Multiple sequences as input and restructuring of output #204
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@nf-core-bot fix-linting |
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@nf-core-bot fix linting |
JoseEspinosa
requested changes
Oct 28, 2024
| @@ -1,3 +0,0 @@ | |||
| sequence,fasta | |||
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Why this file is removed?
It will need to be updated due to #205 instead
| pattern: '*.*' | ||
| ], | ||
| [ | ||
| path: { "${params.outdir}/alphafold2_${params.alphafold2_mode}/best_structures" }, |
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Suggested change
| path: { "${params.outdir}/alphafold2_${params.alphafold2_mode}/best_structures" }, | |
| path: { "${params.outdir}/alphafold2_${params.alphafold2_mode}/top_ranked_structures" }, |
| pattern: '*.*' | ||
| ], | ||
| [ | ||
| path: { "${params.outdir}/alphafold2_${params.alphafold2_mode}/best_structures" }, |
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Suggested change
| path: { "${params.outdir}/alphafold2_${params.alphafold2_mode}/best_structures" }, | |
| path: { "${params.outdir}/alphafold2_${params.alphafold2_mode}/top_ranked_structures" }, |
| pattern: '*.*' | ||
| ], | ||
| [ | ||
| path: { "${params.outdir}/colabfold_${params.colabfold_server}/best_structures" }, |
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Suggested change
| path: { "${params.outdir}/colabfold_${params.colabfold_server}/best_structures" }, | |
| path: { "${params.outdir}/colabfold_${params.colabfold_server}/top_ranked_structures" }, |
| pattern: '*.*' | ||
| ], | ||
| [ | ||
| path: { "${params.outdir}/colabfold_${params.colabfold_server}/best_structures" }, |
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Suggested change
| path: { "${params.outdir}/colabfold_${params.colabfold_server}/best_structures" }, | |
| path: { "${params.outdir}/colabfold_${params.colabfold_server}/top_ranked_structures" }, |
| pattern: '*' | ||
| ], | ||
| [ | ||
| path: { "${params.outdir}/esmfold/best_structures" }, |
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Suggested change
| path: { "${params.outdir}/esmfold/best_structures" }, | |
| path: { "${params.outdir}/esmfold/top_ranked_structures" }, |
| - `<SEQUENCE NAME>.alphafold.pdb` that is the structure with the highest pLDDT score (ranked first) | ||
| - `<SEQUENCE NAME>_plddt_mqc.tsv` that presents the pLDDT scores per residue for each of the 5 predicted models | ||
| - `alphafold_standard/` or `alphafold_split_msa_prediction/` based on the selected mode. Contain the computed MSAs, unrelaxed structures, relaxed structures, ranked structures, raw model outputs, prediction metadata, and section timings. Specifically, `<SEQUENCE NAME>_plddt_mqc.tsv` presents the pLDDT scores per residue for each of the 5 predicted models. | ||
| - `best_structures/<SEQUENCE NAME>.pdb` that is the structure with the highest pLDDT score per input (ranked first) |
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Suggested change
| - `best_structures/<SEQUENCE NAME>.pdb` that is the structure with the highest pLDDT score per input (ranked first) | |
| - `top_ranked_structures/<SEQUENCE NAME>.pdb` that is the structure with the highest pLDDT score per input (ranked first) |
| @@ -35,6 +35,8 @@ The samplesheet can have as many columns as you desire, however, there is a stri | |||
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| An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline. | |||
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| Each FASTA file is assumed to contain a single protein sequence unless you are using multimer mode. If you want to provide a FASTA file with multiple protein sequences, each to be folded individually, you can supply one or more FASTA files containing one or more sequences and use the --split_fasta parameter. In this case, each sequence in the FASTA file will be folded individually and in parallel, as if you had listed each sequence separately in the samplesheet. | |||
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Suggested change
| Each FASTA file is assumed to contain a single protein sequence unless you are using multimer mode. If you want to provide a FASTA file with multiple protein sequences, each to be folded individually, you can supply one or more FASTA files containing one or more sequences and use the --split_fasta parameter. In this case, each sequence in the FASTA file will be folded individually and in parallel, as if you had listed each sequence separately in the samplesheet. | |
| Each FASTA file should contain a single protein sequence unless using multimer mode. To provide a FASTA file with multiple sequences for individual folding, you can use one or more FASTA files with the --split_fasta parameter. This will treat each sequence in the FASTA file as a separate entry, folding them individually and in parallel, as if each sequence were listed separately in the samplesheet. |
| @@ -40,6 +40,11 @@ | |||
| "description": "Run on CPUs (default) or GPUs", | |||
| "fa_icon": "fas fa-microchip" | |||
| }, | |||
| "split_fasta": { | |||
| "type": "boolean", | |||
| "description": "Split input fasta file in multiple fasta files each of them containing one sequence to be folded", | |||
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Suggested change
| "description": "Split input fasta file in multiple fasta files each of them containing one sequence to be folded", | |
| "description": "Split input multi-fasta file in separated fasta files each of them containing one sequence to be folded", |
JoseEspinosa
requested changes
Oct 28, 2024
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I made some suggestions, but let's keep the PR open for discussion as we have to double-check how the different modes use multifasta:
- does
colabfoldprocess them in batch to improve accuracy? - does esmfold/colabfold use the sequence tag in the file?
- should we anyway implement the
split_fastaparameter for all modes so that users can process the sequences in parallel?
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Fixing issues #198 and #199
PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).