Add Picrust2 #307
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Add Picrust2 #307
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erikrikarddaniel
approved these changes
Jul 28, 2021
CITATIONS.md
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| * [PICRUSt2](https://pubmed.ncbi.nlm.nih.gov/32483366/) | ||
| > Douglas GM, Maffei VJ, Zaneveld JR, Yurgel SN, Brown JR, Taylor CM, Huttenhower C, Langille MGI. PICRUSt2 for prediction of metagenome functions. Nat Biotechnol. 2020 Jun;38(6):685-688. doi: 10.1038/s41587-020-0548-6. PMID: 32483366; PMCID: PMC7365738. | ||
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| * PICRUSt2 is using in this pipeline by default [EPA-ng](https://pubmed.ncbi.nlm.nih.gov/30165689/) |
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Grammar is not correct in "is using in", do you mean "is used in" or maybe "is using"? If the latter, maybe "pipeline" is not correct, maybe just "PICRUSt2 is by default using [EPA-ng]"?
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Thanks, will change!
CITATIONS.md
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| * PICRUSt2 is using in this pipeline by default [EPA-ng](https://pubmed.ncbi.nlm.nih.gov/30165689/) | ||
| > Barbera P, Kozlov AM, Czech L, Morel B, Darriba D, Flouri T, Stamatakis A. EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences. Syst Biol. 2019 Mar 1;68(2):365-369. doi: 10.1093/sysbio/syy054. PMID: 30165689; PMCID: PMC6368480. | ||
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| * PICRUSt2 is using in this pipeline by default [MinPath](https://pubmed.ncbi.nlm.nih.gov/19680427/) |
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Thanks, will change!
docs/output.md
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| @@ -27,6 +27,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d | |||
| * [Alpha diversity indices](#alpha-diversity-indices) - Diversity within samples | |||
| * [Beta diversity indices](#beta-diversity-indices) - Diversity between samples (e.g. PCoA plots) | |||
| * [ANCOM](#ancom) - Differential abundance analysis | |||
| * [PICRUSt2](#picrust2) - Predicting functional abundances | |||
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Or "Predicting functional genes", "Predicting functional gene abundances"?
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I changed to "Predict the functional potential of a bacterial community"
nextflow_schema.json
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| @@ -103,6 +103,10 @@ | |||
| "description": "Naming of sequencing files", | |||
| "help_text": "Indicates the naming of sequencing files (default: `\"/*_R{1,2}_001.fastq.gz\"`).\n\nPlease note:\n\n1. The prepended slash (`/`) is required\n2. The star (`*`) is the required wildcard for sample names\n3. The curly brackets (`{}`) enclose the orientation for paired end reads, seperated by a comma (`,`).\n4. The pattern must be enclosed in quotes\n\nFor example for one sample (name: `1`) with forward (file: `1_a.fastq.gz`) and reverse (file: `1_b.fastq.gz`) reads in folder `data`:\n\n```bash\n--input \"data\" --extension \"/*_{a,b}.fastq.gz\"\n```" | |||
| }, | |||
| "picrust": { | |||
| "type": "boolean", | |||
| "description": "If functional abundances are predicted from the marker genes." | |||
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"Functional gene abundances predicted from phylogenetic relationships to marker gene organisms."?
workflows/ampliseq.nf
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| @@ -520,6 +521,18 @@ workflow AMPLISEQ { | |||
| } | |||
| } | |||
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| // | |||
| // MODULE: Predict functional abundances from marker genes with Picrust2 | |||
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"functional gene abundances"?
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The tests fail most likely because Picrust2 needs more than the 6GB RAM that is available for ci tests. It seems that the required RAM is independent of the ASV numbers but might be due to the databases that need to be loaded. I'll keep it in the |
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Den tors 29 juli 2021 kl 09:11 skrev Daniel Straub ***@***.***
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The tests fail most likely because Picrust2 needs more than the 6GB RAM
that is available for ci tests. It seems that the required RAM is
independent of the ASV numbers but might be due to the databases that need
to be loaded. I'll keep it in the test_full profile which is executed in
AWS on demand/release, but not in test_doubleprimers.
Probably the phylogenetic placement. The reference tree is just as large no
matter the number of ASVs.
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This solves the old issue #41
PR checklist
scrape_software_versions.pynf-core lint .).nextflow run . -profile test,docker).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).