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Tiny bugfixes #476

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merged 2 commits into from
Oct 14, 2024
Merged

Tiny bugfixes #476

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9a8c93c
Tiny bugfixes
apeltzer Oct 14, 2024
e5a7cc1
Update CITATIONS.md
apeltzer Oct 14, 2024
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2 changes: 2 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -7,3 +7,5 @@ testing/
testing*
*.pyc
null/
execution_trace*
.nf-test*
1 change: 0 additions & 1 deletion CITATIONS.md
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Expand Up @@ -38,7 +38,6 @@

- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)

> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
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- [Bioconductor](https://www.bioconductor.org/) and [R](https://cran.r-project.org/)
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2 changes: 0 additions & 2 deletions nextflow.config
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Expand Up @@ -90,8 +90,6 @@ params {
help = false
help_full = false
show_hidden = false
help_full = false
show_hidden = false
version = false
pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
// Config options
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16 changes: 8 additions & 8 deletions subworkflows/local/utils_nfcore_smrnaseq_pipeline/main.nf
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Expand Up @@ -94,7 +94,7 @@ workflow PIPELINE_INITIALISATION {
.groupTuple()
.map { samplesheet ->
validateInputSamplesheet(samplesheet)
}
}
.map {
meta, fastqs ->
return [ meta, fastqs.flatten() ]
Expand Down Expand Up @@ -170,34 +170,34 @@ def validateInputParameters() {
genomeExistsError()

if (!params.mirgenedb && !params.mirtrace_species) {
error("Reference species for miRTrace is not defined via the --mirtrace_species parameter.")
error("Reference species for miRTrace is not defined via the `--mirtrace_species` parameter.")
}

if (!params.mirgenedb) {
// Validate mature miRNA fasta file
if (!params.mature) {
error("Mature miRNA fasta file not found. Please specify using the '--mature' parameter.")
error("Mature miRNA fasta file not found. Please specify using the `--mature` parameter.")
}
// Validate hairpin miRNA fasta file
if (!params.hairpin) {
error("Hairpin miRNA fasta file not found. Please specify using the '--hairpin' parameter.")
error("Hairpin miRNA fasta file not found. Please specify using the `--hairpin` parameter.")
}
} else {
// Validate MirGeneDB species
if (!params.mirgenedb_species) {
error("You specified to be using MirGeneDB, but the MirGeneDB species is not set. Please specify using the '--mirgenedb_species' parameter.")
error("You specified to be using MirGeneDB, but the MirGeneDB species is not set. Please specify using the `--mirgenedb_species` parameter.")
}
// Validate MirGeneDB mature miRNA fasta file
if (!params.mirgenedb_mature) {
error("You specified to be using MirGeneDB, but the mature miRNA fasta file is not found. Please provide the file using the '--mirgenedb_mature' parameter.")
error("You specified to be using MirGeneDB, but the mature miRNA fasta file is not found. Please provide the file using the `--mirgenedb_mature` parameter.")
}
// Validate MirGeneDB hairpin miRNA fasta file
if (!params.mirgenedb_hairpin) {
error("You specified to be using MirGeneDB, but the hairpin miRNA fasta file is not found. Please provide the file using the '--mirgenedb_hairpin' parameter.")
error("You specified to be using MirGeneDB, but the hairpin miRNA fasta file is not found. Please provide the file using the `--mirgenedb_hairpin` parameter.")
}
// Validate MirGeneDB GFF file
if (!params.mirgenedb_gff) {
error("You specified to be using MirGeneDB, but the GFF file is not found. Please provide the file using the '--mirgenedb_gff' parameter.")
error("You specified to be using MirGeneDB, but the GFF file is not found. Please provide the file using the `--mirgenedb_gff` parameter.")
}
}
}
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