Open
Conversation
|
mirpedrol
commented
Nov 25, 2025
| // | ||
|
|
||
| withName: "CLUSTALO_GUIDETREE|FAMSA_GUIDETREE|MAFFT_GUIDETREE" { | ||
| withName: "CLUSTALO_GUIDETREE|FAMSA_GUIDETREE|MAGUS_GUIDETREE" { |
Owner
Author
There was a problem hiding this comment.
Mafft guidetree should be part of the sub workflow
Magus guidetree should not be part of it
conf/modules.config
Outdated
| // Alignment from a tree (treealign) | ||
| // | ||
|
|
||
| withName: "CLUSTALO_TREEALIGN|FAMSA_TREEALIGN|MAGUS_TREEALIGN|TCOFFEE_TREEALIGN"{ |
Owner
Author
There was a problem hiding this comment.
check if magus should be part of this subworkflow
mafft should be here too?
Owner
Author
There was a problem hiding this comment.
add t-coffee regressive as part of this class
Owner
Author
There was a problem hiding this comment.
upp should also be part of this and the alignment class
Owner
Author
There was a problem hiding this comment.
this file shouldn't be installed in the pipeline, or change the name to make sure that it only affects the modules repo
| container = "nf-core/ubuntu:22.04" | ||
| } | ||
| withName: 'MSA_ALIGNMENT:TCOFFEE_ALIGN'{ | ||
| ext.args = { "-output fasta_aln" } |
Owner
Author
There was a problem hiding this comment.
maybe modify the module upstream?
| @@ -57,7 +66,7 @@ workflow MULTIPLESEQUENCEALIGN{ | |||
|
|
|||
| take: | |||
| ch_input // channel: [ meta, path(sequence.fasta), path(reference.fasta), path(dependency_files.tar.gz), path(templates.txt) ] | |||
Owner
Author
There was a problem hiding this comment.
the dependency_fiels and templates are the "optional data", these are to run the structural alignments. Currently the structural alignment is not used :( should be implemented.
Templates are optional. If you don't use a template file there is a module that creates it, should be run before the class swf.
| take: | ||
| ch_input // channel: [ meta, path(sequence.fasta), path(reference.fasta), path(dependency_files.tar.gz), path(templates.txt) ] | ||
| ch_tools // channel: [ val(guide_tree_tool), val(args_guide_tree_tool), val(alignment_tool), val(args_alignment_tool) ] | ||
| ch_tools // channel: [ meta_guidetree_treealign, meta_alignment ] |
Owner
Author
There was a problem hiding this comment.
is this channel created like this? does it work?
| // | ||
| if (!params.skip_eval) { | ||
| EVALUATE (ALIGN.out.msa, ch_refs, ch_optional_data_template) | ||
| EVALUATE (ch_alignment_output, ch_refs, ch_optional_data_template) |
Owner
Author
There was a problem hiding this comment.
evaluate could be divided into three classes: reference-free, reference-based and structure-based
Owner
Author
There was a problem hiding this comment.
could this be part of the benchmarking module for the class?
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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
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.
No description provided.