Goalign cleanseqs #1785
Goalign cleanseqs #1785
Conversation
…goalign_cleanseqs
edmundmiller
left a comment
There was a problem hiding this comment.
Great work! Just a few things.
Would it be over-kill to test the other input formats? Again, I'm not familiar with goalign.
| - aln: | ||
| type: file | ||
| description: MultiFASTA/Phylip alignment file | ||
| pattern: "*.{fasta,phy}" |
There was a problem hiding this comment.
| pattern: "*.{fasta,phy}" | |
| pattern: "*.{fasta,fas,fa,phy}" |
This is what's in the output.
There was a problem hiding this comment.
That is true, plus as mentioned below, it can be gzipped. So, I have changed the output file to mirror the input file's extension:
path("*.${aln.getExtension()}"), emit: aln| - aln: | ||
| type: file | ||
| description: MultiFASTA/Phylip alignment file | ||
| pattern: "*.{fasta,phy}" |
There was a problem hiding this comment.
I'm not familiar with goalign, but should this be *.{fasta,fas,fa,phy}?
There was a problem hiding this comment.
The tools also supports compressed inputs, so it should account for those too
| - aln: | ||
| type: file | ||
| description: MultiFASTA/Phylip alignment file | ||
| pattern: "*.{fasta,phy}" |
There was a problem hiding this comment.
The tools also supports compressed inputs, so it should account for those too
|
@emiller88 and @matthdsm thank you for the review. I'll work on it over the weekend. |
|
@andersgs I think you didn't push your work? You added comments but there's no new commits. No rush, just wanted to review them if you were ready! |
|
@emiller88 that is true. I am working on adding the extra tests for different formats. I am also trying to work upstream to allow for compressed output. While the tool allows compressed input, it always outputs uncompressed output. I'll make the push as soon as I can get the test datasets into the test data repo. |
| -t ${task.cpus} \\ | ||
| $args \\ | ||
| -o ${prefix}.${aln.getExtension()} \\ | ||
| -i $aln |
There was a problem hiding this comment.
If input format is phylip, the option -p/--phylip should be specified. Otherwise, if --auto-detect is given, goalign tries to detect the input format in the following order: 1) fasta, 2) nexus, 3) phylip, 4) clustal .
|
@andersgs, are you still to work on this? No pressure, we're just cleaning up for the upcoming nf-core hackathon. |
|
Does anyone have an interest in getting this finished off? I can help get it updated to recent structural changes (including nf-test). @andersgs , @matthdsm , @fredericlemoine ? |
|
Closing due to lack of activity. Can be reopened if someone wants to take over (but will need significant changes to meet the newer module specifications) |
Closes #1782
PR checklist
versions.ymlfile.labelPROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-awarePROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-awarePROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware