Add nf-test for FUSIONCATCHER subworkflow
#591
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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: 3.0.2. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
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alanmmobbs93
commented
Dec 19, 2024
atrigila
reviewed
Dec 19, 2024
rannick
reviewed
Jan 7, 2025
| conda "${projectDir}/environment.yml" | ||
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
| 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d5/d53f36e9e01d14a0ae8e15f8046f52b2883c970c27fe43fdfbd9440a55f5403f/data' : | ||
| 'community.wave.seqera.io/library/fusioncatcher:1.33--4733482b637ef92f' }" |
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It works with 1.33 now because ensembl 113 directory does not contain 37 and 38 which was confusing the build. It is not compatible with ensembl 112 and we can't force to use a certain version. Conclusion: use 113/gencode 47 as default
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And keep 1.33. Add in documentation where to find the references for ensembl 112
rannick
reviewed
Jan 7, 2025
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| input: | ||
| tuple val(meta), path(fasta) | ||
| path reference | ||
| tuple val(meta), path(fastqs, stageAs: "input/*") |
rannick
reviewed
Jan 7, 2025
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| // TODO: Remove fusioncatcher_fusions as parameter. | ||
| // TODO: remove dummy file. Work with Channel.empty() | ||
| // TODO: if the files were already produced and the user want to skip the module because of this, they should be taken them from the sample sheet |
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Open issues?
Using fusioncatcher_fusions is practical if you want to run the last part of rnafusion: fusionreport and fusioninspector
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@rannick thanks for looking into this! Let me understand this correctly, the fusioncatcher_fusions parameter can be used to feed one single file and hence skip the FUSIONCATCHER_DETECT process, am I right? I was wondering whether this single file should contain the data for all the samples that the user want to analyze with fusionreport and fusioninspector, or if the user has to supply one file per sample.
If the second scenario is the correct one, then I got it wrong and this approach is almost ok, just a little bit of fine tunning. But if the first scenario is the correct, then we should change more things
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Yes fusioncatcher_fusions allows to skip FUSIONCATCHER_DETECT.
That is a good point about the samples, the files probably have to be fed per sample
rannick
approved these changes
Jan 7, 2025
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PR checklist
nf-core lint).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).It's important to know that it takes almost and hour to download the references.
Added
FUSIONCATCHER. Note: fusioncatcher reference files are large for testing purposes. After this it would be ideal to dedicate some time to create or obtain a reduced reference, as explained in Create small reference for fusioncatcher (chr4) #580.Changed
fusioncatcherdetect module's input, adding meta components.Perspectives