299 add qc for nanopore data #344
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…icine-sweden/jasen into 299-add-qc-for-nanopore-data confusion with committing
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Confusion with commits, need to check what happened before reviewing and merging |
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No worries, make it a draft until you're ready for review, so we don't use the CI resources:) |
configs/nextflow.base.config
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| @@ -77,7 +77,6 @@ profiles { | |||
| mycobacterium_tuberculosis { | |||
| params.species = 'mycobacterium tuberculosis' | |||
| params.speciesDir = 'mtuberculosis' | |||
| params.resistantLociName = 'resistance_loci' | |||
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This is necessary, please put this back:)
configs/nextflow.base.config
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| @@ -107,10 +106,6 @@ process { | |||
| memory='1 GB' | |||
| cpus=2 | |||
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| withName: add_igv_track { | |||
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Same as above, put back please:)
| @@ -219,6 +214,11 @@ process { | |||
| publishDir = [ path: "${params.outdir}/${params.speciesDir}/mykrobe", mode: 'copy', overwrite: true ] | |||
| ext.args = "--species tb --format csv" | |||
| } | |||
| withName: nanoplot { | |||
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Can you add these to the other contigs?
configs/nextflow.base.config
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| @@ -313,5 +313,5 @@ manifest { | |||
| homePage = 'https://github.com/genomic-medicine-sweden/jasen' | |||
| description = 'Pipeline epitypes numerous bacterial species as well as identifies AMR and virulence genes' | |||
| mainScript = 'main.nf' | |||
| version = '0.9.0' | |||
ryanjameskennedy
requested changes
Sep 10, 2024
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Description
Added module with NanoPlot to check quality of raw input reads produced by ONT technology.
Summary of the changes made:
added new module script, added container URL to Makefile, changed bacterial base workflow script
Primary function of PR
Testing
The pipeline has been run with test data, NanoPlot report is produced in the nanoplot output folder.
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