update readmes for bcftools, htslib, and samtools

Program_Licenses.md

@@ -18,7 +18,7 @@ The licenses of the open-source software that is contained in these Docker image
 | Bakta | GNU GPLv3 | https://github.com/oschwengers/bakta/blob/main/LICENSE |
 | Bandage | GNU GPLv3 | https://github.com/rrwick/Bandage?tab=GPL-3.0-1-ov-file#readme |
 | BBTools | non-standard - see `licence.txt` and `legal.txt` that is included in docker image under `/bbmap/docs/`; Also on sourceforge repo for BBTools | https://jgi.doe.gov/disclaimer/ |
-| bcftools | MIT or **GNU GPLv3** (depends on how bcftools was compiled, I believe GNU GPLv3 applies here) | https://github.com/samtools/bcftools/blob/develop/LICENSE |
+| bcftools | MIT & **GNU GPLv3** | https://github.com/samtools/bcftools/blob/develop/LICENSE |
 | bedtools | MIT | https://github.com/arq5x/bedtools2/blob/master/LICENSE |
 | blast+ | Public Domain | https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/scripts/projects/blast/LICENSE |
 | bowtie2 | GNU GPLv3 | https://github.com/BenLangmead/bowtie2/blob/master/LICENSE |

README.md

@@ -119,7 +119,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [bakta](https://hub.docker.com/r/staphb/bakta) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bakta)](https://hub.docker.com/r/staphb/bakta) | <ul><li>[1.9.2](./bakta/1.9.2/)</li><li>[1.9.2-light](./bakta/1.9.2-5.1-light/)</li><li>[1.9.3](./bakta/1.9.3/)</li><li>[1.9.3-light](./bakta/1.9.3-5.1-light/)</li></ul> | https://github.com/oschwengers/bakta |
 | [bandage](https://hub.docker.com/r/staphb/bandage) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bandage)](https://hub.docker.com/r/staphb/bandage) | <ul><li>[0.8.1](./bandage/0.8.1/)</li></ul> | https://rrwick.github.io/Bandage/ |
 | [BBTools](https://hub.docker.com/r/staphb/bbtools/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bbtools)](https://hub.docker.com/r/staphb/bbtools) | <ul><li>[38.76](./bbtools/38.76/)</li><li>[38.86](./bbtools/38.86/)</li><li>[38.95](./bbtools/38.95/)</li><li>[38.96](./bbtools/38.96/)</li><li>[38.97](./bbtools/38.97/)</li><li>[38.98](./bbtools/38.98/)</li><li>[38.99](./bbtools/38.99/)</li><li>[39.00](./bbtools/39.00/)</li><li>[39.01](./bbtools/39.01/)</li><li>[39.06](./bbtools/39.06/)</li></ul> | https://jgi.doe.gov/data-and-tools/bbtools/ |
-| [bcftools](https://hub.docker.com/r/staphb/bcftools/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bcftools)](https://hub.docker.com/r/staphb/bcftools) | <ul><li>[1.10.2](./bcftools/1.10.2/)</li><li>[1.11](./bcftools/1.11/)</li><li>[1.12](./bcftools/1.12/)</li><li>[1.13](./bcftools/1.13/)</li><li>[1.14](./bcftools/1.14/)</li><li>[1.15](./bcftools/1.15/)</li><li>[1.16](./bcftools/1.16/)</li><li>[1.17](./bcftools/1.17/)</li><li>[1.18](bcftools/1.18/)</li><li>[1.19](./bcftools/1.19/)</li><li>[1.20](./bcftools/1.20/)</li></ul> | https://github.com/samtools/bcftools |
+| [bcftools](https://hub.docker.com/r/staphb/bcftools/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bcftools)](https://hub.docker.com/r/staphb/bcftools) | <ul><li>[1.10.2](./bcftools/1.10.2/)</li><li>[1.11](./bcftools/1.11/)</li><li>[1.12](./bcftools/1.12/)</li><li>[1.13](./bcftools/1.13/)</li><li>[1.14](./bcftools/1.14/)</li><li>[1.15](./bcftools/1.15/)</li><li>[1.16](./bcftools/1.16/)</li><li>[1.17](./bcftools/1.17/)</li><li>[1.18](bcftools/1.18/)</li><li>[1.19](./bcftools/1.19/)</li><li>[1.20](./bcftools/1.20/)</li><li>[1.20.c](./bcftools/1.20.c/)</li></ul> | https://github.com/samtools/bcftools |
 | [bedtools](https://hub.docker.com/r/staphb/bedtools/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bedtools)](https://hub.docker.com/r/staphb/bedtools) | <ul><li>2.29.2</li><li>2.30.0</li><li>[2.31.0](bedtools/2.31.0/)</li><li>[2.31.1](bedtools/2.31.1/)</li></ul> | https://bedtools.readthedocs.io/en/latest/ <br/>https://github.com/arq5x/bedtools2 |
 | [berrywood-report-env](https://hub.docker.com/r/staphb/berrywood-report-env/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/berrywood-report-env)](https://hub.docker.com/r/staphb/berrywood-report-env) | <ul><li>1.0</li></ul> | none |
 | [blast+](https://hub.docker.com/r/staphb/blast/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/blast)](https://hub.docker.com/r/staphb/blast) | <ul><li>[2.13.0](blast/2.13.0/)</li><li>[2.14.0](blast/2.14.0/)</li><li>[2.14.1](blast/2.14.1/)</li><li>[2.15.0](blast/2.15.0/)</li></ul> | https://www.ncbi.nlm.nih.gov/books/NBK279690/ |
@@ -172,7 +172,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [heatcluster](https://hub.docker.com/r/staphb/heatcluster) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/heatcluster)](https://hub.docker.com/r/staphb/heatcluster) | <ul><li>[1.0.2c](./heatcluster/1.0.2c/)</li></ul> | https://github.com/DrB-S/heatcluster/tree/main |
 | [hmmer](https://hub.docker.com/r/staphb/hmmer) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/hmmer)](https://hub.docker.com/r/staphb/hmmer) | <ul><li>[3.3](hmmer/3.3/)</li><li>[3.3.2](hmmer/3.3.2/)</li><li>[3.4](./hmmer/3.4/)</li></ul> | http://hmmer.org/ |
 | [homopolish](https://hub.docker.com/r/staphb/homopolish) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/homopolish)](https://hub.docker.com/r/staphb/homopolish) | <ul><li>0.4.1</li></ul> | https://github.com/ythuang0522/homopolish/ |
-| [htslib](https://hub.docker.com/r/staphb/htslib) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/htslib)](https://hub.docker.com/r/staphb/htslib) | <ul><li>[1.14](./htslib/1.14)</li><li>[1.15](./htslib/1.15)</li><li>[1.16](./htslib/1.16)</li><li>[1.17](./htslib/1.17)</li><li>[1.18](./htslib/1.18/)</li><li>[1.19](./htslib/1.19/)</li><li>[1.20](./htslib/1.20/)</li></ul> | https://www.htslib.org/ |
+| [htslib](https://hub.docker.com/r/staphb/htslib) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/htslib)](https://hub.docker.com/r/staphb/htslib) | <ul><li>[1.14](./htslib/1.14)</li><li>[1.15](./htslib/1.15)</li><li>[1.16](./htslib/1.16)</li><li>[1.17](./htslib/1.17)</li><li>[1.18](./htslib/1.18/)</li><li>[1.19](./htslib/1.19/)</li><li>[1.20](./htslib/1.20/)</li><li>[1.20.c](./htslib/1.20.c/)</li></ul> | https://www.htslib.org/ |
 | [iqtree](https://hub.docker.com/r/staphb/iqtree/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/iqtree)](https://hub.docker.com/r/staphb/iqtree) | <ul><li>1.6.7</li></ul> | http://www.iqtree.org/ |
 | [iqtree2](https://hub.docker.com/r/staphb/iqtree2/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/iqtree2)](https://hub.docker.com/r/staphb/iqtree2) | <ul><li>2.1.2</li><li>2.2.2.2</li><li>[2.2.2.6](iqtree2/2.2.2.6/)</li><li>[2.2.2.7](iqtree2/2.2.2.7/)</li><li>[2.3.1](iqtree2/2.3.1/)</li><li>[2.3.4](iqtree2/2.3.4/)</li></ul> | http://www.iqtree.org/ |
 | [IPA](https://hub.docker.com/r/staphb/pbipa) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/pbipa)](https://hub.docker.com/r/staphb/pbipa) | <ul><li>[1.8.0](./pbipa/1.8.0/)</li></ul> | https://github.com/PacificBiosciences/pbipa |
@@ -255,7 +255,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [Roary](https://hub.docker.com/r/staphb/roary/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/roary)](https://hub.docker.com/r/staphb/roary) | <ul><li>3.12.0</li><li>3.13.0</li></ul> | https://github.com/sanger-pathogens/Roary |
 | [SalmID](https://hub.docker.com/r/staphb/salmid) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/salmid)](https://hub.docker.com/r/staphb/salmid) | <ul><li>0.1.23</li></ul> | https://github.com/hcdenbakker/SalmID |
 | [samclip](https://hub.docker.com/r/staphb/samclip) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/samclip)](https://hub.docker.com/r/staphb/samclip) | <ul><li>[0.4.0](./samclip/0.4.0/)</li></ul>| https://github.com/tseemann/samclip |
-| [Samtools](https://hub.docker.com/r/staphb/samtools) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/samtools)](https://hub.docker.com/r/staphb/samtools) | <ul><li>[1.9](./samtools/1.9/)</li><li>[1.10](./samtools/1.10/)</li><li>[1.11](./samtools/1.11/)</li><li>[1.12](./samtools/1.12/)</li><li>[1.13](./samtools/1.13/)</li><li>[1.14](./samtools/1.14/)</li><li>[1.15](./samtools/1.15/)</li><li>[1.16](./samtools/1.16/)</li><li>[1.16.1](./samtools/1.16.1/)</li><li>[1.17](./samtools/1.17/)</li><li>[1.17-2023-06](./samtools/1.17-2023-06/)</li><li>[1.18](./samtools/1.18/)</li><li>[1.19](./samtools/1.19/)</li><li>[1.20](./samtools/1.20/)</li></ul> | https://github.com/samtools/samtools |
+| [Samtools](https://hub.docker.com/r/staphb/samtools) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/samtools)](https://hub.docker.com/r/staphb/samtools) | <ul><li>[1.9](./samtools/1.9/)</li><li>[1.10](./samtools/1.10/)</li><li>[1.11](./samtools/1.11/)</li><li>[1.12](./samtools/1.12/)</li><li>[1.13](./samtools/1.13/)</li><li>[1.14](./samtools/1.14/)</li><li>[1.15](./samtools/1.15/)</li><li>[1.16](./samtools/1.16/)</li><li>[1.16.1](./samtools/1.16.1/)</li><li>[1.17](./samtools/1.17/)</li><li>[1.17-2023-06](./samtools/1.17-2023-06/)</li><li>[1.18](./samtools/1.18/)</li><li>[1.19](./samtools/1.19/)</li><li>[1.20](./samtools/1.20/)</li><li>[1.20.c](./samtools/1.20.c/)</li></ul> | https://github.com/samtools/samtools |
 | [SeqKit](https://hub.docker.com/r/staphb/SeqKit) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/seqkit)](https://hub.docker.com/r/staphb/seqkit) | <ul><li>[2.3.1](./seqkit/2.3.1/)</li><li>[2.6.1](./seqkit/2.6.1/)</li><li>[2.7.0](./seqkit/2.7.0/)</li><li>[2.8.0](./seqkit/2.8.0/)</li><li>[2.8.1](./seqkit/2.8.1/)</li><li>[2.8.2](./seqkit/2.8.2/)</li></ul> | https://github.com/shenwei356/seqkit |
 | [SeqSero](https://hub.docker.com/r/staphb/seqsero/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/seqsero)](https://hub.docker.com/r/staphb/seqsero) | <ul><li>1.0.1</li></ul> | https://github.com/denglab/SeqSero |
 | [SeqSero2](https://hub.docker.com/r/staphb/seqsero2/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/seqsero2)](https://hub.docker.com/r/staphb/seqsero2) | <ul><li>[0.1.0](./seqsero2/0.1.0/)</li><li>[1.0.0](./seqsero2/1.0.0/)</li><li>[1.0.2](./seqsero2/1.0.2/)</li><li>[1.1.0](./seqsero2/1.1.0/)</li><li>[1.1.1](./seqsero2/1.1.1/)</li><li>[1.2.1](./seqsero2/1.2.1/)</li><li>[1.3.1](./seqsero2/1.3.1/)</li></ul> | https://github.com/denglab/SeqSero2/ |

bcftools/1.20.c/README.md

@@ -1,13 +1,25 @@
 # bcftools container
 
-Main tool:
+Main tool: [bcftools](https://github.com/samtools/bcftools)
 
-* [bcftools](https://github.com/samtools/bcftools)
+Code repository: https://github.com/samtools/bcftools
+
+Basic information on how to use this tool:
+- executable: bcftools
+- help: --help
+- version: --version
+- description: BCFtools is a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF. 
+
+Additional information:
+
+This container includes bcftools v1.20 compiled with **libdeflate** for a better cloud performance. Also, "polysomy" and plugins are enabled in this image.
+
+Full documentation: https://samtools.github.io/bcftools/howtos/index.html
 
 ## Example Usage
 
 ```bash
 bcftools mpileup -A -d 200 -B -Q 0 -f {reference_genome} {bam} | bcftools call -mv -Ov -o bcftools_variants/{sample}.vcf
 ```
 
-Better documentation can be found at [https://www.htslib.org/doc/bcftools.html](https://www.htslib.org/doc/bcftools.html)
+

htslib/1.20.c/README.md

@@ -1,14 +1,25 @@
 # htslib container
 
-Main tool:
+Main tool: [htslib](https://www.htslib.org/)
 
-* [https://www.htslib.org/](https://www.htslib.org/)
-* [GitHub](https://github.com/samtools/htslib)
+Code repository: https://github.com/samtools/htslib
 
 Additional tools:
 
 * perl 5.34.0
 
+Basic information on how to use this tool:
+- executable: htsfile
+- help: --help
+- version: --version
+- description: The htsfile utility attempts to identify what kind of high-throughput sequencing data files the specified files are, and provides minimal viewing capabilities for some kinds of data file.
+
+Additional information:
+
+This container includes htslib v1.20 compiled with **libdeflate** for a better cloud performance.
+
+Full documentation: https://www.htslib.org/doc/samtools.html
+
 ## Example Usage
 
 ```bash
@@ -22,5 +33,3 @@ ce_tag_padded.sam:      SAM version 1.4 sequence text
 # compresses sample.fastq to sample.fastq.gz in BGZF format (blocked GNU Zip Format)
 $ bgzip sample.fastq
 ```
-
-Better documentation can be found at [https://www.htslib.org/doc/samtools.html](https://www.htslib.org/doc/samtools.html)

samtools/1.20.c/README.md

@@ -1,14 +1,25 @@
 # samtools container
 
-Main tool:
+Main tool: [samtools](https://www.htslib.org/)
 
-* [https://www.htslib.org/](https://www.htslib.org/)
-* [GitHub](https://github.com/samtools/samtools)
+Code repository: https://github.com/samtools/samtools
 
 Additional tools:
 
 * perl 5.34.0
 
+Basic information on how to use this tool:
+- executable: samtools
+- help: --help
+- version: --version
+- description: Utilities for the Sequence Alignment/Map (SAM) format
+
+Additional information:
+
+This container includes samtools v1.20 compiled with **libdeflate** for a better cloud performance.
+
+Full documentation: https://www.htslib.org/doc/samtools.html
+
 ## Example Usage
 
 ```bash
@@ -17,4 +28,3 @@ samtools ampliconclip -b bed.file input.bam
 samtools sort -T /tmp/aln.sorted -o aln.sorted.bam aln.bam
 ```
 
-Better documentation can be found at [https://www.htslib.org/doc/samtools.html](https://www.htslib.org/doc/samtools.html)