From 9429ec06db222ee00b615f267b04c23e6a4dd874 Mon Sep 17 00:00:00 2001 From: thanhleviet Date: Mon, 30 Oct 2023 21:33:12 +0000 Subject: [PATCH] deploy: 64efc18cd0eaac9ccdc93a3ce7cb140c7305bbb3 --- about/index.html | 2 +- categories/metagenomics/index.html | 4 ++-- categories/short-read/index.html | 2 +- categories/workflows/index.html | 6 +++--- code-of-conduct/index.html | 2 +- contact/index.html | 2 +- how-to/download-large-dataset/index.html | 2 +- how-to/filter-failed-jobs/index.html | 2 +- how-to/index.html | 6 +++--- how-to/upload-large-dataset/index.html | 2 +- privacy-policy/index.html | 2 +- sitemap.xml | 2 +- tags/assembly/index.html | 2 +- tags/howto/index.html | 6 +++--- tags/index/index.html | 4 ++-- tags/long-read/index.html | 2 +- tags/metagenomics/index.html | 4 ++-- tags/nanopore/index.html | 2 +- tags/privacy/index.html | 2 +- tags/profiling/index.html | 2 +- tags/short-read/index.html | 4 ++-- workflows/index.html | 6 +++--- workflows/long-read-assembly/index.html | 2 +- workflows/metagenomics/index.html | 4 ++-- workflows/taxonomic-profiling/index.html | 4 ++-- 25 files changed, 39 insertions(+), 39 deletions(-) diff --git a/about/index.html b/about/index.html index de65db6..342545a 100644 --- a/about/index.html +++ b/about/index.html @@ -1 +1 @@ -About

About Us

Made with ❤️ by the Hugo Bootstrap Theme team.

\ No newline at end of file +About

About Us

Made with ❤️ by the Hugo Bootstrap Theme team.

\ No newline at end of file diff --git a/categories/metagenomics/index.html b/categories/metagenomics/index.html index 27abbcd..8f104a8 100644 --- a/categories/metagenomics/index.html +++ b/categories/metagenomics/index.html @@ -8,13 +8,13 @@ profiling  howto  index  -Privacy 
featured image metagenomics-1.png

Short Read Metagenomics

+Privacy 
featured image metagenomics-1.png

Short Read Metagenomics

workflows metagenomics metagenomics short-read
This version is built with Go 1.21.1 which contains some relevant security fixes for the html/template package, see Issue 62196 and Issue 62197. This is the main reason Hugo 0.119.0 is released sooner rather than later. But this release also comes with a dependency refresh and some useful image processing improvements: A new general-purpose Process method and filter. A new Opacity filter. -Release …
featured image profilling-1.png

Taxonomic Profiling

+Release …
featured image profilling-1.png

Taxonomic Profiling

workflows metagenomics short-read diff --git a/categories/short-read/index.html b/categories/short-read/index.html index cc1a42a..be1c0eb 100644 --- a/categories/short-read/index.html +++ b/categories/short-read/index.html @@ -8,7 +8,7 @@ profiling  howto  index  -Privacy 
featured image profilling-1.png

Taxonomic Profiling

+Privacy 
featured image profilling-1.png

Taxonomic Profiling

workflows metagenomics short-read diff --git a/categories/workflows/index.html b/categories/workflows/index.html index 3e00932..07cf147 100644 --- a/categories/workflows/index.html +++ b/categories/workflows/index.html @@ -8,17 +8,17 @@ profiling  howto  index  -Privacy 
featured image metagenomics-1.png

Short Read Metagenomics

+Privacy 
featured image metagenomics-1.png

Short Read Metagenomics

workflows metagenomics metagenomics short-read
This version is built with Go 1.21.1 which contains some relevant security fixes for the html/template package, see Issue 62196 and Issue 62197. This is the main reason Hugo 0.119.0 is released sooner rather than later. But this release also comes with a dependency refresh and some useful image processing improvements: A new general-purpose Process method and filter. A new Opacity filter. -Release …
featured image dna.png

De-novo assembly long read

+Release …
featured image dna.png

De-novo assembly long read

workflows nanopore long-read -assembly
This is pseudo content generated by ChatGPT. De-novo Assembly for Long Read Nanopore Data De-novo assembly refers to the process of assembling genomes from scratch, without the use of a reference genome. This is particularly useful for studying novel organisms or strains. Long-read sequencing technologies, such as Oxford Nanopore, provide reads that are much longer than those generated by …
featured image profilling-1.png

Taxonomic Profiling

+assembly
This is pseudo content generated by ChatGPT. De-novo Assembly for Long Read Nanopore Data De-novo assembly refers to the process of assembling genomes from scratch, without the use of a reference genome. This is particularly useful for studying novel organisms or strains. Long-read sequencing technologies, such as Oxford Nanopore, provide reads that are much longer than those generated by …
featured image profilling-1.png

Taxonomic Profiling

workflows metagenomics short-read diff --git a/code-of-conduct/index.html b/code-of-conduct/index.html index d185d59..3304fb5 100644 --- a/code-of-conduct/index.html +++ b/code-of-conduct/index.html @@ -1,4 +1,4 @@ -Code of Conduct

Contributor Covenant Code of Conduct

Our Pledge

We as members, contributors, and leaders pledge to make participation in our +Code of Conduct

Contributor Covenant Code of Conduct

Our Pledge

We as members, contributors, and leaders pledge to make participation in our community a harassment-free experience for everyone, regardless of age, body size, visible or invisible disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, diff --git a/contact/index.html b/contact/index.html index a7ae3dd..754b32e 100644 --- a/contact/index.html +++ b/contact/index.html @@ -1 +1 @@ -Contact

Contact

Open an issue on GitHub.

\ No newline at end of file +Contact

Contact

Open an issue on GitHub.

\ No newline at end of file diff --git a/how-to/download-large-dataset/index.html b/how-to/download-large-dataset/index.html index 5a24eeb..5dc203d 100644 --- a/how-to/download-large-dataset/index.html +++ b/how-to/download-large-dataset/index.html @@ -1 +1 @@ -Download large files from Galaxy

If you want to download large files from Galaxy, you can use the tool Get Galaxy data. This tool will transfer data from the Galaxy to the location transfer/incoming/galaxy_staging/your-email@quadram.ac.uk

\ No newline at end of file +Download large files from Galaxy

If you want to download large files from Galaxy, you can use the tool Get Galaxy data. This tool will transfer data from the Galaxy to the location transfer/incoming/galaxy_staging/your-email@quadram.ac.uk

\ No newline at end of file diff --git a/how-to/filter-failed-jobs/index.html b/how-to/filter-failed-jobs/index.html index 57ce069..dc5bc79 100644 --- a/how-to/filter-failed-jobs/index.html +++ b/how-to/filter-failed-jobs/index.html @@ -1 +1 @@ -Filter failed jobs from a collection

In Galaxy, users can effectively manage collections with failed samples using the Filter failed datasets tool. This functionality allows for quick and easy removal of problematic samples, ensuring that only passed samples are used in next downstream analyses.

filter-failed-datasets

\ No newline at end of file +Filter failed jobs from a collection

In Galaxy, users can effectively manage collections with failed samples using the Filter failed datasets tool. This functionality allows for quick and easy removal of problematic samples, ensuring that only passed samples are used in next downstream analyses.

filter-failed-datasets

\ No newline at end of file diff --git a/how-to/index.html b/how-to/index.html index b34cce6..40f2b07 100644 --- a/how-to/index.html +++ b/how-to/index.html @@ -8,7 +8,7 @@ profiling  howto  index  -Privacy 
featured image download-galaxy.png

Download large files from Galaxy

-howto
Download large files to Galaxy via HPC location
featured image filter-failed-jobs.png

Filter failed jobs from a collection

-howto
Removing failed jobs from a collection
featured image upload-galaxy-1.png

Upload large files to Galaxy

+Privacy 
featured image download-galaxy.png

Download large files from Galaxy

+howto
Download large files to Galaxy via HPC location
featured image filter-failed-jobs.png

Filter failed jobs from a collection

+howto
Removing failed jobs from a collection
featured image upload-galaxy-1.png

Upload large files to Galaxy

howto
Uploading large files to Galaxy via HPC location
\ No newline at end of file diff --git a/how-to/upload-large-dataset/index.html b/how-to/upload-large-dataset/index.html index 2ce8940..d04385b 100644 --- a/how-to/upload-large-dataset/index.html +++ b/how-to/upload-large-dataset/index.html @@ -1 +1 @@ -Upload large files to Galaxy

You can transfer your data to transfer/incoming/galaxy_ftp/your-email@quadram.ac.uk

\ No newline at end of file +Upload large files to Galaxy

You can transfer your data to transfer/incoming/galaxy_ftp/your-email@quadram.ac.uk

\ No newline at end of file diff --git a/privacy-policy/index.html b/privacy-policy/index.html index b194c25..761315e 100644 --- a/privacy-policy/index.html +++ b/privacy-policy/index.html @@ -1 +1 @@ -Privacy Policy

Privacy Policy

TLDR: We do not use cookies and we do not collect any personal data.

Website visitors

  • No personal information is collected.
  • No information is stored in the browser.
  • No information is shared with, sent to or sold to third-parties.
  • No information is shared with advertising companies.
  • No information is mined and harvested for personal and behavioral trends.
  • No information is monetized.

Information we collect and what we use it for

The server hosting this site can collect the following information:

  • Page URL
  • HTTP Referrer
  • Browser
  • Operating system
  • Device type
  • IP address

All logs are discarded in every release.

Contact us

Contact us if you have any questions.

Effective Date: 15th May 2022

\ No newline at end of file +Privacy Policy

Privacy Policy

TLDR: We do not use cookies and we do not collect any personal data.

Website visitors

  • No personal information is collected.
  • No information is stored in the browser.
  • No information is shared with, sent to or sold to third-parties.
  • No information is shared with advertising companies.
  • No information is mined and harvested for personal and behavioral trends.
  • No information is monetized.

Information we collect and what we use it for

The server hosting this site can collect the following information:

  • Page URL
  • HTTP Referrer
  • Browser
  • Operating system
  • Device type
  • IP address

All logs are discarded in every release.

Contact us

Contact us if you have any questions.

Effective Date: 15th May 2022

\ No newline at end of file diff --git a/sitemap.xml b/sitemap.xml index aed939d..2310448 100644 --- a/sitemap.xml +++ b/sitemap.xml @@ -1 +1 @@ -/2023-10-30T21:30:58+00:00weekly0.5/categories/2023-10-30T21:30:58+00:00weekly0.5/tags/metagenomics/2023-10-30T21:30:58+00:00weekly0.5/categories/metagenomics/2023-10-30T21:30:58+00:00weekly0.5/workflows/metagenomics/2023-10-30T21:30:58+00:00weekly0.5/tags/short-read/2023-10-30T21:30:58+00:00weekly0.5/tags/2023-10-30T21:30:58+00:00weekly0.5/categories/workflows/2023-10-30T21:30:58+00:00weekly0.5/tags/assembly/2023-10-30T21:30:58+00:00weekly0.5/workflows/long-read-assembly/2023-10-30T21:30:58+00:00weekly0.5/tags/long-read/2023-10-30T21:30:58+00:00weekly0.5/tags/nanopore/2023-10-30T21:30:58+00:00weekly0.5/tags/profiling/2023-10-30T21:30:58+00:00weekly0.5/categories/short-read/2023-10-30T21:30:58+00:00weekly0.5/workflows/taxonomic-profiling/2023-10-30T21:30:58+00:00weekly0.5/about/2023-10-30T21:30:58+00:00weekly0.5/authors/2023-10-30T21:30:58+00:00weekly0.5/code-of-conduct/2023-10-30T21:30:58+00:00weekly0.5/contact/2023-10-30T21:30:58+00:00weekly0.5/authors/core-team/2023-10-30T21:30:58+00:00weekly0.5/how-to/download-large-dataset/2023-10-30T21:30:58+00:00weekly0.5/authors/filipe-carneiro/2023-10-30T21:30:58+00:00weekly0.5/how-to/filter-failed-jobs/2023-10-30T21:30:58+00:00weekly0.5/how-to/2023-10-30T21:30:58+00:00weekly0.5/tags/howto/2023-10-30T21:30:58+00:00weekly0.5/tags/index/2023-10-30T21:30:58+00:00weekly0.5/tags/privacy/2023-10-30T21:30:58+00:00weekly0.5/privacy-policy/2023-10-30T21:30:58+00:00weekly0.5/series/weekly0.5/authors/thanh.le-viet/2023-10-30T21:30:58+00:00weekly0.5/how-to/upload-large-dataset/2023-10-30T21:30:58+00:00weekly0.5/workflows/2023-10-30T21:30:58+00:00weekly0.5 \ No newline at end of file +/2023-10-30T21:33:06+00:00weekly0.5/categories/2023-10-30T21:33:06+00:00weekly0.5/tags/metagenomics/2023-10-30T21:33:06+00:00weekly0.5/categories/metagenomics/2023-10-30T21:33:06+00:00weekly0.5/workflows/metagenomics/2023-10-30T21:33:06+00:00weekly0.5/tags/short-read/2023-10-30T21:33:06+00:00weekly0.5/tags/2023-10-30T21:33:06+00:00weekly0.5/categories/workflows/2023-10-30T21:33:06+00:00weekly0.5/tags/assembly/2023-10-30T21:33:06+00:00weekly0.5/workflows/long-read-assembly/2023-10-30T21:33:06+00:00weekly0.5/tags/long-read/2023-10-30T21:33:06+00:00weekly0.5/tags/nanopore/2023-10-30T21:33:06+00:00weekly0.5/tags/profiling/2023-10-30T21:33:06+00:00weekly0.5/categories/short-read/2023-10-30T21:33:06+00:00weekly0.5/workflows/taxonomic-profiling/2023-10-30T21:33:06+00:00weekly0.5/about/2023-10-30T21:33:06+00:00weekly0.5/authors/2023-10-30T21:33:06+00:00weekly0.5/code-of-conduct/2023-10-30T21:33:06+00:00weekly0.5/contact/2023-10-30T21:33:06+00:00weekly0.5/authors/core-team/2023-10-30T21:33:06+00:00weekly0.5/how-to/download-large-dataset/2023-10-30T21:33:06+00:00weekly0.5/authors/filipe-carneiro/2023-10-30T21:33:06+00:00weekly0.5/how-to/filter-failed-jobs/2023-10-30T21:33:06+00:00weekly0.5/how-to/2023-10-30T21:33:06+00:00weekly0.5/tags/howto/2023-10-30T21:33:06+00:00weekly0.5/tags/index/2023-10-30T21:33:06+00:00weekly0.5/tags/privacy/2023-10-30T21:33:06+00:00weekly0.5/privacy-policy/2023-10-30T21:33:06+00:00weekly0.5/series/weekly0.5/authors/thanh.le-viet/2023-10-30T21:33:06+00:00weekly0.5/how-to/upload-large-dataset/2023-10-30T21:33:06+00:00weekly0.5/workflows/2023-10-30T21:33:06+00:00weekly0.5 \ No newline at end of file diff --git a/tags/assembly/index.html b/tags/assembly/index.html index 31053ab..8c27976 100644 --- a/tags/assembly/index.html +++ b/tags/assembly/index.html @@ -8,7 +8,7 @@ profiling  howto  index  -Privacy 
featured image dna.png

De-novo assembly long read

+Privacy 
featured image dna.png

De-novo assembly long read

workflows nanopore long-read diff --git a/tags/howto/index.html b/tags/howto/index.html index b0a5766..50d1af5 100644 --- a/tags/howto/index.html +++ b/tags/howto/index.html @@ -8,7 +8,7 @@ profiling  howto  index  -Privacy 
featured image download-galaxy.png

Download large files from Galaxy

-howto
Download large files to Galaxy via HPC location
featured image filter-failed-jobs.png

Filter failed jobs from a collection

-howto
Removing failed jobs from a collection
featured image upload-galaxy-1.png

Upload large files to Galaxy

+Privacy 
featured image download-galaxy.png

Download large files from Galaxy

+howto
Download large files to Galaxy via HPC location
featured image filter-failed-jobs.png

Filter failed jobs from a collection

+howto
Removing failed jobs from a collection
featured image upload-galaxy-1.png

Upload large files to Galaxy

howto
Uploading large files to Galaxy via HPC location
\ No newline at end of file diff --git a/tags/index/index.html b/tags/index/index.html index 693ef41..5a11b88 100644 --- a/tags/index/index.html +++ b/tags/index/index.html @@ -8,6 +8,6 @@ profiling  howto  index  -Privacy 

How-to

-index

Workflows

+Privacy 

How-to

+index

Workflows

index
\ No newline at end of file diff --git a/tags/long-read/index.html b/tags/long-read/index.html index 737dafc..71099e1 100644 --- a/tags/long-read/index.html +++ b/tags/long-read/index.html @@ -8,7 +8,7 @@ profiling  howto  index  -Privacy 
featured image dna.png

De-novo assembly long read

+Privacy 
featured image dna.png

De-novo assembly long read

workflows nanopore long-read diff --git a/tags/metagenomics/index.html b/tags/metagenomics/index.html index 4665ddf..d3f8364 100644 --- a/tags/metagenomics/index.html +++ b/tags/metagenomics/index.html @@ -8,13 +8,13 @@ profiling  howto  index  -Privacy 
featured image metagenomics-1.png

Short Read Metagenomics

+Privacy 
featured image metagenomics-1.png

Short Read Metagenomics

workflows metagenomics metagenomics short-read
This version is built with Go 1.21.1 which contains some relevant security fixes for the html/template package, see Issue 62196 and Issue 62197. This is the main reason Hugo 0.119.0 is released sooner rather than later. But this release also comes with a dependency refresh and some useful image processing improvements: A new general-purpose Process method and filter. A new Opacity filter. -Release …
featured image profilling-1.png

Taxonomic Profiling

+Release …
featured image profilling-1.png

Taxonomic Profiling

workflows metagenomics short-read diff --git a/tags/nanopore/index.html b/tags/nanopore/index.html index 73f7db2..b5f1482 100644 --- a/tags/nanopore/index.html +++ b/tags/nanopore/index.html @@ -8,7 +8,7 @@ profiling  howto  index  -Privacy 
featured image dna.png

De-novo assembly long read

+Privacy 
featured image dna.png

De-novo assembly long read

workflows nanopore long-read diff --git a/tags/privacy/index.html b/tags/privacy/index.html index 0fa2ac7..0bcd760 100644 --- a/tags/privacy/index.html +++ b/tags/privacy/index.html @@ -8,6 +8,6 @@ profiling  howto  index  -Privacy 

Privacy Policy

+Privacy 

Privacy Policy

Privacy
Privacy Policy TLDR: We do not use cookies and we do not collect any personal data. Website visitors No personal information is collected. No information is stored in the browser. No information is shared with, sent to or sold to third-parties. No information is shared with advertising companies. No information is mined and harvested for personal and behavioral trends. No information is monetized. …
\ No newline at end of file diff --git a/tags/profiling/index.html b/tags/profiling/index.html index 79c223c..2d2bdca 100644 --- a/tags/profiling/index.html +++ b/tags/profiling/index.html @@ -8,7 +8,7 @@ profiling  howto  index  -Privacy 
featured image profilling-1.png

Taxonomic Profiling

+Privacy 
featured image profilling-1.png

Taxonomic Profiling

workflows metagenomics short-read diff --git a/tags/short-read/index.html b/tags/short-read/index.html index d0d876b..8b9a1e6 100644 --- a/tags/short-read/index.html +++ b/tags/short-read/index.html @@ -8,13 +8,13 @@ profiling  howto  index  -Privacy 
featured image metagenomics-1.png

Short Read Metagenomics

+Privacy 
featured image metagenomics-1.png

Short Read Metagenomics

workflows metagenomics metagenomics short-read
This version is built with Go 1.21.1 which contains some relevant security fixes for the html/template package, see Issue 62196 and Issue 62197. This is the main reason Hugo 0.119.0 is released sooner rather than later. But this release also comes with a dependency refresh and some useful image processing improvements: A new general-purpose Process method and filter. A new Opacity filter. -Release …
featured image profilling-1.png

Taxonomic Profiling

+Release …
featured image profilling-1.png

Taxonomic Profiling

workflows metagenomics short-read diff --git a/workflows/index.html b/workflows/index.html index 33447f6..8e07eed 100644 --- a/workflows/index.html +++ b/workflows/index.html @@ -8,17 +8,17 @@ profiling  howto  index  -Privacy 
featured image metagenomics-1.png

Short Read Metagenomics

+Privacy 
featured image metagenomics-1.png

Short Read Metagenomics

workflows metagenomics metagenomics short-read
This version is built with Go 1.21.1 which contains some relevant security fixes for the html/template package, see Issue 62196 and Issue 62197. This is the main reason Hugo 0.119.0 is released sooner rather than later. But this release also comes with a dependency refresh and some useful image processing improvements: A new general-purpose Process method and filter. A new Opacity filter. -Release …
featured image dna.png

De-novo assembly long read

+Release …
featured image dna.png

De-novo assembly long read

workflows nanopore long-read -assembly
This is pseudo content generated by ChatGPT. De-novo Assembly for Long Read Nanopore Data De-novo assembly refers to the process of assembling genomes from scratch, without the use of a reference genome. This is particularly useful for studying novel organisms or strains. Long-read sequencing technologies, such as Oxford Nanopore, provide reads that are much longer than those generated by …
featured image profilling-1.png

Taxonomic Profiling

+assembly
This is pseudo content generated by ChatGPT. De-novo Assembly for Long Read Nanopore Data De-novo assembly refers to the process of assembling genomes from scratch, without the use of a reference genome. This is particularly useful for studying novel organisms or strains. Long-read sequencing technologies, such as Oxford Nanopore, provide reads that are much longer than those generated by …
featured image profilling-1.png

Taxonomic Profiling

workflows metagenomics short-read diff --git a/workflows/long-read-assembly/index.html b/workflows/long-read-assembly/index.html index 56ab5fc..6cb2f7d 100644 --- a/workflows/long-read-assembly/index.html +++ b/workflows/long-read-assembly/index.html @@ -1,4 +1,4 @@ -De-novo assembly long read

Bootstrap 5 3

De-novo Assembly for Long Read Nanopore Data

De-novo assembly refers to the process of assembling genomes from scratch, without the use of a reference genome. This is particularly useful for studying novel organisms or strains. Long-read sequencing technologies, such as Oxford Nanopore, provide reads that are much longer than those generated by short-read technologies, allowing for more accurate and contiguous genome assemblies.

Prerequisites

  • Quality Long-Read Data: Ensure that you have high-quality nanopore sequencing data.
  • Computational Resources: Access to a computer with sufficient memory and computational power.
  • Software Installation: Install required bioinformatics tools and software.

Steps

1. Data Quality Check

  • FastQC: Use FastQC or a similar tool to assess the quality of your sequencing data.

    fastqc input_reads.fastq
+De-novo assembly long read
    Bootstrap 5 3
    De-novo Assembly for Long Read Nanopore Data
    De-novo assembly refers to the process of assembling genomes from scratch, without the use of a reference genome. This is particularly useful for studying novel organisms or strains. Long-read sequencing technologies, such as Oxford Nanopore, provide reads that are much longer than those generated by short-read technologies, allowing for more accurate and contiguous genome assemblies.
    Prerequisites
    • Quality Long-Read Data: Ensure that you have high-quality nanopore sequencing data.
    • Computational Resources: Access to a computer with sufficient memory and computational power.
    • Software Installation: Install required bioinformatics tools and software.
    Steps
    1. Data Quality Check
    • FastQC: Use FastQC or a similar tool to assess the quality of your sequencing data.
      fastqc input_reads.fastq
 
    2. Read Trimming and Filtering
    • NanoFilt: Trim adapters and filter reads based on quality and length.
      cat input_reads.fastq | NanoFilt -q 7 --minlength 1000 > filtered_reads.fastq
 
    3. De-novo Assembly
    • Canu: Use Canu or a similar assembler for nanopore data.
      canu -p assembly -d assembly_out genomeSize=your_genome_size -nanopore-raw filtered_reads.fastq
 
    4. Assembly Polishing
    • Racon: Use Racon to correct errors in the assembly using the original reads.
      racon -t number_of_threads input_reads.fastq assembly.sam assembly.fasta > polished_assembly.fasta
diff --git a/workflows/metagenomics/index.html b/workflows/metagenomics/index.html
index 1e99be7..54e760d 100644
--- a/workflows/metagenomics/index.html
+++ b/workflows/metagenomics/index.html
@@ -2,7 +2,7 @@
 A new general-purpose Process method and filter. A new Opacity filter.
 Release Notes on GitHub.">
      Metagenomics
      This version is built with Go 1.21.1 which contains some relevant security fixes for the html/template package, see Issue 62196 and Issue 62197. This is the main reason Hugo 0.119.0 is released sooner rather than later. But this release also comes with a dependency refresh and some useful image processing improvements:
      A new general-purpose Process method and filter.
+Release Notes on GitHub.">
      Metagenomics
      This version is built with Go 1.21.1 which contains some relevant security fixes for the html/template package, see Issue 62196 and Issue 62197. This is the main reason Hugo 0.119.0 is released sooner rather than later. But this release also comes with a dependency refresh and some useful image processing improvements:
      A new general-purpose Process method and filter.
 A new Opacity filter.
      Release Notes on GitHub.
      
\ No newline at end of file
diff --git a/workflows/taxonomic-profiling/index.html b/workflows/taxonomic-profiling/index.html
index 4dd14ba..83411c6 100644
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 Input dataset collection:
 The workflow starts with an input dataset collection, which is likely to be a set of sequencing reads. Kraken2:
 A tool for taxonomic classification, which assigns taxonomic labels to short DNA sequences. Fastp:
-A tool for fast all-in-one preprocessing for FastQ files, including quality control and read trimming.">
      profilling
      Workflow Summary
      This workflow is designed for metagenomic profiling, involving steps for quality control, taxonomic classification, and data retrieval:
      1. Input dataset collection:
        • The workflow starts with an input dataset collection, which is likely to be a set of sequencing reads.
      2. Kraken2:
        • A tool for taxonomic classification, which assigns taxonomic labels to short DNA sequences.
      3. Fastp:
        • A tool for fast all-in-one preprocessing for FastQ files, including quality control and read trimming.
      4. Bracken:
        • A tool for estimating the abundance of species in DNA sequences from a metagenomics sample.
      5. Get Galaxy Data:
        • This tool appears multiple times in the workflow and seems to be used for retrieving and passing data between different steps in the workflow.
      6. HUMAnN3_QIB:
        • This tool is likely used for functional annotation of metagenomic data, although the specific details are not clear from the provided information.
      The workflow includes steps for data preprocessing, taxonomic classification, and abundance estimation, which are common tasks in metagenomic analysis. The repeated use of the “Get Galaxy Data” tool suggests that data from different steps are being retrieved and used in subsequent analyses, highlighting the interconnectivity of the workflow.
      Run the workflow
      Step NameTool VersionTool ID
      Input dataset collectionN/AN/A
      Kraken22.1.1+galaxy0toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy0
      Fastp0.23.2+galaxy0toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0
      Bracken2.2testtoolshed.g2.bx.psu.edu/repos/thanhlv/bracken/bracken/2.2
      Get Galaxy Data1.0.0get_galaxy_data
      Get Galaxy Data1.0.0get_galaxy_data
      HUMAnN3_QIB3.6.0+galaxy0humann3_qib
      Get Galaxy Data1.0.0get_galaxy_data
      Get Galaxy Data1.0.0get_galaxy_data
      Get Galaxy Data1.0.0get_galaxy_data
      Get Galaxy Data1.0.0get_galaxy_data
      Get Galaxy Data1.0.0get_galaxy_data
      
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+A tool for fast all-in-one preprocessing for FastQ files, including quality control and read trimming.">
      profilling
      Workflow Summary
      This workflow is designed for metagenomic profiling, involving steps for quality control, taxonomic classification, and data retrieval:
      1. Input dataset collection:
        • The workflow starts with an input dataset collection, which is likely to be a set of sequencing reads.
      2. Kraken2:
        • A tool for taxonomic classification, which assigns taxonomic labels to short DNA sequences.
      3. Fastp:
        • A tool for fast all-in-one preprocessing for FastQ files, including quality control and read trimming.
      4. Bracken:
        • A tool for estimating the abundance of species in DNA sequences from a metagenomics sample.
      5. Get Galaxy Data:
        • This tool appears multiple times in the workflow and seems to be used for retrieving and passing data between different steps in the workflow.
      6. HUMAnN3_QIB:
        • This tool is likely used for functional annotation of metagenomic data, although the specific details are not clear from the provided information.
      The workflow includes steps for data preprocessing, taxonomic classification, and abundance estimation, which are common tasks in metagenomic analysis. The repeated use of the “Get Galaxy Data” tool suggests that data from different steps are being retrieved and used in subsequent analyses, highlighting the interconnectivity of the workflow.
      Run the workflow
      Step NameTool VersionTool ID
      Input dataset collectionN/AN/A
      Kraken22.1.1+galaxy0toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy0
      Fastp0.23.2+galaxy0toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0
      Bracken2.2testtoolshed.g2.bx.psu.edu/repos/thanhlv/bracken/bracken/2.2
      Get Galaxy Data1.0.0get_galaxy_data
      Get Galaxy Data1.0.0get_galaxy_data
      HUMAnN3_QIB3.6.0+galaxy0humann3_qib
      Get Galaxy Data1.0.0get_galaxy_data
      Get Galaxy Data1.0.0get_galaxy_data
      Get Galaxy Data1.0.0get_galaxy_data
      Get Galaxy Data1.0.0get_galaxy_data
      Get Galaxy Data1.0.0get_galaxy_data
      
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