-
If you use HERRO via `dorado correct` (https://github.com/nanoporetech/dorado?tab=readme-ov-file#read-error-correction) it outputs the reads as fasta instead of fastq. Will this pipeline work on those…
-
Hello,
I have about 200 samples. There are 2 fastq.gz file (sample.R1.fq.gz and sample.R2.fq.gz) for every file. Each file is very large (more than 50G compressed file). How can I unzip them and…
-
Hello shang-qian,
I am currently trying to replicate data from this [paper](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02302-5) using SCSit.
In short they perform a SPLiT…
-
## Bug report
When using the publishDir directive to send outputs to an s3 location, it looks like Nextflow creates a zero-sized object with a key ending in a slash at the publishDir location. Whi…
-
Hi aMeta team!
Thanks for providing such a great ancient metagenome pipe. I found a very minor issue when downloading the krakendb from https://doi.org/10.17044/scilifelab.20518251. After wget, th…
-
Hi,
this problem was considered in issue 104 and I have been following the instructions given there. I am running Salmon in alignment mode on bam files generated by STAR (unsorted and in transcriptom…
-
**Description of the issue**
For dataset [Distinct microbial and immune niches of the human colon](https://data.humancellatlas.org/explore/projects/83f5188e-3bf7-4956-9544-cea4f8997756), the pipelines…
-
Currently workflow does k-mer counting on the individual fastqs from each bam, but then goes on to combine the fastq. Should k-mer counting be performed on the combined fastq or the parts?
-
Hi,
First of all, congratulations on this amazing tool!
I've tried running the Docker with 6 FASTQ files divided into 2 groups, without environment. However, it seems to stop at the end of t…
-
### Need
As a developer, I need the pipeline to have a test profile with accompanying relevant test data, which should test if not all then at least the majority of the pipeline.
### Suggested a…