General refactor and format #142
Open
Conversation
This file contains hidden or 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
|
| cpus = { 1 * task.attempt } | ||
| memory = { 6.GB * task.attempt } | ||
| time = { 4.h * task.attempt } | ||
| cpus = { 1 * task.attempt } |
There was a problem hiding this comment.
I see what you've done here, and I'm fine with it. There is a general approach that people seem to like anf that the template generates that the equals sighs are vertical.
| @@ -14,12 +14,12 @@ process { | |||
| resourceLimits = [ | |||
| cpus: 2, | |||
| memory: '6.GB', | |||
| time: '1.h' | |||
| time: '1.h', | |||
There was a problem hiding this comment.
I thought the last item doesn't require a comma?
| @@ -5,25 +5,25 @@ | |||
| Defines input files and everything required to run a fast and simple pipeline test. | |||
|
|
|||
| Use as follows: | |||
| nextflow run nf-core/dualrnaseq -profile test_hackathon,<docker/singularity> --outdir <OUTDIR> | |||
| nextflow run nf-core/dualrnaseq -profile test_2_fasta_pathogen,<docker/singularity> --outdir <OUTDIR> | |||
There was a problem hiding this comment.
I agree the naming should be different. This naming doesn't quite make sense as the fasta contains host and pathogen reads.
Perhaps test_small as the files are small and were designed on purpose for fast testing run-times
Comment on lines
-25
to
-37
| tuple val(meta), path('*d.out.bam') , emit: bam | ||
| tuple val(meta), path('*Log.final.out') , emit: log_final | ||
| tuple val(meta), path('*Log.out') , emit: log_out | ||
| tuple val(meta), path('*d.out.bam'), emit: bam | ||
| tuple val(meta), path('*Log.final.out'), emit: log_final | ||
| tuple val(meta), path('*Log.out'), emit: log_out | ||
| tuple val(meta), path('*Log.progress.out'), emit: log_progress | ||
| path "versions.yml" , emit: versions | ||
| path "versions.yml", emit: versions | ||
|
|
||
| tuple val(meta), path('*sortedByCoord.out.bam') , optional:true, emit: bam_sorted | ||
| tuple val(meta), path('*sortedByCoord.out.bam'), optional: true, emit: bam_sorted | ||
| // tuple val(meta), path('*toTranscriptome.out.bam'), optional:true, emit: bam_transcript | ||
| tuple val(meta), path('*Aligned.unsort.out.bam') , optional:true, emit: bam_unsorted | ||
| tuple val(meta), path('*fastq.gz') , optional:true, emit: fastq | ||
| tuple val(meta), path('*.tab') , optional:true, emit: tab | ||
| tuple val(meta), path('*.out.junction') , optional:true, emit: junction | ||
| tuple val(meta), path('*.out.sam') , optional:true, emit: sam |
There was a problem hiding this comment.
You can see here why they vertically align the outputs - when there's lots, it does become easier to read.
| @@ -115,14 +112,18 @@ params { | |||
| // -------------- | |||
| libtype = 'A' | |||
| // gene_feature_gff_to_create_transcriptome_host = ["exon"] // old | |||
| gene_feature_gff_to_create_transcriptome_host = "exon" // new | |||
| gene_feature_gff_to_create_transcriptome_host = "exon" | |||
| // new | |||
| gene_attribute_gff_to_create_transcriptome_host = "transcript_id" | |||
| // gene_feature_gff_to_create_transcriptome_pathogen = ["gene", "sRNA", "tRNA", "rRNA"] //old | |||
There was a problem hiding this comment.
If yo are wondering why there are a bunch of these comments that I've commented out and left. I've kept them in until all three tools successfully run and the output looks reliable. Otherwise if something isn't quite correct somewhere, these are a quick reference point
| quantMode = 'TranscriptomeSAM' // Create a transcriptome Bam (to use with Salmon) - also generates a genome bam (use with STAR genome alignment) | ||
| quantTranscriptomeBan = 'Singleend' // Regarding transcriptome alignments - allowing for insertions, deletions and soft-clips (Singleend option). To prohibit this behaviour, specify IndelSoftclipSingleend | ||
| limitBAMsortRAM = 0 // Option to limit RAM when sorting BAM file. If 0, will be set to the genome index size, which can be quite large when running on a desktop or laptop | ||
| outSAMunmapped = 'Within' |
There was a problem hiding this comment.
I think you need to shift all these comments to above the param?
| }, | ||
| "pathogen_organism": { | ||
| "type": "string", | ||
| "description": "Change to custom name if desired, ie Salmonella_SL1344", | ||
| "fa_icon": "far fa-file" | ||
| "fa_icon": "far fa-file", | ||
| "default": "pathogen" |
There was a problem hiding this comment.
Same as above - unless I'm missing something obvious
There was a problem hiding this comment.
these 2 were caught by the linter nf-core pipelines schema lint as not having defaults in the schema but they are actually set with default values in the config already
reganhayward
approved these changes
Apr 25, 2025
reganhayward
approved these changes
Apr 25, 2025
I thought I'd have to tick (viewed) on all files before approving - good to know |
|
grand, not sure why but all of my replies got marked as reviews |
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.
Overview
everything still runs
PR checklist
scrape_software_versions.pynf-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).