Tag: nf-core

pipeline launch from nf-core website

pipeline launch from nf-core website – input csv bug · Issue #811 · nf-core/sarek · GitHub Labels bug Something isn’t working You can’t perform that action at this time. You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window….

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nf-core presentation – HackMD

<!– .slide: data-background=”raw.githubusercontent.com/maxulysse/maxulysse.github.io/main/assets/img/svg/green_white_bg.svg&#8221; –> <a href=”nf-co.re”><img src=”raw.githubusercontent.com/nf-core/logos/master/nf-core-logos/nf-core-logo-darkbg.svg&#8221; width=”60%”></img></a> # What is nf-core\? [Maxime U Garcia](https://maxulysse.github.io/) ▸ [<i class=”fa fa-twitter” aria-hidden=”true”></i>@gau](https://twitter.com/gau/) | [<i class=”fa fa-github” aria-hidden=”true”></i>@maxulysse](https://github.com/maxulysse/) [Karolinska Institutet](https://ki.se/) | [Science for Life Laboratory](https://www.scilifelab.se/) Sweden — ## Overview – 🗄️ [Barntumörbanken](https://ki.se/forskning/barntumorbanken/) – 🧬 [NGI](https://ngisweden.scilifelab.se/) – 🍬 [Nextflow](https://www.nextflow.io/) – 🧙 [nf-core](https://nf-co.re/) — ##…

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Implement tests with pytest-workflow – githubhot

Pytest workflow makes it easier to maintain larger test suites and also allows to check outputs. cf. github.com/nf-core/tools/issues/605, github.com/nf-core/rnaseq/pull/546, github.com/nf-core/sarek/tree/dev/tests Testing scenarios: Run pipeline with more than one file different parameter combinations different filenames and folder structures for cellranger run subworkflows with and without index different protocols, if we manage…

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Mapped reference id is not an id of the genome file genome_nowhitespace.fa

miRDeep2: Mapped reference id is not an id of the genome file genome_nowhitespace.fa 1 Hi everyone, I’m trying to run nf-co.re/smrnaseq pipeline and I’m having a problem with mirdeep2. Command: nextflow run nf-core/smrnaseq -profile ijcluster –input /home/794_both.fastq.gz –outdir /home/results –genome GRCh38 –protocol qiaseq –mature mirbase.org/ftp/CURRENT/mature.fa.gz –hairpin mirbase.org/ftp/CURRENT/hairpin.fa.gz Error message: Command…

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bam – Detect mutation context in a read of a sam file

That kind of custom fiddling with reads and variants is very cumbersome, non-standard and also error-prone. Do a standard variant callign pipeline and then filter for the mutations that you want. Then extract the variant position (so the coordinates) and get the variant context from the reference genome. Using individual…

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Any suggestion on metagenomics pipelines for processing shotgun metagenomics whole genome sequencing samples?

Any suggestion on metagenomics pipelines for processing shotgun metagenomics whole genome sequencing samples? 0 Hi, I have some shotgun metagenomics gonorrhea samples and I want to use metagenomics pipeline to process the samples and then detect antimicrobial resistance. I looked into few pipelines so far for metagenomics data such as…

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How to pass custom software specific variables to nf-core/sarek nextflow pipeline?

How to pass custom software specific variables to nf-core/sarek nextflow pipeline? 0 I’m attempting to call whole genome variants using nf-core/sarek nextflow pipeline. In QC step there is an option that invokes trim_galore quality trimming, but i don’t know how to pass my custom adapters to be cut as well….

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