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nf-core
Assembly and binning of metagenomes
### Description of feature Following up on my Slack message (10/16/2023) and as per @jfy133 to post a feature request: "It is possible to only annotate the refined or binned...
### Description of the bug We are trying to redirect the scratch to /tmp on the BOWTIE2 task but it fails with: > FATAL: container creation failed: mount /tmp/nxf.cN0zaFFBsi->/tmp/nxf.cN0zaFFBsi error:...
### Description of feature As originally suggested by @ramprasadn here: https://github.com/nf-core/mag/pull/499#discussion_r1318384733
### Description of feature The following processes do nothing but unpack tars or handle files. We can remove some or all of them to make the pipeline much more efficient:...
### Description of feature Currently, all contigs that were assembled by an assembler will be passed on to pyDamage when the `--ancient_dna` workflow is activated. However, from simulations we know...
### Description of feature Hi, In the host removal module, the bowtie index needs to be recomputed from `--host_fasta` for each execution. Would it be possible to add `--host_bt2` or...
### Description of feature BUSCO has a batch mode, where the input to the BUSCO call is a directory of fasta files rather than an individual file. As binning can...
### Description of feature As per the latest template
### Description of feature e.g. valid options for `--binning_map_mode`
### Description of feature Due to the high fragmentation of ancient DNA data, there is not much gain in using long-read DNA sequencing methods for assembling ancient DNA samples. However,...