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Hello!
I am trying to run the mRNAseq pipeline on the provided test data, but I can't seem to be able to get past the following error. Unfortunately the STAR .log is empty.
Error in rule STAR:
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**Describe the bug**
I was able to run the ECODE chip seq pipeline on my own dataset starting from adapter-trimmed fastq.gz files. However, near the end of the pipeline I encountered a few errors whi…
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Thanks! It's one of those unwritten rules that we've discussed and implemented to various degrees in some of the main pipelines but haven't had the time to officially document :sweat_smile: You could …
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Hi Jin
I was going to post my question and ask your help for multiple runs that are failing. but I cannot find metadata.json.
after updating the chip and atac pipeline, out of 20 runs at Stanford r…
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**Describe the bug**
spp fails in step call-call_peak_pr2 for shard-1 , but has not problem with shard-0
**OS/Platform**
-Centos 6.10 and UGE
- Conda version: 4.7.12
- Pipeline version: v1.3.…
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Hello,
It is not really an issue but more a call for help. (I wanted to ask on slack but got a 404 for this page https://nf-co.re/join/slack/).
I have not been able to understand how to configu…
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Error:
```
[CaperURI] copying from gcs to local, src: gs://caper_out/bpnet_anna/atac/d47e2acb-cd7b-4ce4-b342-b9bbbe3e54fe/call-qc_report/glob-3440f922973abb7a616aaf203e0db08b/qc.json
[CaperURI] …
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Hey @SweetiePi
I've had this design idea for a bit to make an email flyer / poster out of. I put it together but I still think it's missing a little bit of a design element to tie it all together.…
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Can we add SICER2 support for ChIP-seq peak calling?
I'm working on a bioconda recipe here:
https://github.com/bioconda/bioconda-recipes/pull/20017
Here are some URLs with more details:
- http…
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**Describe the bug**
I tried to run atac-seq-pipeline using example json file at https://raw.githubusercontent.com/ENCODE-DCC/atac-seq-pipeline/master/example_input_json/caper/ENCSR356KRQ_subsampled_…