Update modules #63
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Update modules #63
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JoseEspinosa
requested changes
Sep 29, 2023
| @@ -0,0 +1,3 @@ | |||
| id,fasta,reference,structures | |||
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Is this needed or is it an error?
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This is just an extra file I am keeping now for testing - will remove it for the release :)
| @@ -0,0 +1,25 @@ | |||
| process MTMALIGN_ALIGN { | |||
| tag "$meta.id" | |||
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Even if it is a local module you could provide its biocontainer
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There is none at the moment, if you prefer i can remove the module from the PR but maybe we can leave it and solve it in the next PR ( i already have an issue open for it and i plan to make it an nf-core module :)
subworkflows/local/compute_trees.nf
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| ch_fastas_fortrees = ch_fastas.combine(tree_tools) | ||
| .map( it -> [it[0] + it[2], it[1]] ) | ||
| .branch{ | ||
| famsa_guidetree: it[0]["tree"] == "FAMSA_GUIDETREE" | ||
| mbed: it[0]["tree"] == "MBED" | ||
| famsa: it[0]["tree"] == "FAMSA" | ||
| clustalo: it[0]["tree"] == "CLUSTALO" | ||
| } |
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Suggested change
| ch_fastas_fortrees = ch_fastas.combine(tree_tools) | |
| .map( it -> [it[0] + it[2], it[1]] ) | |
| .branch{ | |
| famsa_guidetree: it[0]["tree"] == "FAMSA_GUIDETREE" | |
| mbed: it[0]["tree"] == "MBED" | |
| famsa: it[0]["tree"] == "FAMSA" | |
| clustalo: it[0]["tree"] == "CLUSTALO" | |
| } | |
| ch_fastas | |
| .combine(tree_tools) | |
| .map{ it -> [ it[0] + it[2], it[1] ] } | |
| .branch { | |
| famsa: it[0]["tree"] == "FAMSA" | |
| clustalo: it[0]["tree"] == "CLUSTALO" | |
| } | |
| .set { ch_fastas_fortrees } |
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I don't have anymore the branches mbed and famsa_guidetree. I changed the name convention to the name of the module as we discussed the other day in the meeting w/ Cedric :)
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Yeah sorry, I copy pasted it wrongly, I was complaining about the formatting of the code
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I updated the comment but double check I did it correctly
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It would not allow me to change it here directly. I changed it directly in the code and pushed again.
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
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This was referenced Sep 29, 2023
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Closes #35, #45, #58, #60, #61
Add new modules (learnMSA and tcoffee align) from nf-core
Add local mtmalign module
Fix issues to enable structural alignments modes
PR checklist
nf-core lint).nextflow run . -profile 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).