Prokka and prodigal modules update #87
Merged
Conversation
This file contains 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
danilodileo
changed the title
|
added 2 commits
January 22, 2023 18:30
added 2 commits
January 22, 2023 18:43
modules/local/format_prodigal.nf
Outdated
| 'quay.io/biocontainers/gzip:1.11 ' }" | ||
|
|
||
| input: | ||
| tuple val(meta), path(eggnog) |
There was a problem hiding this comment.
Why eggnog? Confusing.
There was a problem hiding this comment.
I used eggnog_table.nf as template but I forgot to change the names in some areas :) I changed it.
modules/local/format_prodigal.nf
Outdated
| prefix = task.ext.prefix ?: "${meta.id}" | ||
|
|
||
| """ | ||
|
|
There was a problem hiding this comment.
Remove the empty line (I think; i.e. follow conventions).
subworkflows/local/prodigal.nf
Outdated
Comment on lines
18
to
19
|
|
||
|
|
subworkflows/local/prodigal.nf
Outdated
|
|
||
| include { PRODIGAL as PRODIGAL_MODULE } from '../../modules/nf-core/prodigal/main' | ||
| include { FORMAT_PRODIGAL } from '../../modules/local/format_prodigal.nf' | ||
| include { UNPIGZ as UNPIGZ_FASTA_PROTEIN } from '../../modules/local/unpigz.nf' |
There was a problem hiding this comment.
You're not using this, I think.
There was a problem hiding this comment.
right. I removed it . I noticed that I didn't need to unpigz while I was working on it but I forgot it there.
| @@ -72,7 +72,6 @@ ch_multiqc_custom_methods_description = params.multiqc_methods_description ? fil | |||
| // MODULE: local | |||
| // | |||
| include { MEGAHIT_INTERLEAVED } from '../modules/local/megahit/interleaved.nf' | |||
| include { UNPIGZ as UNPIGZ_FASTA_PROTEIN } from '../modules/local/unpigz.nf' | |||
There was a problem hiding this comment.
You moved this to the new subworkflow, but never used it. This makes me wonder which output files from the three orf callers are gzipped and which are not; and do we need to do something about this?
There was a problem hiding this comment.
it seems that transdecoder still needs to unpigz
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).I made changes in prodigal output + added a '--metagenome' to prokka.
as mentioned in prokka's website tseemann/prokka#399 prokka doesn't provide the same output as prodigal, it turns out with less gene predicted. Prokka people might not be interested in fix this issue. As the author wrote on GitHub "Prokka is not really designed for metagenomes."