General refactor and format #142
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conf/base.config
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| cpus = { 1 * task.attempt } | ||
| memory = { 6.GB * task.attempt } | ||
| time = { 4.h * task.attempt } | ||
| cpus = { 1 * task.attempt } |
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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.
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| 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 | ||
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| 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 |
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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 | |||
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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
nextflow.config
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| 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' |
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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" |
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Same as above - unless I'm missing something obvious
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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 |
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grand, not sure why but all of my replies got marked as reviews |
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.2.0. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
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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).