RiboCode - prepare_transcripts, metaplots, ribocode #9485
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pinin4fjords
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pinin4fjords
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Good work! Just need some bits and pieces to fix it up
| 'biocontainers/ribocode:1.2.15--pyhfa5458b_0' }" | ||
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| input: | ||
| path fasta |
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Inputs and outputs will need to be tuples with meta elements
| path gtf | ||
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| output: | ||
| path "annotation" , emit: annotation |
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| output: | ||
| path "annotation" , emit: annotation | ||
| path "versions.yml" , emit: versions |
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Versions will be collected via topic channels from now on (there's a bulk conversion in process). You might as well have that in place now- check out https://github.com/nf-core/modules/blob/master/modules/nf-core/ribodetector/main.nf for how it's done.
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| """ | ||
| # nf-core: ensure FASTA is uncompressed | ||
| GENOME="$fasta" |
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We shouldn't bake this sort of concern into modules I think, keep things simple, pipelines can input gunzip processes.
| fi | ||
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| # Update the GTF | ||
| GTFupdate \\ |
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This should probably be a separate module
| identifier: "" | ||
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| input: | ||
| - fasta: |
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This will be updated to allow for the meta structure I indicated above
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "test_ORFs_category.pdf:md5,a56356649534ea846fe7aa3aac6684ff" |
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We probably shouldn't try to snapshot pdfs, they tend not to be stable over multiple machines because of differences in underlying libraries.
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "SRX11780887.Aligned.toTranscriptome.out_psites.hd5:md5,802ec4fe5545dec4fe8affd79716faeb" |
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hd5 is a binary format also likely to work poorly with snapshots
| ext.args = '-f0_percent 0.1 -pv1 1 -pv2 1' | ||
| } | ||
| withName: RIBOCODE_RIBOCODE { | ||
| ext.args = '' |
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Don't need this if you're not setting anything
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| input: | ||
| tuple val(meta), path(bam) | ||
| path annotation |
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Still need a tuple with a meta
I had added the three module required for running the RiboCode application for detecting translated regions from Ribo-Seq data. This involves preparing the annotations (
ribocode/prepare), assessing the alignment files (ribocode/metaplots) and finally running the calling (ribocode/ribocode)PR checklist
Closes Very Old Issue
versions.ymlfile.labelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda