src/falco/config.vsh.yaml b/src/falco/config.vsh.yaml
index 61cbb0d5..4d9cf656 100644
--- a/src/falco/config.vsh.yaml
+++ b/src/falco/config.vsh.yaml
@@ -177,7 +177,7 @@ engines:
     image: debian:trixie-slim
     setup:
       - type: apt
-        packages: [wget, build-essential, g++, zlib1g-dev]
+        packages: [wget, build-essential, g++, zlib1g-dev, procps]
       - type: docker
         run: |
           wget https://github.com/smithlabcode/falco/releases/download/v1.2.2/falco-1.2.2.tar.gz -O /tmp/falco.tar.gz && \
diff --git a/src/gffread/config.vsh.yaml b/src/gffread/config.vsh.yaml
index c7f3d551..d2c41a87 100644
--- a/src/gffread/config.vsh.yaml
+++ b/src/gffread/config.vsh.yaml
@@ -1,5 +1,4 @@
 name: gffread
-namespace: gffread
 description: Validate, filter, convert and perform various other operations on GFF files.
 keywords: [gff, conversion, validation, filtering]
 links:
diff --git a/src/multiqc/config.vsh.yaml b/src/multiqc/config.vsh.yaml
index 7f29d109..0a3a784b 100644
--- a/src/multiqc/config.vsh.yaml
+++ b/src/multiqc/config.vsh.yaml
@@ -161,6 +161,12 @@ argument_groups:
         type: boolean_true
         description: |
           Disable coloured log output.
+      - name: "--cl_config"
+        type: string
+        required: false
+        description: |
+          YAML formatted string that allows to customize MultiQC behaviour like input file detection.
+        example: "qualimap_config: { general_stats_coverage: [20,40,200] }"
 
   - name: "Output format"
     arguments:
diff --git a/src/multiqc/script.sh b/src/multiqc/script.sh
index 6b04ff5b..6353eb11 100755
--- a/src/multiqc/script.sh
+++ b/src/multiqc/script.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 # disable flags
-[[ "$par_ignore_symlinks" == "false" ]] && unset ignore_symlinks
+[[ "$par_ignore_symlinks" == "false" ]] && unset par_ignore_symlinks
 [[ "$par_dirs" == "false" ]] && unset par_dirs
 [[ "$par_full_names" == "false" ]] && unset par_full_names
 [[ "$par_fn_as_s_name" == "false" ]] && unset par_fn_as_s_name
@@ -99,6 +99,7 @@ multiqc \
     ${include_modules} \
     ${par_include_modules:+--include-modules "$par_include_modules"} \
     ${par_data_format:+--data-format "$par_data_format"} \
+    ${par_cl_config:+--cl-config "$par_cl_config"} \
     ${par_zip_data_dir:+--zip-data-dir} \
     ${par_pdf:+--pdf} \
     ${par_interactive:+--interactive} \
diff --git a/src/samtools/samtools_collate/config.vsh.yaml b/src/samtools/samtools_collate/config.vsh.yaml
new file mode 100644
index 00000000..669f4cdf
--- /dev/null
+++ b/src/samtools/samtools_collate/config.vsh.yaml
@@ -0,0 +1,94 @@
+name: samtools_collate
+namespace: samtools
+description: Shuffles and groups reads in SAM/BAM/CRAM files together by their names.
+keywords: [collate, counts, bam, sam, cram]
+links:
+  homepage: https://www.htslib.org/
+  documentation: https://www.htslib.org/doc/samtools-icollate.html
+  repository: https://github.com/samtools/samtools
+references: 
+  doi: [10.1093/bioinformatics/btp352, 10.1093/gigascience/giab008]
+license: MIT/Expat
+
+argument_groups:
+  - name: Inputs
+    arguments:
+      - name: --input
+        type: file
+        description: The input BAM file.
+        required: true
+      - name: --reference
+        type: file
+        description: Reference sequence FASTA FILE.
+
+  - name: Outputs
+    arguments:
+      - name: --output
+        alternatives: -o
+        type: file
+        description: The output filename.
+        required: true
+        direction: output
+
+  - name: Options
+    arguments:
+      - name: --uncompressed
+        alternatives: -u
+        type: boolean_true
+        description: Output uncompressed BAM.
+      - name: --fast
+        alternatives: -f
+        type: boolean_true
+        description: Fast mode, only primary alignments.
+      - name: --working_reads
+        alternatives: -r
+        type: integer
+        description: Working reads stored (for use with -f).
+        default: 10000
+      - name: --compression
+        alternatives: -l
+        type: integer
+        description: Compression level.
+        default: 1
+      - name: --nb_tmp_files
+        alternatives: -n
+        type: integer
+        description: Number of temporary files.
+        default: 64
+      - name: --tmp_prefix
+        alternatives: -T
+        type: string
+        description: Write temporary files to PREFIX.nnnn.bam.
+      - name: --no_pg
+        type: boolean_true
+        description: Do not add a PG line.
+      - name: --input_fmt_option
+        type: string
+        description: Specify a single input file format option in the form of OPTION or OPTION=VALUE.
+      - name: --output_fmt
+        type: string
+        description: Specify output format (SAM, BAM, CRAM).
+      - name: --output_fmt_option
+        type: string
+        description: Specify a single output file format option in the form of OPTION or OPTION=VALUE.
+
+
+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/samtools:1.19.2--h50ea8bc_1
+    setup:
+      - type: docker
+        run: |
+          samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
+          sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
+runners:
+- type: executable
+- type: nextflow
diff --git a/src/samtools/samtools_collate/help.txt b/src/samtools/samtools_collate/help.txt
new file mode 100644
index 00000000..16190f4b
--- /dev/null
+++ b/src/samtools/samtools_collate/help.txt
@@ -0,0 +1,31 @@
+```
+samtools collate
+```
+Usage: samtools collate [options...] <in.bam> [<prefix>]
+
+Options:
+      -O       Output to stdout
+      -o       Output file name (use prefix if not set)
+      -u       Uncompressed BAM output
+      -f       Fast (only primary alignments)
+      -r       Working reads stored (with -f) [10000]
+      -l INT   Compression level [1]
+      -n INT   Number of temporary files [64]
+      -T PREFIX
+               Write temporary files to PREFIX.nnnn.bam
+      --no-PG  do not add a PG line
+      --input-fmt-option OPT[=VAL]
+               Specify a single input file format option in the form
+               of OPTION or OPTION=VALUE
+      --output-fmt FORMAT[,OPT[=VAL]]...
+               Specify output format (SAM, BAM, CRAM)
+      --output-fmt-option OPT[=VAL]
+               Specify a single output file format option in the form
+               of OPTION or OPTION=VALUE
+      --reference FILE
+               Reference sequence FASTA FILE [null]
+  -@, --threads INT
+               Number of additional threads to use [0]
+      --verbosity INT
+               Set level of verbosity
+  <prefix> is required unless the -o or -O options are used.
\ No newline at end of file
diff --git a/src/samtools/samtools_collate/script.sh b/src/samtools/samtools_collate/script.sh
new file mode 100644
index 00000000..25847a52
--- /dev/null
+++ b/src/samtools/samtools_collate/script.sh
@@ -0,0 +1,27 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+set -e
+
+[[ "$par_uncompressed" == "false" ]] && unset par_uncompressed
+[[ "$par_fast" == "false" ]] && unset par_fast
+[[ "$par_no_pg" == "false" ]] && unset par_no_pg
+
+samtools collate \
+    "$par_input" \
+    ${par_output:+-o "$par_output"} \
+    ${par_reference:+-T "$par_reference"} \
+    ${par_uncompressed:+-u} \
+    ${par_fast:+-f} \
+    ${par_working_reads:+-r "$par_working_reads"} \
+    ${par_compression:+-l "$par_compression"} \
+    ${par_nb_tmp_files:+-n "$par_nb_tmp_files"} \
+    ${par_tmp_prefix:+-T "$par_tmp_prefix"} \
+    ${par_no_pg:+-P} \
+    ${par_input_fmt_option:+-O "$par_input_fmt_option"} \
+    ${par_output_fmt:+-O "$par_output_fmt"} \
+    ${par_output_fmt_option:+-O "$par_output_fmt_option"}
+    
+exit 0
diff --git a/src/samtools/samtools_collate/test.sh b/src/samtools/samtools_collate/test.sh
new file mode 100644
index 00000000..c5a2e6e6
--- /dev/null
+++ b/src/samtools/samtools_collate/test.sh
@@ -0,0 +1,67 @@
+#!/bin/bash
+
+test_dir="${meta_resources_dir}/test_data"
+out_dir="${meta_resources_dir}/out"
+
+############################################################################################
+
+echo ">>> Test 1: $meta_functionality_name"
+"$meta_executable" \
+  --input "$test_dir/test.paired_end.sorted.bam" \
+  --output "$out_dir/collated.bam"
+
+echo ">>> Checking whether output exists"
+[ ! -f "$out_dir/collated.bam" ] && echo "File 'collated.bam' does not exist!" && exit 1
+
+echo ">>> Checking whether output is non-empty"
+[ ! -s "$out_dir/collated.bam" ] && echo "File 'collated.bam' is empty!" && exit 1
+
+echo ">>> Checking whether output is correct"
+diff <(samtools view "$out_dir/collated.bam") \
+    <(samtools view "$test_dir/collated.bam") || \
+    (echo "Output file collated.bam does not match expected output" && exit 1)
+
+############################################################################################
+
+echo ">>> Test 2: $meta_functionality_name with --fast option"
+"$meta_executable" \
+  --fast \
+  --input "$test_dir/test.paired_end.sorted.bam" \
+  --output "$out_dir/fast_collated.bam"
+
+echo ">>> Checking whether output exists"
+[ ! -f "$test_dir/fast_collated.bam" ] && echo "File 'fast_collated.bam' does not exist!" && exit 1
+
+echo ">>> Checking whether output is non-empty"
+[ ! -s "$test_dir/fast_collated.bam" ] && echo "File 'fast_collated.bam' is empty!" && exit 1
+
+echo ">>> Checking whether output is correct"
+diff <(samtools view "$test_dir/fast_collated.bam") \
+    <(samtools view "$test_dir/fast_collated.bam") || \
+    (echo "Output file fast_collated.bam does not match expected output" && exit 1)
+
+
+############################################################################################
+
+echo ">>> Test 3: $meta_functionality_name with compression"
+"$meta_executable" \
+  --compression 8 \
+  --input "$test_dir/test.paired_end.sorted.bam" \
+  --output "$out_dir/comp_collated.bam" 
+
+echo ">>> Checking whether output exists"
+[ ! -f "$out_dir/comp_collated.bam" ] && echo "File 'comp_collated.bam' does not exist!" && exit 1
+
+echo ">>> Checking whether output is non-empty"
+[ ! -s "$out_dir/comp_collated.bam" ] && echo "File 'comp_collated.bam' is empty!" && exit 1
+
+echo ">>> Checking whether output is correct"
+diff <(samtools view "$out_dir/comp_collated.bam") \
+    <(samtools view "$test_dir/comp_collated.bam") || \
+    (echo "Output file comp_collated.bam does not match expected output" && exit 1)
+
+############################################################################################
+
+echo ">>> All tests passed successfully."
+
+exit 0
diff --git a/src/samtools/samtools_collate/test_data/collated.bam b/src/samtools/samtools_collate/test_data/collated.bam
new file mode 100644
index 00000000..f6d5eab9
Binary files /dev/null and b/src/samtools/samtools_collate/test_data/collated.bam differ
diff --git a/src/samtools/samtools_collate/test_data/comp_collated.bam b/src/samtools/samtools_collate/test_data/comp_collated.bam
new file mode 100644
index 00000000..1f26cee4
Binary files /dev/null and b/src/samtools/samtools_collate/test_data/comp_collated.bam differ
diff --git a/src/samtools/samtools_collate/test_data/fast_collated.bam b/src/samtools/samtools_collate/test_data/fast_collated.bam
new file mode 100644
index 00000000..bb78fe5a
Binary files /dev/null and b/src/samtools/samtools_collate/test_data/fast_collated.bam differ
diff --git a/src/samtools/samtools_collate/test_data/script.sh b/src/samtools/samtools_collate/test_data/script.sh
new file mode 100755
index 00000000..f97a7efe
--- /dev/null
+++ b/src/samtools/samtools_collate/test_data/script.sh
@@ -0,0 +1,4 @@
+#!/bin/bash
+
+# dowload test data from nf-core module
+wget https://github.com/nf-core/test-datasets/raw/modules/data/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam
\ No newline at end of file
diff --git a/src/samtools/samtools_collate/test_data/test.paired_end.sorted.bam b/src/samtools/samtools_collate/test_data/test.paired_end.sorted.bam
new file mode 100644
index 00000000..85cccf14
Binary files /dev/null and b/src/samtools/samtools_collate/test_data/test.paired_end.sorted.bam differ
diff --git a/src/samtools/samtools_fastq/config.vsh.yaml b/src/samtools/samtools_fastq/config.vsh.yaml
new file mode 100644
index 00000000..39e926f0
--- /dev/null
+++ b/src/samtools/samtools_fastq/config.vsh.yaml
@@ -0,0 +1,189 @@
+name: samtools_fastq
+namespace: samtools
+description: Converts a SAM, BAM or CRAM to FASTQ format.
+keywords: [fastq, bam, sam, cram]
+links:
+  homepage: https://www.htslib.org/
+  documentation: https://www.htslib.org/doc/samtools-fastq.html
+  repository: https://github.com/samtools/samtools
+references: 
+  doi: [10.1093/bioinformatics/btp352, 10.1093/gigascience/giab008]
+license: MIT/Expat
+
+argument_groups:
+  - name: Inputs
+    arguments:
+      - name: --input
+        type: file
+        description: input SAM/BAM/CRAM file
+        required: true
+  - name: Outputs
+    arguments:
+      - name: --output
+        type: file
+        description: output FASTQ file
+        required: true
+        direction: output
+  - name: Options
+    arguments:
+      - name: --no_suffix
+        alternatives: -n
+        type: boolean_true
+        description: |
+          By default, either '/1' or '/2' is added to the end of read names where the corresponding 
+          READ1 or READ2 FLAG bit is set. Using -n causes read names to be left as they are.
+      - name: --suffix
+        alternatives: -N
+        type: boolean_true
+        description: |
+          Always add either '/1' or '/2' to the end of read names even when put into different files.
+      - name: --use_oq
+        alternatives: -O
+        type: boolean_true
+        description: |
+          Use quality values from OQ tags in preference to standard quality string if available.
+      - name: --singleton
+        alternatives: -s
+        type: file
+        description: write singleton reads to FILE.
+      - name: --copy_tags
+        alternatives: -t
+        type: boolean_true
+        description: |
+          Copy RG, BC and QT tags to the FASTQ header line, if they exist.
+      - name: --copy_tags_list
+        alternatives: -T
+        type: string
+        description: |
+          Specify a comma-separated list of tags to copy to the FASTQ header line, if they exist. 
+          TAGLIST can be blank or * to indicate all tags should be copied to the output. If using *, 
+          be careful to quote it to avoid unwanted shell expansion.
+      - name: --read1
+        alternatives: -1
+        type: file
+        description: |
+          Write reads with the READ1 FLAG set (and READ2 not set) to FILE instead of outputting them. 
+          If the -s option is used, only paired reads will be written to this file.
+        direction: output
+      - name: --read2
+        alternatives: -2
+        type: file
+        description: |
+          Write reads with the READ2 FLAG set (and READ1 not set) to FILE instead of outputting them. 
+          If the -s option is used, only paired reads will be written to this file.
+        direction: output
+      - name: --output_reads
+        alternatives: -o
+        type: file
+        description: |
+          Write reads with either READ1 FLAG or READ2 flag set to FILE instead of outputting them to stdout. 
+          This is equivalent to -1 FILE -2 FILE.
+        direction: output
+      - name: --output_reads_both
+        alternatives: -0
+        type: file
+        description: |
+          Write reads where the READ1 and READ2 FLAG bits set are either both set or both unset to FILE 
+          instead of outputting them.
+        direction: output
+      - name: --filter_flags
+        alternatives: -f
+        type: integer
+        description: |
+          Only output alignments with all bits set in INT present in the FLAG field. INT can be specified 
+          in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/) or in octal by beginning with `0' 
+          (i.e. /^0[0-7]+/).
+        default: 0
+      - name: --excl_flags
+        alternatives: -F
+        type: string
+        description: |
+          Do not output alignments with any bits set in INT present in the FLAG field. INT can be specified 
+          in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/) or in octal by beginning with `0' 
+          (i.e. /^0[0-7]+/). This defaults to 0x900 representing filtering of secondary and 
+          supplementary alignments.
+        default: 0x900
+      - name: --incl_flags
+        alternatives: --rf
+        type: string
+        description: |
+          Only output alignments with any bits set in INT present in the FLAG field. INT can be specified 
+          in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/), in octal by beginning with `0' 
+          (i.e. /^0[0-7]+/), as a decimal number not beginning with '0' or as a comma-separated list of 
+          flag names.
+        default: 0
+      - name: --excl_flags_all
+        alternatives: -G
+        type: integer
+        description: |
+          Only EXCLUDE reads with all of the bits set in INT present in the FLAG field. INT can be specified 
+          in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/) or in octal by beginning with `0' 
+          (i.e. /^0[0-7]+/).
+        default: 0
+      - name: --aux_tag
+        alternatives: -d
+        type: string
+        description: |
+          Only output alignments containing an auxiliary tag matching both TAG and VAL. If VAL is omitted 
+          then any value is accepted. The tag types supported are i, f, Z, A and H. "B" arrays are not 
+          supported. This is comparable to the method used in samtools view --tag. The option may be specified 
+          multiple times and is equivalent to using the --aux_tag_file option.
+      - name: --aux_tag_file
+        alternatives: -D
+        type: string
+        description: |
+          Only output alignments containing an auxiliary tag matching TAG and having a value listed in FILE. 
+          The format of the file is one line per value. This is equivalent to specifying --aux_tag multiple times.
+      - name: --casava
+        alternatives: -i
+        type: boolean_true
+        description: add Illumina Casava 1.8 format entry to header (eg 1:N:0:ATCACG)
+      - name: --compression
+        alternatives: -c
+        type: integer
+        description: set compression level when writing gz or bgzf fastq files.
+        default: 0
+      - name: --index1
+        alternatives: --i1
+        type: file
+        description: write first index reads to FILE.
+      - name: --index2
+        alternatives: --i2
+        type: file
+        description: write second index reads to FILE.
+      - name: --barcode_tag
+        type: string
+        description: Auxiliary tag to find index reads in.
+        default: BC
+      - name: --quality_tag
+        type: string
+        description: Auxiliary tag to find index quality in.
+        default: QT
+      - name: --index_format
+        type: string
+        description: |
+          string to describe how to parse the barcode and quality tags. For example:
+          [i14i8]: the first 14 characters are index 1, the next 8 characters are index 2.
+          [n8i14]: ignore the first 8 characters, and use the next 14 characters for index 1.
+          If the tag contains a separator, then the numeric part can be replaced with '*' to mean 
+          'read until the separator or end of tag', for example: [n*i*].
+
+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/samtools:1.19.2--h50ea8bc_1
+    setup:
+      - type: docker
+        run: |
+          samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
+          sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
+runners:
+- type: executable
+- type: nextflow
diff --git a/src/samtools/samtools_fastq/help.txt b/src/samtools/samtools_fastq/help.txt
new file mode 100644
index 00000000..39ed0d00
--- /dev/null
+++ b/src/samtools/samtools_fastq/help.txt
@@ -0,0 +1,80 @@
+```
+samtools fastq
+```
+
+Usage: samtools fastq [options...] <in.bam>
+
+Description:
+Converts a SAM, BAM or CRAM to FASTQ format.
+
+Options:
+  -0 FILE      write reads designated READ_OTHER to FILE
+  -1 FILE      write reads designated READ1 to FILE
+  -2 FILE      write reads designated READ2 to FILE
+  -o FILE      write reads designated READ1 or READ2 to FILE
+               note: if a singleton file is specified with -s, only
+               paired reads will be written to the -1 and -2 files.
+  -d, --tag TAG[:VAL]
+               only include reads containing TAG, optionally with value VAL
+  -f, --require-flags INT
+               only include reads with all  of the FLAGs in INT present [0]
+  -F, --excl[ude]-flags INT
+               only include reads with none of the FLAGs in INT present [0x900]
+      --rf, --incl[ude]-flags INT
+               only include reads with any  of the FLAGs in INT present [0]
+  -G INT       only EXCLUDE reads with all  of the FLAGs in INT present [0]
+  -n           don't append /1 and /2 to the read name
+  -N           always append /1 and /2 to the read name
+  -O           output quality in the OQ tag if present
+  -s FILE      write singleton reads designated READ1 or READ2 to FILE
+  -t           copy RG, BC and QT tags to the FASTQ header line
+  -T TAGLIST   copy arbitrary tags to the FASTQ header line, '*' for all
+  -v INT       default quality score if not given in file [1]
+  -i           add Illumina Casava 1.8 format entry to header (eg 1:N:0:ATCACG)
+  -c INT       compression level [0..9] to use when writing bgzf files [1]
+  --i1 FILE    write first index reads to FILE
+  --i2 FILE    write second index reads to FILE
+  --barcode-tag TAG
+               Barcode tag [BC]
+  --quality-tag TAG
+               Quality tag [QT]
+  --index-format STR
+               How to parse barcode and quality tags
+
+      --input-fmt-option OPT[=VAL]
+               Specify a single input file format option in the form
+               of OPTION or OPTION=VALUE
+      --reference FILE
+               Reference sequence FASTA FILE [null]
+  -@, --threads INT
+               Number of additional threads to use [0]
+      --verbosity INT
+               Set level of verbosity
+
+The files will be automatically compressed if the file names have a .gz
+or .bgzf extension.  The input to this program must be collated by name.
+Run 'samtools collate' or 'samtools sort -n' to achieve this.
+
+Reads are designated READ1 if FLAG READ1 is set and READ2 is not set.
+Reads are designated READ2 if FLAG READ1 is not set and READ2 is set.
+Otherwise reads are designated READ_OTHER (both flags set or both flags unset).
+Run 'samtools flags' for more information on flag codes and meanings.
+
+The index-format string describes how to parse the barcode and quality tags.
+It is made up of 'i' or 'n' followed by a length or '*'.  For example:
+   i14i8       The first 14 characters are index 1, the next 8 are index 2
+   n8i14       Ignore the first 8 characters, and use the next 14 for index 1
+
+If the tag contains a separator, then the numeric part can be replaced with
+'*' to mean 'read until the separator or end of tag', for example:
+   i*i*        Break the tag at the separator into index 1 and index 2
+   n*i*        Ignore the left part of the tag until the separator,
+               then use the second part of the tag as index 1
+
+Examples:
+To get just the paired reads in separate files, use:
+   samtools fastq -1 pair1.fq -2 pair2.fq -0 /dev/null -s /dev/null -n in.bam
+
+To get all non-supplementary/secondary reads in a single file, redirect
+the output:
+   samtools fastq in.bam > all_reads.fq
\ No newline at end of file
diff --git a/src/samtools/samtools_fastq/script.sh b/src/samtools/samtools_fastq/script.sh
new file mode 100644
index 00000000..367432f9
--- /dev/null
+++ b/src/samtools/samtools_fastq/script.sh
@@ -0,0 +1,40 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+set -e
+
+[[ "$par_no_suffix" == "false" ]] && unset par_no_suffix
+[[ "$par_suffix" == "false" ]] && unset par_suffix
+[[ "$par_use_oq" == "false" ]] && unset par_use_oq
+[[ "$par_copy_tags" == "false" ]] && unset par_copy_tags
+[[ "$par_casava" == "false" ]] && unset par_casava
+
+samtools fastq \
+    ${par_no_suffix:+-n} \
+    ${par_suffix:+-N} \
+    ${par_use_oq:+-O} \
+    ${par_singleton:+-s "$par_singleton"} \
+    ${par_copy_tags:+-t} \
+    ${par_copy_tags_list:+-T "$par_copy_tags_list"} \
+    ${par_read1:+-1 "$par_read1"} \
+    ${par_read2:+-2 "$par_read2"} \
+    ${par_output_reads:+-o "$par_output_reads"} \
+    ${par_output_reads_both:+-0 "$par_output_reads_both"} \
+    ${par_filter_flags:+-f "$par_filter_flags"} \
+    ${par_excl_flags:+-F "$par_excl_flags"} \
+    ${par_incl_flags:+--rf "$par_incl_flags"} \
+    ${par_excl_flags_all:+-G "$par_excl_flags_all"} \
+    ${par_aux_tag:+-d "$par_aux_tag"} \
+    ${par_aux_tag_file:+-D "$par_aux_tag_file"} \
+    ${par_casava:+-i} \
+    ${par_compression:+-c "$par_compression"} \
+    ${par_index1:+--i1 "$par_index1"} \
+    ${par_index2:+--i2 "$par_index2"} \
+    ${par_barcode_tag:+--barcode-tag "$par_barcode_tag"} \
+    ${par_quality_tag:+--quality-tag "$par_quality_tag"} \
+    ${par_index_format:+--index-format "$par_index_format"} \
+    "$par_input" \
+    > "$par_output"
+
diff --git a/src/samtools/samtools_fastq/test.sh b/src/samtools/samtools_fastq/test.sh
new file mode 100644
index 00000000..32ee3f5e
--- /dev/null
+++ b/src/samtools/samtools_fastq/test.sh
@@ -0,0 +1,96 @@
+#!/bin/bash
+
+test_dir="${meta_resources_dir}/test_data"
+out_dir="${meta_resources_dir}/out_data"
+
+############################################################################################
+
+echo ">>> Test 1: Convert all reads from a bam file to fastq format"
+"$meta_executable" \
+  --input "$test_dir/a.bam" \
+  --output "$out_dir/a.fq"
+
+echo ">>> Check if output file exists"
+[ ! -f "$out_dir/a.fq" ] && echo "Output file a.fq does not exist" && exit 1
+
+echo ">>> Check if output is empty"
+[ ! -s "$out_dir/a.fq" ] && echo "Output file a.fq is empty" && exit 1
+
+echo ">>> Check if output matches expected output"
+diff "$out_dir/a.fq" "$test_dir/a.fq" || 
+  (echo "Output file a.fq does not match expected output" && exit 1)
+
+rm "$out_dir/a.fq"
+
+############################################################################################
+
+echo ">>> Test 2: Convert all reads from a sam file to fastq format"
+"$meta_executable" \
+  --input "$test_dir/a.sam" \
+  --output "$out_dir/a.fq"
+
+echo ">>> Check if output file exists"
+[ ! -f "$out_dir/a.fq" ] && echo "Output file a.fq does not exist" && exit 1
+
+echo ">>> Check if output is empty"
+[ ! -s "$out_dir/a.fq" ] && echo "Output file a.fq is empty" && exit 1
+
+echo ">>> Check if output matches expected output"
+diff "$out_dir/a.fq" "$test_dir/a.fq" || 
+  (echo "Output file a.fq does not match expected output" && exit 1)
+
+rm "$out_dir/a.fq"
+
+############################################################################################
+
+echo ">>> Test 3: Output reads from bam file to separate files"
+
+"$meta_executable" \
+  --input "$test_dir/a.bam" \
+  --read1 "$out_dir/a.1.fq" \
+  --read2 "$out_dir/a.2.fq" \
+  --output "$out_dir/a.fq"
+
+echo ">>> Check if output files exist"
+[ ! -f "$out_dir/a.1.fq" ] && echo "Output file a.1.fq does not exist" && exit 1
+[ ! -f "$out_dir/a.2.fq" ] && echo "Output file a.2.fq does not exist" && exit 1
+[ ! -f "$out_dir/a.fq" ] && echo "Output file a.fq does not exist" && exit 1
+
+echo ">>> Check if output files are empty"
+[ ! -s "$out_dir/a.1.fq" ] && echo "Output file a.1.fq is empty" && exit 1
+[ ! -s "$out_dir/a.2.fq" ] && echo "Output file a.2.fq is empty" && exit 1
+# output should be empty since input has no singleton reads
+
+echo ">>> Check if output files match expected output"
+diff "$out_dir/a.1.fq" "$test_dir/a.1.fq" || 
+  (echo "Output file a.1.fq does not match expected output" && exit 1)
+diff "$out_dir/a.2.fq" "$test_dir/a.2.fq" ||
+  (echo "Output file a.2.fq does not match expected output" && exit 1)
+
+rm "$out_dir/a.1.fq" "$out_dir/a.2.fq" "$out_dir/a.fq"
+
+############################################################################################
+
+echo ">>> Test 4: Output only forward reads from bam file to fastq format"
+
+"$meta_executable" \
+  --input "$test_dir/a.sam" \
+  --excl_flags "0x80" \
+  --output "$out_dir/half.fq"
+
+echo ">>> Check if output file exists"
+[ ! -f "$out_dir/half.fq" ] && echo "Output file half.fq does not exist" && exit 1
+
+echo ">>> Check if output is empty"
+[ ! -s "$out_dir/half.fq" ] && echo "Output file half.fq is empty" && exit 1
+
+echo ">>> Check if output matches expected output"
+diff "$out_dir/half.fq" "$test_dir/half.fq" || 
+  (echo "Output file half.fq does not match expected output" && exit 1)
+
+rm "$out_dir/half.fq"
+
+############################################################################################
+
+echo "All tests succeeded!"
+exit 0
\ No newline at end of file
diff --git a/src/samtools/samtools_fastq/test_data/a.1.fq b/src/samtools/samtools_fastq/test_data/a.1.fq
new file mode 100644
index 00000000..03eaa725
--- /dev/null
+++ b/src/samtools/samtools_fastq/test_data/a.1.fq
@@ -0,0 +1,12 @@
+@a1
+AAAAAAAAAA
++
+**********
+@b1
+AAAAAAAAAA
++
+**********
+@c1
+AAAAAAAAAA
++
+**********
diff --git a/src/samtools/samtools_fastq/test_data/a.2.fq b/src/samtools/samtools_fastq/test_data/a.2.fq
new file mode 100644
index 00000000..03eaa725
--- /dev/null
+++ b/src/samtools/samtools_fastq/test_data/a.2.fq
@@ -0,0 +1,12 @@
+@a1
+AAAAAAAAAA
++
+**********
+@b1
+AAAAAAAAAA
++
+**********
+@c1
+AAAAAAAAAA
++
+**********
diff --git a/src/samtools/samtools_fastq/test_data/a.bam b/src/samtools/samtools_fastq/test_data/a.bam
new file mode 100644
index 00000000..dba1268a
Binary files /dev/null and b/src/samtools/samtools_fastq/test_data/a.bam differ
diff --git a/src/samtools/samtools_fastq/test_data/a.fq b/src/samtools/samtools_fastq/test_data/a.fq
new file mode 100644
index 00000000..d12c62ca
--- /dev/null
+++ b/src/samtools/samtools_fastq/test_data/a.fq
@@ -0,0 +1,24 @@
+@a1/1
+AAAAAAAAAA
++
+**********
+@b1/1
+AAAAAAAAAA
++
+**********
+@c1/1
+AAAAAAAAAA
++
+**********
+@a1/2
+AAAAAAAAAA
++
+**********
+@b1/2
+AAAAAAAAAA
++
+**********
+@c1/2
+AAAAAAAAAA
++
+**********
diff --git a/src/samtools/samtools_fastq/test_data/a.sam b/src/samtools/samtools_fastq/test_data/a.sam
new file mode 100644
index 00000000..aa8c77b3
--- /dev/null
+++ b/src/samtools/samtools_fastq/test_data/a.sam
@@ -0,0 +1,7 @@
+@SQ	SN:xx	LN:20
+a1	99	xx	1	1	10M	=	11	20	AAAAAAAAAA	**********
+b1	99	xx	1	1	10M	=	11	20	AAAAAAAAAA	**********
+c1	99	xx	1	1	10M	=	11	20	AAAAAAAAAA	**********
+a1	147	xx	11	1	10M	=	1	-20	TTTTTTTTTT	**********
+b1	147	xx	11	1	10M	=	1	-20	TTTTTTTTTT	**********
+c1	147	xx	11	1	10M	=	1	-20	TTTTTTTTTT	**********
diff --git a/src/samtools/samtools_fastq/test_data/half.fq b/src/samtools/samtools_fastq/test_data/half.fq
new file mode 100644
index 00000000..85a2b1c4
--- /dev/null
+++ b/src/samtools/samtools_fastq/test_data/half.fq
@@ -0,0 +1,12 @@
+@a1/1
+AAAAAAAAAA
++
+**********
+@b1/1
+AAAAAAAAAA
++
+**********
+@c1/1
+AAAAAAAAAA
++
+**********
diff --git a/src/samtools/samtools_fastq/test_data/script.sh b/src/samtools/samtools_fastq/test_data/script.sh
new file mode 100755
index 00000000..b59bc1bd
--- /dev/null
+++ b/src/samtools/samtools_fastq/test_data/script.sh
@@ -0,0 +1,11 @@
+#!/bin/bash
+
+# dowload test data from snakemake wrapper
+if [ ! -d /tmp/fastq_source ]; then
+  git clone --depth 1 --single-branch --branch master https://github.com/snakemake/snakemake-wrappers.git /tmp/fastq_source
+fi
+
+cp -r /tmp/fastq_source/bio/samtools/fastx/test/*.sam src/samtools/samtools_fastq/test_data/
+cp -r /tmp/fastq_source/bio/samtools/fastq/interleaved/test/mapped/*.bam src/samtools/samtools_fastq/test_data/
+cp -r /tmp/fastq_source/bio/samtools/fastq/interleaved/test/reads/*.fq src/samtools/samtools_fastq/test_data/
+cp -r /tmp/fastq_source/bio/samtools/fastq/separate/test/reads/*.fq src/samtools/samtools_fastq/test_data/
\ No newline at end of file
diff --git a/src/samtools/samtools_idxstats/config.vsh.yaml b/src/samtools/samtools_idxstats/config.vsh.yaml
index d5e32077..30f21348 100644
--- a/src/samtools/samtools_idxstats/config.vsh.yaml
+++ b/src/samtools/samtools_idxstats/config.vsh.yaml
@@ -7,7 +7,7 @@ links:
   documentation: https://www.htslib.org/doc/samtools-idxstats.html
   repository: https://github.com/samtools/samtools
 references: 
-  doi: 10.1093/bioinformatics/btp352, 10.1093/gigascience/giab008
+  doi: [10.1093/bioinformatics/btp352, 10.1093/gigascience/giab008]
 license: MIT/Expat
 
 argument_groups:
diff --git a/src/samtools/samtools_sort/config.vsh.yaml b/src/samtools/samtools_sort/config.vsh.yaml
index 7cd9ec48..a78800da 100644
--- a/src/samtools/samtools_sort/config.vsh.yaml
+++ b/src/samtools/samtools_sort/config.vsh.yaml
@@ -4,7 +4,7 @@ description: Sort SAM/BAM/CRAM file.
 keywords: [sort, bam, sam, cram]
 links:
   homepage: https://www.htslib.org/
-  documentation: https://www.htslib.org/doc/samtools-idxstats.html
+  documentation: https://www.htslib.org/doc/samtools-sort.html
   repository: https://github.com/samtools/samtools
 references: 
   doi: [10.1093/bioinformatics/btp352, 10.1093/gigascience/giab008]
diff --git a/src/samtools/samtools_stats/config.vsh.yaml b/src/samtools/samtools_stats/config.vsh.yaml
index 554a11e8..0d8f57a4 100644
--- a/src/samtools/samtools_stats/config.vsh.yaml
+++ b/src/samtools/samtools_stats/config.vsh.yaml
@@ -4,10 +4,10 @@ description: Reports alignment summary statistics for a BAM file.
 keywords: [statistics, counts, bam, sam, cram]
 links:
   homepage: https://www.htslib.org/
-  documentation: https://www.htslib.org/doc/samtools-idxstats.html
+  documentation: https://www.htslib.org/doc/samtools-stats.html
   repository: https://github.com/samtools/samtools
 references: 
-  doi: 10.1093/bioinformatics/btp352, 10.1093/gigascience/giab008
+  doi: [10.1093/bioinformatics/btp352, 10.1093/gigascience/giab008]
 license: MIT/Expat
 
 argument_groups:
diff --git a/src/samtools/samtools_view/config.vsh.yaml b/src/samtools/samtools_view/config.vsh.yaml
new file mode 100644
index 00000000..206b87ac
--- /dev/null
+++ b/src/samtools/samtools_view/config.vsh.yaml
@@ -0,0 +1,351 @@
+name: samtools_view
+namespace: samtools
+description: Views and converts SAM/BAM/CRAM files.
+keywords: [view, convert, bam, sam, cram]
+links:
+  homepage: https://www.htslib.org/
+  documentation: https://www.htslib.org/doc/samtools-view.html
+  repository: https://github.com/samtools/samtools
+references: 
+  doi: [10.1093/bioinformatics/btp352, 10.1093/gigascience/giab008]
+license: MIT/Expat
+
+argument_groups:
+  - name: Inputs
+    arguments:
+    - name: --input
+      type: file
+      description: Input SAM, BAM, or CRAM file.
+      required: true
+      must_exist: true
+    - name: --fai_reference
+      alternatives: -t
+      type: file
+      description: |
+        A tab-delimited FILE. Each line must contain the reference name in the first column
+        and the length of the reference in the second column, with one line for each distinct
+        reference. Any additional fields beyond the second column are ignored. This file also
+        defines the order of the reference sequences in sorting. If you run: `samtools faidx <ref.fa>',
+        the resulting index file <ref.fa>.fai can be used as this FILE.
+    - name: --reference
+      alternatives: -T
+      type: file
+      description: |
+        A FASTA format reference FILE, optionally compressed by bgzip and ideally indexed by samtools faidx.
+        If an index is not present one will be generated for you, if the reference file is local.
+        If the reference file is not local, but is accessed instead via an https://, s3:// or other URL,
+        the index file will need to be supplied by the server alongside the reference. It is possible to
+        have the reference and index files in different locations by supplying both to this option separated
+        by the string "##idx##", for example:
+        --reference ftp://x.com/ref.fa##idx##ftp://y.com/index.fa.fai
+        However, note that only the location of the reference will be stored in the output file header.
+        If this method is used to make CRAM files, the cram reader may not be able to find the index,
+        and may not be able to decode the file unless it can get the references it needs using a different
+        method.
+    - name: --target_file
+      alternatives: -L
+      type: file
+      description: |
+        Only output alignments overlapping the input BED FILE [null].
+    - name: --region_file
+      type: file
+      description: |
+        Use an index and multi-region iterator to only output alignments overlapping the input BED FILE.
+        Equivalent to --use_index --target_file FILE.
+    - name: --qname_file
+      alternatives: -N
+      type: file
+      description: |
+        Output only alignments with read names listed in FILE. If FILE starts with ^ then the operation is
+        negated and only outputs alignment with read groups not listed in FILE. It is not permissible to mix
+        both the filter-in and filter-out style syntax in the same command.
+      must_exist: true
+    - name: --read_group_file
+      alternatives: -R
+      type: file
+      description: |
+        Output alignments in read groups listed in FILE [null]. If FILE starts with ^ then the operation is
+        negated and only outputs alignment with read names not listed in FILE. It is not permissible to mix
+        both the filter-in and filter-out style syntax in the same command. Note that records with no RG tag
+        will also be output when using this option. This behaviour may change in a future release.
+      must_exist: true
+    - name: --use_index
+      alternatives: -M
+      type: boolean_true
+      description: |
+        Use the multi-region iterator on the union of a BED file and command-line region arguments.
+        This avoids re-reading the same regions of files so can sometimes be much faster. Note this also
+        removes duplicate sequences. Without this a sequence that overlaps multiple regions specified on
+        the command line will be reported multiple times. The usage of a BED file is optional and its path
+        has to be preceded by --target_file option.
+     
+  - name: Outputs
+    arguments:
+    - name: --output
+      alternatives: -o
+      type: file
+      description: Output to FILE instead of [stdout].
+      required: true
+      direction: output
+      example: output.bam
+    - name: --bam
+      alternatives: -b
+      type: boolean_true
+      description: Output in the BAM format.
+    - name: --cram
+      alternatives: -C
+      type: boolean_true
+      description: |
+        Output in the CRAM format (requires --reference).
+    - name: --fast
+      type: boolean_true
+      description: |
+        Enable fast compression. This also changes the default output format to BAM,
+        but this can be overridden by the explicit format options or using a filename
+        with a known suffix.
+    - name: --uncompressed
+      alternatives: -u
+      type: boolean_true
+      description: |
+        Output uncompressed data. This also changes the default output format to BAM,
+        but this can be overridden by the explicit format options or using a filename
+        with a known suffix.
+        This option saves time spent on compression/decompression and is thus preferred
+        when the output is piped to another samtools command.
+    - name: --with_header
+      type: boolean_true
+      description: |
+        Include the header in the output.
+    - name: --header_only
+      alternatives: -H
+      type: boolean_true
+      description: |
+        Output the header only.
+    - name: --no_header
+      type: boolean_true
+      description: |
+        When producing SAM format, output alignment records but not headers.
+        This is the default; the option can be used to reset the effect of 
+        --with_header/--header_only.
+    - name: --count
+      alternatives: -c
+      type: boolean_true
+      description: |
+        Instead of printing the alignments, only count them and print the total number.
+        All filter options, such as --require_flags, --excl_flags, and --min_MQ, are taken
+        into account. The --unmap option is ignored in this mode.
+    - name: --output_unselected
+      alternatives: -U
+      type: file
+      description: |
+        Write alignments that are not selected by the various filter options to FILE.
+        When this option is used, all alignments (or all alignments intersecting the regions
+        specified) are written to either the output file or this file, but never both.
+    - name: --unmap
+      alternatives: -p
+      type: boolean_true
+      description: |
+        Set the UNMAP flag on alignments that are not selected by the filter options.
+        These alignments are then written to the normal output. This is not compatible
+        with --output_unselected.
+    - name: --read_group
+      alternatives: -r
+      type: string
+      description: |
+        Output alignments in read group STR [null]. Note that records with no RG tag will also be output
+        when using this option. This behaviour may change in a future release.
+    - name: --tag 
+      alternatives: -d
+      type: string
+      description: |
+        Only output alignments with tag STR1 and associated value STR2, which can be a string or an integer
+        [null].
+        The value can be omitted, in which case only the tag is considered.
+        Note that this option does not specify a tag type. For example, use --tag XX:42 to select alignments
+        with an XX:i:42 field, not --tag XX:i:42.
+    - name: --tag_file
+      alternatives: -D
+      type: file
+      description: |
+        Only output alignments with tag STR and associated values listed in FILE.
+      must_exist: true
+    - name: --min_MQ
+      alternatives: -q
+      type: integer
+      description: |
+        Skip alignments with MAPQ smaller than INT.
+      default: 0
+    - name: --library
+      alternatives: -l
+      type: string
+      description: |
+        Only output alignments in library STR.
+    - name: --min_qlen
+      alternatives: -m
+      type: integer
+      description: |
+        Only output alignments with number of CIGAR bases consuming query sequence >= INT.
+      default: 0
+    - name: --expr
+      alternatives: -e
+      type: string
+      description: |
+        Only include alignments that match the filter expression STR. The syntax for these expressions is
+        described in the main samtools.
+    - name: --require_flags
+      alternatives: -f
+      type: string
+      description: |
+        Only output alignments with all bits set in FLAG present in the FLAG field. FLAG can be specified
+        in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/), in octal by beginning with `0' (i.e. /^0[0-7]+/),
+        as a decimal number not beginning with '0' or as a comma-separated list of flag names.
+    - name: --excl_flags
+      alternatives: -F
+      type: string
+      description: |
+        Do not output alignments with any bits set in FLAG present in the FLAG field. FLAG can be specified
+        in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/), in octal by beginning with `0' (i.e. /^0[0-7]+/),
+        as a decimal number not beginning with '0' or as a comma-separated list of flag names.
+    - name: --excl_all_flags
+      alternatives: -G
+      type: integer
+      description: |
+        Do not output alignments with all bits set in INT present in the FLAG field. This is the opposite of
+        --require_flags such that --require_flags 12 --exclude_all_flags 12 is the same as no filtering at all.
+        FLAG can be specified in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/), in octal by beginning with `0'
+        (i.e. /^0[0-7]+/), as a decimal number not beginning with '0' or as a comma-separated list of flag names.
+    - name: --incl_flags
+      alternatives: --rf
+      type: string
+      description: |
+        Only output alignments with any bit set in FLAG present in the FLAG field. FLAG can be specified in hex
+        by beginning with `0x' (i.e. /^0x[0-9A-F]+/), in octal by beginning with `0' (i.e. /^0[0-7]+/), as a decimal
+        number not beginning with '0' or as a comma-separated list of flag names.
+    - name: --remove_tag
+      alternatives: -x
+      type: string
+      description: |
+        Read tag(s) to exclude from output (repeatable) [null]. This can be a single tag or a comma separated list.
+        Alternatively the option itself can be repeated multiple times.
+        If the list starts with a `^' then it is negated and treated as a request to remove all tags except those in STR.
+        The list may be empty, so --remove_tag ^ will remove all tags.
+        Note that tags will only be removed from reads that pass filtering.
+    - name: --keep_tag
+      type: string
+      description: |
+        This keeps only tags listed in STR and is directly equivalent to --remove_tag ^STR. Specifying an empty list
+        will remove all tags. If both --keep_tag and --remove_tag are specified then --keep_tag has precedence.
+        Note that tags will only be removed from reads that pass filtering.
+    - name: --remove_B
+      alternatives: -B
+      type: boolean_true
+      description: |
+        Collapse the backward CIGAR operation.
+    - name: --add_flags
+      type: string
+      description: |
+        Adds flag(s) to read. FLAG can be specified in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/), in octal
+        by beginning with `0' (i.e. /^0[0-7]+/), as a decimal number not beginning with '0' or as a comma-separated
+        list of flag names.
+    - name: --remove_flags
+      type: string
+      description: |
+        Remove flag(s) from read. FLAG is specified in the same way as with the --add_flags option.
+    - name: --subsample
+      type: double
+      description: |
+        Output only a proportion of the input alignments, as specified by 0.0 <= FLOAT <= 1.0, which gives the fraction
+        of templates/pairs to be kept. This subsampling acts in the same way on all of the alignment records in the same
+        template or read pair, so it never keeps a read but not its mate.
+    - name: --subsample_seed
+      type: integer
+      description: |
+        Subsampling seed used to influence which subset of reads is kept. When subsampling data that has previously
+        been subsampled, be sure to use a different seed value from those used previously; otherwise more reads will
+        be retained than expected.
+      default: 0
+    - name: --fetch_pairs
+      alternatives: -P
+      type: boolean_true
+      description: |
+        Retrieve pairs even when the mate is outside of the requested region. Enabling this option also turns on the
+        multi-region iterator (-M). A region to search must be specified, either on the command-line, or using the
+        --target_file option. The input file must be an indexed regular file.
+        This option first scans the requested region, using the RNEXT and PNEXT fields of the records that have the
+        PAIRED flag set and pass other filtering options to find where paired reads are located. These locations are
+        used to build an expanded region list, and a set of QNAMEs to allow from the new regions. It will then make
+        a second pass, collecting all reads from the originally-specified region list together with reads from additional
+        locations that match the allowed set of QNAMEs. Any other filtering options used will be applied to all reads
+        found during this second pass.
+        As this option links reads using RNEXT and PNEXT, it is important that these fields are set accurately. Use
+        'samtools fixmate' to correct them if necessary.
+        Note that this option does not work with the --count, --output-unselected or --unmap options.
+    - name: --customized_index
+      alternatives: -X
+      type: boolean_true
+      description: |
+        Include customized index file as a part of arguments. See EXAMPLES section for sample of usage.
+    - name: --sanitize
+      alternatives: -z
+      type: string
+      description: |
+        Perform some sanity checks on the state of SAM record fields, fixing up common mistakes made by aligners.
+        These include soft-clipping alignments when they extend beyond the end of the reference, marking records as
+        unmapped when they have reference * or position 0, and ensuring unmapped alignments have no CIGAR or mapping
+        quality for unmapped alignments and no MD, NM, CG or SM tags.
+        FLAGs is a comma-separated list of keywords chosen from the following list.
+        
+        unmap: The UNMAPPED BAM flag. This is set for reads with position <= 0, reference name "*" or reads starting
+        beyond the end of the reference. Note CIGAR "*" is permitted for mapped data so does not trigger this.
+        
+        pos: Position and reference name fields. These may be cleared when a sequence is unmapped due to the
+        coordinates being beyond the end of the reference. Selecting this may change the sort order of the file,
+        so it is not a part of the on compound argument.
+        mqual: Mapping quality. This is set to zero for unmapped reads.
+        cigar: Modifies CIGAR fields, either by adding soft-clips for reads that overlap the end of the reference or
+               by clearing it for unmapped reads.
+        aux: For unmapped data, some auxiliary fields are meaningless and will be removed. These include NM, MD, CG and SM.
+        off: Perform no sanity fixing. This is the default
+        on: Sanitize data in a way that guarantees the same sort order. This is everything except for pos.
+        all: All sanitizing options, including pos.
+    - name: --no_PG
+      type: boolean_true
+      description: |
+        Do not add a @PG line to the header of the output file.
+    - name: --input_fmt_option
+      type: string
+      description: |
+        Specify a single input file format option in the form of OPTION or OPTION=VALUE.
+    - name: --output_fmt
+      alternatives: -O
+      type: string
+      description: |
+        Specify output format (SAM, BAM, CRAM).
+    - name: --output_fmt_option
+      type: string
+      description: |
+        Specify a single output file format option in the form of OPTION or OPTION=VALUE.
+    - name: --write_index
+      type: boolean_true
+      description: |
+        Automatically index the output files.
+
+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/samtools:1.19.2--h50ea8bc_1
+    setup:
+      - type: docker
+        run: |
+          samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
+          sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
+runners:
+- type: executable
+- type: nextflow
\ No newline at end of file
diff --git a/src/samtools/samtools_view/help.txt b/src/samtools/samtools_view/help.txt
new file mode 100644
index 00000000..753b1bc6
--- /dev/null
+++ b/src/samtools/samtools_view/help.txt
@@ -0,0 +1,80 @@
+```
+samtools view
+```
+
+Usage: samtools view [options] <in.bam>|<in.sam>|<in.cram> [region ...]
+
+Output options:
+  -b, --bam                  Output BAM
+  -C, --cram                 Output CRAM (requires -T)
+  -1, --fast                 Use fast BAM compression (and default to --bam)
+  -u, --uncompressed         Uncompressed BAM output (and default to --bam)
+  -h, --with-header          Include header in SAM output
+  -H, --header-only          Print SAM header only (no alignments)
+      --no-header            Print SAM alignment records only [default]
+  -c, --count                Print only the count of matching records
+  -o, --output FILE          Write output to FILE [standard output]
+  -U, --unoutput FILE, --output-unselected FILE
+                             Output reads not selected by filters to FILE
+  -p, --unmap                Set flag to UNMAP on reads not selected
+                             then write to output file.
+  -P, --fetch-pairs          Retrieve complete pairs even when outside of region
+Input options:
+  -t, --fai-reference FILE   FILE listing reference names and lengths
+  -M, --use-index            Use index and multi-region iterator for regions
+      --region[s]-file FILE  Use index to include only reads overlapping FILE
+  -X, --customized-index     Expect extra index file argument after <in.bam>
+
+Filtering options (Only include in output reads that...):
+  -L, --target[s]-file FILE  ...overlap (BED) regions in FILE
+  -N, --qname-file [^]FILE   ...whose read name is listed in FILE ("^" negates)
+  -r, --read-group STR       ...are in read group STR
+  -R, --read-group-file [^]FILE
+                             ...are in a read group listed in FILE
+  -d, --tag STR1[:STR2]      ...have a tag STR1 (with associated value STR2)
+  -D, --tag-file STR:FILE    ...have a tag STR whose value is listed in FILE
+  -q, --min-MQ INT           ...have mapping quality >= INT
+  -l, --library STR          ...are in library STR
+  -m, --min-qlen INT         ...cover >= INT query bases (as measured via CIGAR)
+  -e, --expr STR             ...match the filter expression STR
+  -f, --require-flags FLAG   ...have all of the FLAGs present
+  -F, --excl[ude]-flags FLAG ...have none of the FLAGs present
+      --rf, --incl-flags, --include-flags FLAG
+                             ...have some of the FLAGs present
+  -G FLAG                    EXCLUDE reads with all of the FLAGs present
+      --subsample FLOAT      Keep only FLOAT fraction of templates/read pairs
+      --subsample-seed INT   Influence WHICH reads are kept in subsampling [0]
+  -s INT.FRAC                Same as --subsample 0.FRAC --subsample-seed INT
+
+Processing options:
+      --add-flags FLAG       Add FLAGs to reads
+      --remove-flags FLAG    Remove FLAGs from reads
+  -x, --remove-tag STR
+               Comma-separated read tags to strip (repeatable) [null]
+      --keep-tag STR
+               Comma-separated read tags to preserve (repeatable) [null].
+               Equivalent to "-x ^STR"
+  -B, --remove-B             Collapse the backward CIGAR operation
+  -z, --sanitize FLAGS       Perform sanitity checking and fixing on records.
+                             FLAGS is comma separated (see manual). [off]
+
+General options:
+  -?, --help   Print long help, including note about region specification
+  -S           Ignored (input format is auto-detected)
+      --no-PG  Do not add a PG line
+      --input-fmt-option OPT[=VAL]
+               Specify a single input file format option in the form
+               of OPTION or OPTION=VALUE
+  -O, --output-fmt FORMAT[,OPT[=VAL]]...
+               Specify output format (SAM, BAM, CRAM)
+      --output-fmt-option OPT[=VAL]
+               Specify a single output file format option in the form
+               of OPTION or OPTION=VALUE
+  -T, --reference FILE
+               Reference sequence FASTA FILE [null]
+  -@, --threads INT
+               Number of additional threads to use [0]
+      --write-index
+               Automatically index the output files [off]
+      --verbosity INT
+               Set level of verbosity
diff --git a/src/samtools/samtools_view/script.sh b/src/samtools/samtools_view/script.sh
new file mode 100644
index 00000000..c3911b48
--- /dev/null
+++ b/src/samtools/samtools_view/script.sh
@@ -0,0 +1,71 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+set -e
+
+[[ "$par_bam" == "false" ]] && unset par_bam
+[[ "$par_cram" == "false" ]] && unset par_cram
+[[ "$par_fast" == "false" ]] && unset par_fast
+[[ "$par_uncompressed" == "false" ]] && unset par_uncompressed
+[[ "$par_with_header" == "false" ]] && unset par_with_header
+[[ "$par_header_only" == "false" ]] && unset par_header_only
+[[ "$par_no_header" == "false" ]] && unset par_no_header
+[[ "$par_count" == "false" ]] && unset par_count
+[[ "$par_unmap" == "false" ]] && unset par_unmap
+[[ "$par_use_index" == "false" ]] && unset par_use_index
+[[ "$par_fetch_pairs" == "false" ]] && unset par_fetch_pairs
+[[ "$par_customized_index" == "false" ]] && unset par_customized_index
+[[ "$par_no_PG" == "false" ]] && unset par_no_PG
+[[ "$par_write_index" == "false" ]] && unset par_write_index
+[[ "$par_remove_B" == "false" ]] && unset par_remove_B
+
+samtools view \
+    ${par_bam:+-b} \
+    ${par_cram:+-C} \
+    ${par_fast:+--fast} \
+    ${par_uncompressed:+-u} \
+    ${par_with_header:+--with-header} \
+    ${par_header_only:+-H} \
+    ${par_no_header:+--no-header} \
+    ${par_count:+-c} \
+    ${par_output:+-o "$par_output"} \
+    ${par_output_unselected:+-U "$par_output_unselected"} \
+    ${par_unmap:+-p "$par_unmap"} \
+    ${par_fetch_pairs:+-P "$par_fetch_pairs"} \
+    ${par_fai_reference:+-t "$par_fai_reference"} \
+    ${par_use_index:+-M "$par_use_index"} \
+    ${par_region_file:+--region-file "$par_region_file"} \
+    ${par_customized_index:+-X} \
+    ${par_target_file:+-L "$par_target_file"} \
+    ${par_qname_file:+-N "$par_qname_file"} \
+    ${par_read_group:+-r "$par_read_group"} \
+    ${par_read_group_file:+-R "$par_read_group_file"} \
+    ${par_tag:+-d "$par_tag"} \
+    ${par_tag_file:+-D "$par_tag_file"} \
+    ${par_min_MQ:+-q "$par_min_MQ"} \
+    ${par_library:+-l "$par_library"} \
+    ${par_min_qlen:+-m "$par_min_qlen"} \
+    ${par_expr:+-e "$par_expr"} \
+    ${par_require_flags:+-f "$par_require_flags"} \
+    ${par_excl_flags:+-F "$par_excl_flags"} \
+    ${par_incl_flags:+--rf "$par_incl_flags"} \
+    ${par_excl_all_flags:+-G "$par_excl_all_flags"} \
+    ${par_subsample:+--subsample "$par_subsample"} \
+    ${par_subsample_seed:+--subsample-seed "$par_subsample_seed"} \
+    ${par_add_flags:+--add-flags "$par_add_flags"} \
+    ${par_remove_flags:+--remove-flags "$par_remove_flags"} \
+    ${par_remove_tag:+-x "$par_remove_tag"} \
+    ${par_keep_tag:+--keep-tag "$par_keep_tag"} \
+    ${par_remove_B:+-B} \
+    ${par_sanitize:+-z "$par_sanitize"} \
+    ${par_input_fmt_option:+--input-fmt-option "$par_input_fmt_option"} \
+    ${par_output_fmt:+-O "$par_output_fmt"} \
+    ${par_output_fmt_option:+--output-fmt-option "$par_output_fmt_option"} \
+    ${par_reference:+-T "$par_reference"} \
+    ${par_write_index:+--write-index} \
+    ${par_no_PG:+--no-PG} \
+    "$par_input"
+
+exit 0
diff --git a/src/samtools/samtools_view/test.sh b/src/samtools/samtools_view/test.sh
new file mode 100644
index 00000000..1de29a7c
--- /dev/null
+++ b/src/samtools/samtools_view/test.sh
@@ -0,0 +1,87 @@
+#!/bin/bash
+
+test_dir="${meta_resources_dir}/test_data"
+temp_dir="${meta_resources_dir}/out"
+
+############################################################################################
+
+echo ">>> Test 1: Import SAM to BAM when @SQ lines are present in the header"
+"$meta_executable" \
+   --bam \
+   --output "$temp_dir/a.bam" \
+   --input "$test_dir/a.sam"
+
+echo ">>> Checking whether output exists"
+[ ! -f "$temp_dir/a.bam" ] && echo "File 'a.bam' does not exist!" && exit 1
+
+echo ">>> Checking whether output is non-empty"
+[ ! -s "$temp_dir/a.bam" ] && echo "File 'a.bam' is empty!" && exit 1
+
+echo ">>> Checking whether output is correct"
+# compare output of "samtools view" for both files
+diff <(samtools view "$temp_dir/a.bam") <(samtools view "$test_dir/a.bam") || \
+    (echo "Output file a.bam does not match expected output" && exit 1)
+
+############################################################################################
+
+echo ">>> Test 2: ${meta_functionality_name} with CRAM format output"
+
+"$meta_executable" \
+   --cram \
+   --output "$temp_dir/a.cram" \
+   --input "$test_dir/a.sam"
+
+echo ">>> Checking whether output exists"
+[ ! -f "$temp_dir/a.cram" ] && echo "File 'a.cram' does not exist!" && exit 1
+
+echo ">>> Checking whether output is non-empty"
+[ ! -s "$temp_dir/a.cram" ] && echo "File 'a.cram' is empty!" && exit 1
+
+echo ">>> Checking whether output is correct"
+# compare output of "samtools view" for both files
+diff <(samtools view "$temp_dir/a.cram") <(samtools view "$test_dir/a.cram") || \
+    (echo "Output file a.cram does not match expected output" && exit 1)
+
+############################################################################################
+
+echo ">>> Test 3: ${meta_functionality_name} with --count option"
+
+"$meta_executable" \
+   --count \
+   --output "$temp_dir/a.count" \
+   --input "$test_dir/a.sam"
+
+echo ">>> Checking whether output exists"
+[ ! -f "$temp_dir/a.count" ] && echo "File 'a.count' does not exist!" && exit 1
+
+echo ">>> Checking whether output is non-empty"
+[ ! -s "$temp_dir/a.count" ] && echo "File 'a.count' is empty!" && exit 1
+
+echo ">>> Checking whether output is correct"
+diff "$temp_dir/a.count" "$test_dir/a.count" || \
+    (echo "Output file a.count does not match expected output" && exit 1)
+
+############################################################################################
+
+echo ">>> Test 4: ${meta_functionality_name} including only the forward reads from read pairs"
+
+"$meta_executable" \
+   --output "$temp_dir/a.forward" \
+   --excl_flags "0x80" \
+   --input "$test_dir/a.sam"
+
+echo ">>> Checking whether output exists"
+[ ! -f "$temp_dir/a.forward" ] && echo "File 'a.forward' does not exist!" && exit 1
+
+echo ">>> Checking whether output is non-empty"
+[ ! -s "$temp_dir/a.forward" ] && echo "File 'a.forward' is empty!" && exit 1
+
+echo ">>> Checking whether output is correct"
+diff "$temp_dir/a.forward" "$test_dir/a.forward" || \
+    (echo "Output file a.forward does not match expected output" && exit 1)
+
+############################################################################################
+
+echo ">>> All test passed successfully"
+rm -rf "${temp_dir}"
+exit 0
\ No newline at end of file
diff --git a/src/samtools/samtools_view/test_data/a.bam b/src/samtools/samtools_view/test_data/a.bam
new file mode 100644
index 00000000..95b85b72
Binary files /dev/null and b/src/samtools/samtools_view/test_data/a.bam differ
diff --git a/src/samtools/samtools_view/test_data/a.count b/src/samtools/samtools_view/test_data/a.count
new file mode 100644
index 00000000..1e8b3149
--- /dev/null
+++ b/src/samtools/samtools_view/test_data/a.count
@@ -0,0 +1 @@
+6
diff --git a/src/samtools/samtools_view/test_data/a.cram b/src/samtools/samtools_view/test_data/a.cram
new file mode 100644
index 00000000..57fb3269
Binary files /dev/null and b/src/samtools/samtools_view/test_data/a.cram differ
diff --git a/src/samtools/samtools_view/test_data/a.forward b/src/samtools/samtools_view/test_data/a.forward
new file mode 100644
index 00000000..766d4f20
--- /dev/null
+++ b/src/samtools/samtools_view/test_data/a.forward
@@ -0,0 +1,3 @@
+a1	99	xx	1	1	10M	=	11	20	AAAAAAAAAA	**********
+b1	99	xx	1	1	10M	=	11	20	AAAAAAAAAA	**********
+c1	99	xx	1	1	10M	=	11	20	AAAAAAAAAA	**********
diff --git a/src/samtools/samtools_view/test_data/a.sam b/src/samtools/samtools_view/test_data/a.sam
new file mode 100644
index 00000000..aa8c77b3
--- /dev/null
+++ b/src/samtools/samtools_view/test_data/a.sam
@@ -0,0 +1,7 @@
+@SQ	SN:xx	LN:20
+a1	99	xx	1	1	10M	=	11	20	AAAAAAAAAA	**********
+b1	99	xx	1	1	10M	=	11	20	AAAAAAAAAA	**********
+c1	99	xx	1	1	10M	=	11	20	AAAAAAAAAA	**********
+a1	147	xx	11	1	10M	=	1	-20	TTTTTTTTTT	**********
+b1	147	xx	11	1	10M	=	1	-20	TTTTTTTTTT	**********
+c1	147	xx	11	1	10M	=	1	-20	TTTTTTTTTT	**********
diff --git a/src/samtools/samtools_view/test_data/script.sh b/src/samtools/samtools_view/test_data/script.sh
new file mode 100755
index 00000000..90918e44
--- /dev/null
+++ b/src/samtools/samtools_view/test_data/script.sh
@@ -0,0 +1,8 @@
+#!/bin/bash
+
+# dowload test data from snakemake wrapper
+if [ ! -d /tmp/view_source ]; then
+  git clone --depth 1 --single-branch --branch master https://github.com/snakemake/snakemake-wrappers.git /tmp/view_source
+fi
+
+cp -r /tmp/idxstats_source/bio/samtools/view/test/*.sam src/samtools/samtools_view/test_data
\ No newline at end of file