eager
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nf-core
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
I realised that in DSL2 there is possibly one way to reduce the size of the console logging of all the processes (which is currently very large for eager, and...
For many projects having a 'common' sheet that is reused across all analyses and contains all relevant metadata for all libraries/samples is useful to have. It would be nice if...
Hello, it seems that for some processes, e.g., picard - markduplicates, is memory limit passed as an argument, for example -Xms ${task.memory.toMega()}M. However, the same limit is used as container...
## Check Documentation I have checked the following places for your error: - [x] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting) - [x] [nf-core/eager pipeline documentation](https://nf-co.re/nf-core/eager/usage) ## Description of the bug `hostremoval_input_fastq` fails on...
The MetaPhlAn series of taxonomic classifiers are very popular in metagenomics, and have very low overhead. It also allows exporting of physical alignments to the gene databases that theoretically (but...
It would be very useful to have automated splitting of large fastq files to parallelise alignment, and then have automated concatenation of the output aligned files. BWA alignment is often...
## Is your feature request related to a problem? Please describe For microbiome/metagenomic screening analysis, typically the main file type is an OTU table. We already have this with Kraken,...
Whelp, I guess we have to tackle the bull. First thoughts, we need to work out what nf-core/modules we would need, check what are already available and what we would...
Just to note things down while they are fresh: The CircularMapper step should actually be a subworkflow in the DSL2 version, as it encompasses multiple steps that have already existing...
Some approaches in medical genomics use the blanks to subtract the data sequenced there from the actual samples to remove background noise. Something we should also consider and could easily...