POC using module classes v2 #6
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mirpedrol
commented
Nov 25, 2025
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| withName: "CLUSTALO_GUIDETREE|FAMSA_GUIDETREE|MAFFT_GUIDETREE" { | ||
| withName: "CLUSTALO_GUIDETREE|FAMSA_GUIDETREE|MAGUS_GUIDETREE" { |
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Mafft guidetree should be part of the sub workflow
Magus guidetree should not be part of it
conf/modules.config
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| // Alignment from a tree (treealign) | ||
| // | ||
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| withName: "CLUSTALO_TREEALIGN|FAMSA_TREEALIGN|MAGUS_TREEALIGN|TCOFFEE_TREEALIGN"{ |
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check if magus should be part of this subworkflow
mafft should be here too?
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add t-coffee regressive as part of this class
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upp should also be part of this and the alignment class
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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" } |
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maybe modify the module upstream?
| workflow MULTIPLESEQUENCEALIGN{ | ||
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| take: | ||
| ch_input // channel: [ meta, path(sequence.fasta), path(reference.fasta), path(dependency_files.tar.gz), path(templates.txt) ] |
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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 ] |
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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) |
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evaluate could be divided into three classes: reference-free, reference-based and structure-based
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could this be part of the benchmarking module for the class?
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