Jbrowse indexer - track3 - current progress #66
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
vikasguptaebi
requested review from
mberacochea,
SantiagoSanchezF and
tgurbich
mberacochea
requested changes
Oct 18, 2024
There was a problem hiding this comment.
Nice stuff folks. I think it needs a bit of tiding up before mering:
- Publishing dirs is responsability of the pipelines so remove the bespoke processes to do so
- Don't use TAB is the input file is a GFF, it makes reading that trickier with no need (for the output use _gff to make it clear that is a modified version of the file
- I would consider merged GFF_TRIM_FASTA and the indexation process (under a flag).. it will make it faster as there will be less file-copy over done by nextflow (ask me if there are questions around this)
There was a problem hiding this comment.
This module shouldn't be under jbrowse, this is a generic GFF sorting tool
| tuple val(meta), path(tab) | ||
|
|
||
| output: | ||
| tuple val(meta), path("${meta.id}_sorted.gff"), optional: true, emit: gff |
There was a problem hiding this comment.
The output shouldn't be optional, why is it optional?
| container 'quay.io/biocontainers/coreutils:8.25--0' | ||
|
|
||
| input: | ||
| tuple val(meta), path(tab) |
There was a problem hiding this comment.
Suggested change
| tuple val(meta), path(tab) | |
| tuple val(meta), path(gff) |
| tuple val(meta), path(tab) | ||
|
|
||
| output: | ||
| tuple val(meta), path("${meta.id}_sorted.gff"), optional: true, emit: gff |
There was a problem hiding this comment.
Suggested change
| tuple val(meta), path("${meta.id}_sorted.gff"), optional: true, emit: gff | |
| tuple val(meta), path("${meta.id}_sorted.gff"), emit: sorted_gff |
| label 'process_single' | ||
|
|
||
| conda "${moduleDir}/environment.yml" | ||
| container 'quay.io/biocontainers/coreutils:8.25--0' |
There was a problem hiding this comment.
This needs to consider the singularity image too, like this example:
conda "bioconda::blast=2.14.1"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/blast:2.14.1--pl5321h6f7f691_0':
'biocontainers/blast:2.14.1--pl5321h6f7f691_0' }"
Was this module created with the nf-core tools?
| } | ||
|
|
||
| // PUBLISH_OUTPUT_FILES process to save the output files | ||
| process PUBLISH_OUTPUT_FILES { |
There was a problem hiding this comment.
I would remove this process
| @@ -0,0 +1,36 @@ | |||
| # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json | |||
| name: "index_fasta" | |||
| description: Generate fasta indices | |||
There was a problem hiding this comment.
Suggested change
| description: Generate fasta indices | |
| description: Generate fasta indices using BGZIP and FADIX |
| versions = ch_versions // Channel: [ versions.yml ] | ||
|
|
||
| // Call the process to publish files | ||
| PUBLISH_OUTPUT_FILES(gff_gz, tbi_files, output_dir) |
There was a problem hiding this comment.
The same as for the index one, this one should not be here
| @@ -0,0 +1,37 @@ | |||
| # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json | |||
| name: "index_gff" | |||
| description: Generate gff indices | |||
There was a problem hiding this comment.
Suggested change
| description: Generate gff indices | |
| description: Create an indexed GFF without the FASTA sequence |
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.
following are addressed for now --