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Using command `stub` blocks in Nextflow is useful when developing syntax and quickly testing pipelines. However, its use within nf-core is limited because the vast majority of nf-core modules do not h…
ewels updated
4 weeks ago
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STAR is awesome RNASeq aligner.
I'm running a pipeline that runs the STAR version 2.7.9a , but when trying to mapping with the Human genome(hg38) using the bam file as input on the HPC platform wit…
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## Bug report
Using storeDir makes the pipeline crash complaining that the required output file is not there any more.
### Expected behavior and actual behavior
In past storeDir was copying…
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## Bug report
Cached images duplicated by Nextflow and Apptainer/Singularity when ociAutoPull set to true
### Expected behavior and actual behavior
Expection is that on copy of each image fi…
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```
I have been using STAR with Illumina 101bp paired end reads. The first set of
libraries I sequenced work great going through the pipeline, but I have had a
very strange problem with the most rec…
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Based off of the work in :
https://github.com/icgc-argo/workflow-roadmap/issues/438
Add to RNA-Seq alignment pipeline
edsu7 updated
2 months ago
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Hi Alex,
Thank you so much for all of the resources you've provided to the community.
I'm working with PE150 bulk RNAseq data. My library adds an 8nt UMI to read2. I first extracted the UMIs fro…
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#### Provide the command used or report the bug here
De-duplication of annotations needed
#### What version are you using?
current
#### Add error message here (if applicable)
Related to htt…
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Experiment: Single Cell RNAseq from 10x genomics
File Format: I have 2 Lanes (L001 and L002) and I also have for each of the lanes an R1 and R2 file
Reference Genome: Multiple HIV proviral sequences…
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### Description of the bug
Dear Researchers and Developers,
Thank you for developing this pipeline.
I am trying to go from FASTQ files to Salmon pseudo-alignment and quantification, as per th…