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
| @@ -3,6 +3,6 @@ process { | |||
| resourceLimits = [ | |||
| cpus: 4, | |||
| memory: '15.GB', | |||
| time: '1.h' | |||
| time: '4.h' | |||
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I know this is not optimal, maybe skip this change until using fusioncatcher_download properly
atrigila
reviewed
Dec 19, 2024
Comment on lines
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| "references", | ||
| "references/ensembl", | ||
| "references/ensembl/Homo_sapiens.GRCh38.102.chr.gtf", | ||
| "references/ensembl/Homo_sapiens.GRCh38.102.dna.primary_assembly.fa", | ||
| "references/ensembl/Homo_sapiens.GRCh38.102.dna.primary_assembly.fa.fai", | ||
| "references/ensembl/Homo_sapiens.GRCh38.102.genepred", | ||
| "references/ensembl/Homo_sapiens.GRCh38.102.gtf", | ||
| "references/ensembl/Homo_sapiens.GRCh38.102.refflat", | ||
| "references/ensembl/Homo_sapiens.GRCh38.102_rrna_intervals.gtf.interval_list", | ||
| "references/hgnc", | ||
| "references/hgnc/HGNC-DB-timestamp.txt", | ||
| "references/hgnc/hgnc_complete_set.txt", | ||
| "rrnatranscripts", | ||
| "rrnatranscripts/Homo_sapiens.GRCh38.102_rrna_intervals.gtf" |
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Why are all of these references being removed?
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@atrigila Sorry for this but I'm having many issues when running the pipeline's test. I wanted to talk to you and @nschcolnicov about that because I don't know which ones are known to fail or succeed
| @@ -6,8 +6,8 @@ process FUSIONCATCHER_DOWNLOAD { | |||
| container "community.wave.seqera.io/library/fusioncatcher:1.33--4733482b637ef92f" | |||
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| output: | |||
| path "*" , emit: reference | |||
| path "versions.yml" , emit: versions | |||
| tuple env(meta), path("*"), emit: reference | |||
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Interesting. Did you find a change in behaviour with or without env()?
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| if (( run_fusioncatcher || all) && !fusioninspector_only ) { | ||
| if (fusioncatcher_fusions){ | ||
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| ch_fusioncatcher_fusions = reads.combine(Channel.value(file(fusioncatcher_fusions, checkIfExists:true))) | ||
| .map { meta, reads, fusions -> [ meta, fusions ] } | ||
| } else { | ||
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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