A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

How does oncoanalyser handle with samples sequenced in multiple lanes? That is, identical sample names with different filenames on the samplesheet. Are the fastq files concatenated before analysis as in other nf-core pipelines?

In this scenario we differentiate FASTQs that are from the same sample split across multiple lanes by lane information, which must be provided in the samplesheet by the user. See <https://nf-co.re/oncoanalyser/2.3.0/docs/usage/#fastq|these docs> for an example

And in terms of running such an analysis, the same approach is taken as Sarek: align each FASTQ file independently in parallel and then subsequently merge alignments

I see. In my case, I have RNA samples from different lanes, aligned by STAR and merged by sambamba after the alignment.