Skip to content

Update MAGs-generation to 0.5 #1221

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
SantaMcCloud wants to merge 9 commits into
base: main
Choose a base branch
from
Open

Update MAGs-generation to 0.5 #1221

Show file tree
Hide file tree
Changes from 3 commits
Commits
Show all changes
9 commits
Select commit Hold shift + click to select a range
f970f79
Update MAGs-generation to 0.5
SantaMcCloud Apr 26, 2026
baae55e
change labeling
SantaMcCloud Apr 26, 2026
a7f0444
typo and fix linting
SantaMcCloud Apr 26, 2026
c00d3f5
Update workflows/microbiome/mags-building/CHANGELOG.md
SantaMcCloud May 8, 2026
a5c9b49
swap from nested to rule based tool
SantaMcCloud May 9, 2026
2c58dec
fix linting
SantaMcCloud May 9, 2026
6b5b834
Update MAGs-generation.ga
SantaMcCloud May 9, 2026
f4a0b74
remove last nested
SantaMcCloud May 9, 2026
6fdf97c
fix wf
SantaMcCloud May 10, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
8 changes: 8 additions & 0 deletions workflows/microbiome/mags-building/CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,13 @@
# Changelog

## [0.5] - 2026-26-04

- **metaSPAdes** now can use optional long reads as input
- remove certain steps of the workflow into sub-workflows for example taxonomy annotation
Comment thread
SantaMcCloud marked this conversation as resolved.
Outdated
- Change COMEBin to be a optional binner

### Changed

## [0.4] - 2025-10-07

### Changed
Expand Down
190 changes: 164 additions & 26 deletions workflows/microbiome/mags-building/MAGs-generation-tests.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,66 +1,204 @@
- doc: Test for Metagenome-Assembled-Genomes-(MAGs)-generation
- doc: Test for Metagenome-Assembled-Genomes-(MAGs)-generation short read only
job:
Trimmed reads:
class: Collection
collection_type: list:paired
elements:
- class: Collection
type: paired
identifier: 50contig_reads
identifier: test_minigut
elements:
- class: File
identifier: forward
location: https://zenodo.org/records/15089018/files/MAG_reads_forward.fastqsanger.gz
location: https://zenodo.org/records/19235149/files/test_minigut_R1.fastq.gz
- class: File
identifier: reverse
location: https://zenodo.org/records/15089018/files/MAG_reads_reverse.fastqsanger.gz
Trimmed reads from grouped samples:
location: https://zenodo.org/records/19235149/files/test_minigut_R2.fastq.gz
Trimmed paired reads from grouped samples:
class: Collection
collection_type: list:paired
elements:
- class: Collection
type: paired
identifier: 50contig_reads
identifier: test_minigut
elements:
- class: File
identifier: forward
location: https://zenodo.org/records/15089018/files/MAG_reads_forward.fastqsanger.gz
- class: File
identifier: reverse
location: https://zenodo.org/records/15089018/files/MAG_reads_reverse.fastqsanger.gz
- class: File
identifier: forward
location: https://zenodo.org/records/19235149/files/test_minigut_R1.fastq.gz
- class: File
identifier: reverse
location: https://zenodo.org/records/19235149/files/test_minigut_R2.fastq.gz
Choose Assembler: MEGAHIT
Custom Assemblies: null
Minimum length of contigs to output: '200'
Minimum length of contigs to output: '100'
Read length (CONCOCT): '100'
Environment for the built-in model (SemiBin): global
Contamination weight (Binette): '2'
Contamination weight (Binette): '100'
Copy link
Copy Markdown
Collaborator

@paulzierep paulzierep May 8, 2026

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

why 100 ?

Copy link
Copy Markdown
Contributor Author

@SantaMcCloud SantaMcCloud May 8, 2026

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

If i use a low weight Binette favor complete bins which i dont want to happen because of dRep need more bins as input so i try to create a lot of "useless" bin for testing

CheckM2 Database: 1.0.2
Minimum MAG completeness percentage: '1'
Maximum MAG contamination percentage: '25'
Maximum MAG contamination percentage: '1'
Copy link
Copy Markdown
Collaborator

@paulzierep paulzierep May 8, 2026

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

this will probably fail, I would go for 99 for the test

Copy link
Copy Markdown
Contributor Author

@SantaMcCloud SantaMcCloud May 8, 2026

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

The test i did run this didnt failed since i wanted to create more MAGs so dRep get more input therefor i set the limit low.

Minimum MAG length: '100'
ANI threshold for dereplication: '0.95'
GTDB-tk Database: full_database_release_220_downloaded_2024-10-19
Bakta Database: V5.1_2024-01-19
AMRFinderPlus Database for Bakta: amrfinderplus_V3.12_2024-05-02.2
Run Bakta on MAGs: true
Run GTDB-Tk on MAGs: false
ANI threshold for dereplication: '0.99'
Run COMEBin: false
outputs:
Full MultiQC Report:
asserts:
- that: has_text
text: "50contig_reads_bin"
text: "minigut_reads_binette_bin10_fasta"
- that: has_text
text: "QUAST"
- that: has_text
text: "CheckM"
Assembly Report:
element_tests:
50contig_reads:
minigut_reads:
asserts:
- that: has_text
text: "All statistics are based on contigs of size"
- that: has_size
value: 372000
value: 373800
delta: 50000


Primary clustering dendrogram:
asserts:
- that: has_size
value: 169000
delta: 20000
Cluster Assignment:
asserts:
- that: has_text
text: "genome"
- that: has_text
text: "primary_cluster"
- that: has_text
text: "minigut_reads_binette_bin49.fasta"
Dereplicated Bins:
element_tests:
minigut_reads_binette_bin1.fasta:
asserts:
- that: has_size
value: 715700
delta: 10000
Merged CoverM Output:
asserts:
- that: has_text
text: "Genome"
- that: has_text
text: "minigut_reads_binette_bin10"
Merged Quast Output:
asserts:
- that: has_text
text: "Assembly"
- that: has_text
text: "118"
- that: has_text
text: "minigut_reads_binette_bin10.fasta"
- doc: Test for Metagenome-Assembled-Genomes-(MAGs)-generation long read test
job:
Trimmed reads:
class: Collection
collection_type: list:paired
elements:
- class: Collection
type: paired
identifier: test_minigut
elements:
- class: File
identifier: forward
location: https://zenodo.org/records/19235149/files/test_minigut_R1.fastq.gz
- class: File
identifier: reverse
location: https://zenodo.org/records/19235149/files/test_minigut_R2.fastq.gz
Trimmed paired reads from grouped samples:
class: Collection
collection_type: list:paired
elements:
- class: Collection
type: paired
identifier: test_minigut
elements:
- class: File
identifier: forward
location: https://zenodo.org/records/19235149/files/test_minigut_R1.fastq.gz
- class: File
identifier: reverse
location: https://zenodo.org/records/19235149/files/test_minigut_R2.fastq.gz
Trimmed nanopore reads from grouped samples:
class: Collection
collection_type: list
elements:
- class: File
identifier: minigut_reads
location: https://zenodo.org/records/19235149/files/minigut_reads.fastq.gz
Choose Assembler: metaSPAdes
Custom Assemblies: null
Minimum length of contigs to output: '100'
Read length (CONCOCT): '100'
Environment for the built-in model (SemiBin): global
Contamination weight (Binette): '100'
CheckM2 Database: 1.0.2
Minimum MAG completeness percentage: '1'
Maximum MAG contamination percentage: '1'
Minimum MAG length: '100'
ANI threshold for dereplication: '0.99'
Run COMEBin: false
outputs:
Full MultiQC Report:
asserts:
- that: has_text
text: "minigut_reads_binette_bin1_fasta"
- that: has_text
text: "QUAST"
- that: has_text
text: "CheckM"
Assembly Report:
element_tests:
minigut_reads:
asserts:
- that: has_text
text: "All statistics are based on contigs of size"
- that: has_size
value: 361400
delta: 50000
out cn:
element_tests:
minigut_reads:
asserts:
- that: has_size
value: 1736000
delta: 200000
Primary clustering dendrogram:
asserts:
- that: has_size
value: 131000
delta: 20000
Cluster Assignment:
asserts:
- that: has_text
text: "genome"
- that: has_text
text: "primary_cluster"
- that: has_text
text: "minigut_reads_binette_bin2.fasta"
Dereplicated Bins:
element_tests:
minigut_reads_binette_bin1.fasta:
asserts:
- that: has_size
value: 848000
delta: 10000
Merged CoverM Output:
asserts:
- that: has_text
text: "Genome"
- that: has_text
text: "unmapped"
- that: has_text
text: "minigut_reads_binette_bin2"
Merged Quast Output:
asserts:
- that: has_text
text: "Assembly"
- that: has_text
text: "4"
- that: has_text
text: "minigut_reads_binette_bin2.fasta"
Loading
Loading