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Determine the requirements and potential options for the basis of the Pangenome Annotation RNA-seq pipeline.
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## New feature
It's a fairly common request to get automatic notifications about Nextflow pipeline completion within Slack or MS Teams. We have implemented this within the nf-core template and it w…
ewels updated
7 months ago
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Hello Jvivian,
I tried to run the rnaseq-cgl-pipeline:3.2.1-1 version to process RNA-Seq data. My command is as follows:
docker run -v $(pwd):$(pwd) -v $(pwd)/sample_fq_SLE:/samples -v /home/yangz…
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I do not really dare to ask, knowing how much you are investing into guix, but on the other hand, for the same reason you can also well estimate how much an effort it is to maintain the same packages …
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Currently, all of the Github Actions CI tests that we use to test that the pipeline functions (using a minimal dataset) are run as `-profile test,docker`. This just tests whether the pipeline will r…
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We should change the way how the sample sheet is parsed /accessed (here https://github.com/BIMSBbioinfo/pigx_bsseq/blob/master/pigx-bsseq.in#L142-L184) to the way how the rna-seq did (here https://gi…
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I receive the following error when running the bcbio RNAseq pipeline. It appears to be a R package version conflict but I'm not sure how to resolve it. Thanks in advance for any advice.
```
[202…
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I am running on `apptainer version 1.1.3-1.el7` in an HPC system.
#### Expected behaviour
I am currently running nextflow pipelines (https://github.com/nf-core/rnaseq) using singularity images,…
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Do we still need the six.moves library for urlretrieve?
https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/blob/update-rnannot/rnannot/RNAseq_annotate.py#L12
This might be a moot issue i…
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Please convert each of this as an issue when you start working on one.
(That can be done by clicking on the circle dot `⊙` at the end of the line in the list below, hover on a list item to see it)
A…