From 9a8c93cf4dce775989a7a73a437585a3bda43156 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Mon, 14 Oct 2024 09:06:50 +0000 Subject: [PATCH 1/2] Tiny bugfixes --- .gitignore | 2 ++ CITATIONS.md | 1 - nextflow.config | 2 -- .../local/utils_nfcore_smrnaseq_pipeline/main.nf | 16 ++++++++-------- 4 files changed, 10 insertions(+), 11 deletions(-) diff --git a/.gitignore b/.gitignore index a42ce016..24fc8b91 100644 --- a/.gitignore +++ b/.gitignore @@ -7,3 +7,5 @@ testing/ testing* *.pyc null/ +execution_trace* +.nf-test* diff --git a/CITATIONS.md b/CITATIONS.md index 99535fc7..f473604a 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -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. - [Bioconductor](https://www.bioconductor.org/) and [R](https://cran.r-project.org/) diff --git a/nextflow.config b/nextflow.config index c45ce2f9..e4f0e71e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -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 diff --git a/subworkflows/local/utils_nfcore_smrnaseq_pipeline/main.nf b/subworkflows/local/utils_nfcore_smrnaseq_pipeline/main.nf index bda2a7cf..c1494948 100644 --- a/subworkflows/local/utils_nfcore_smrnaseq_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_smrnaseq_pipeline/main.nf @@ -94,7 +94,7 @@ workflow PIPELINE_INITIALISATION { .groupTuple() .map { samplesheet -> validateInputSamplesheet(samplesheet) - } + } .map { meta, fastqs -> return [ meta, fastqs.flatten() ] @@ -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.") } } } From e5a7cc1a524cf2dfce08dc40a7978372c4c63cd2 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Mon, 14 Oct 2024 11:09:41 +0200 Subject: [PATCH 2/2] Update CITATIONS.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- CITATIONS.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CITATIONS.md b/CITATIONS.md index f473604a..4996b65f 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -38,7 +38,7 @@ - [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. - [Bioconductor](https://www.bioconductor.org/) and [R](https://cran.r-project.org/)