Update MAGs-generation to 0.5 #1221
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@@ -16,4 +16,4 @@ workflows: | |
| - name: "Patrick Bühler" | ||
| orcid: 0000-0003-2982-388X | ||
| - name: Santino Faack | ||
| orcid: 0009-0004-0382-2023 | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,66 +1,207 @@ | ||
| - 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: 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: null | ||
| Trimmed PacBio reads from grouped samples: null | ||
| Choose Assembler: MEGAHIT | ||
| 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' | ||
|
Collaborator
There was a problem hiding this comment. this will probably fail, I would go for 99 for the test
Contributor
Author
There was a problem hiding this comment. 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: '0.99' | ||
| Run COMEBin: false | ||
| outputs: | ||
| Full MultiQC Report: | ||
| asserts: | ||
| - that: has_text | ||
| text: "minigut_reads_binette_bin10_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: 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 | ||
| Trimmed PacBio reads from grouped samples: null | ||
| 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" | ||
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why 100 ?
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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