RF2NA: use multi-chain FASTA input and drop interactions sheet #420
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
|
JoseEspinosa
requested changes
Dec 5, 2025
Member
JoseEspinosa
left a comment
JoseEspinosa
left a comment
There was a problem hiding this comment.
Very nice! Only few small suggestions
Comment on lines
14
to
15
| tuple val(meta), path("rf2na_input", type: "dir"), emit: prepared_input | ||
| path "versions.yml" , emit: versions |
Member
There was a problem hiding this comment.
Suggested change
| tuple val(meta), path("rf2na_input", type: "dir"), emit: prepared_input | |
| path "versions.yml" , emit: versions | |
| tuple val(meta), path("rf2na_input", type: "dir"), emit: rf2na_input | |
| path "versions.yml" , emit: versions |
|
|
||
| script: | ||
| """ | ||
| python3 - <<'PY' "${meta.id}" "${fasta}" |
Member
There was a problem hiding this comment.
For using the script this way and given it is quite long, I will put it in the bin folder instead and only call it here:
fasta_to_rosettafold.py "${meta.id}" "${fasta}"
Actually, probably we should join the different scripts that perform this for different modes in a single one in bin, but this will be for a follow-up PR
| @@ -0,0 +1,4 @@ | |||
| >DNA_binding_protein type=protein | |||
Member
There was a problem hiding this comment.
I have opened a PR in https://github.com/nf-core/test-datasets/tree/proteinfold to put all these files here
So please get rid of them here.
conf/test_rosettafold2na.config
Outdated
| rosettafold2na_db = "${projectDir}/assets/dummy_db_dir" | ||
| input = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.2/samplesheet.csv' | ||
| interactions = params.pipelines_testdata_base_path + 'proteinfold/testdata/interactions/v1.2/interactions.csv' | ||
| input = "${projectDir}/assets/examples/rosettafold2na/samplesheet.csv" |
Member
There was a problem hiding this comment.
After, nf-core/test-datasets#1816 is merged, please update:
Suggested change
| input = "${projectDir}/assets/examples/rosettafold2na/samplesheet.csv" | |
| input = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v2.0/rna_complex.fastasamplesheet.csv' |
workflows/rosettafold2na.nf
Outdated
|
|
||
| RUN_ROSETTAFOLD2NA ( | ||
| ch_protein_interaction, | ||
| ROSETTAFOLD2NA_FASTA.out.prepared_input, |
Member
There was a problem hiding this comment.
Suggested change
| ROSETTAFOLD2NA_FASTA.out.prepared_input, | |
| ROSETTAFOLD2NA_FASTA.out.rf2na_input, |
Merge remote-tracking branch 'upstream/dev' into feat/rf2na-fasta-input
JoseEspinosa
approved these changes
Jan 8, 2026
Member
JoseEspinosa
left a comment
JoseEspinosa
left a comment
There was a problem hiding this comment.
LGTM 🚀
Only three small suggestions about formatting issues, feel free to merge once addressed.
| @@ -0,0 +1,139 @@ | |||
| #!/usr/bin/env python3 | |||
Comment on lines
25
to
27
| "${task.process}": | ||
| python: \$(python3 --version | sed 's/Python //g') | ||
| END_VERSIONS |
Member
There was a problem hiding this comment.
Suggested change
| "${task.process}": | |
| python: \$(python3 --version | sed 's/Python //g') | |
| END_VERSIONS | |
| "${task.process}": | |
| python: \$(python3 --version | sed 's/Python //g') | |
| END_VERSIONS |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
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).