Advice for beginner trying to run this

Question

Advice for beginner trying to run this

bradclass opened this issue 2 years ago · 7 comments

I have been trying to get this pipeline working, but feel like I am missing something. Are there some unwritten steps that a beginner would not know about?

Answer 1 · 2022-10-20T17:36:26.000Z

Having a cup of coffee by your side helps. More seriously, try to be more specific so we can help On 20 Oct 2022, at 18:33, bradclass ***@***.******@***.***>> wrote: I have been trying to get this pipeline working, but feel like I am missing something. Are there some unwritten steps that a beginner would not know about? — Reply to this email directly, view it on GitHub [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_cancerit_NanoSeq_issues_46&d=DwMCaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=v9-R7fUmjpv-9Zaqyk1nlnlOC3qPkTEJz5tyYxg2uec&m=8fyVebprVcBbQeLMewqXjiFFlDINnVoUMMPsKBi8wAWeAY6BLgiXxO7FCeRr_B68&s=fP1Y76WpM3nIKENbMpMeIe6iTg1kQimB4Pio5ytIDDk&e=>, or unsubscribe [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ADNUT3NBP5ED5APHTKEN65LWEF66LANCNFSM6AAAAAARKMDMGY&d=DwMCaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=v9-R7fUmjpv-9Zaqyk1nlnlOC3qPkTEJz5tyYxg2uec&m=8fyVebprVcBbQeLMewqXjiFFlDINnVoUMMPsKBi8wAWeAY6BLgiXxO7FCeRr_B68&s=GCVLFDFgUAHMcRMnCzSNpwbHYfrnlQEIL2YqO9SZDVo&e=>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

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Answer 2 · 2022-10-20T17:37:34.000Z

Have been getting this error:

-- Check script 'NanoSeq_main.nf' at line: 22 or see '.nextflow.log' file for more details

Answer 3 · 2022-10-20T17:38:59.000Z

I am trying to use the NanoSeq_main.nf workflow

Answer 4 · 2022-10-20T17:39:37.000Z

*going to get coffee now :-)

Answer 5 · 2022-10-20T20:32:45.000Z

The Nextflow pipeline may not be mature enough. For first time users we would recommend to run the pipeline manually, doing the preprocessing of the bam, the preparation of the matched normal, verifybamid + efficiency, and then running the different steps in runNanoSeq.py. This would also make it easier for us to find out what’s going wrong with your analysis. On 20 Oct 2022, at 18:39, bradclass ***@***.******@***.***>> wrote: I am trying to use the NanoSeq_main.nf workflow — Reply to this email directly, view it on GitHub [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_cancerit_NanoSeq_issues_46-23issuecomment-2D1285918286&d=DwMCaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=v9-R7fUmjpv-9Zaqyk1nlnlOC3qPkTEJz5tyYxg2uec&m=CiraT41qsobdujsIzeiTDdkcy5_TS-Jmj85FWrS_SgmsvV4dvbgT_4RQoqJUrlvS&s=Zg7Olm_6AM2QA_wgMqh7dioei00q8cyNLyNjCZATkog&e=>, or unsubscribe [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ADNUT3NWDKORADFKLTCY4JLWEF7T3ANCNFSM6AAAAAARKMDMGY&d=DwMCaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=v9-R7fUmjpv-9Zaqyk1nlnlOC3qPkTEJz5tyYxg2uec&m=CiraT41qsobdujsIzeiTDdkcy5_TS-Jmj85FWrS_SgmsvV4dvbgT_4RQoqJUrlvS&s=rSuyULmaevSxap-v-7Mv2G6zalN5SCZdBGfGhHEpzQM&e=>. You are receiving this because you commented.Message ID: ***@***.***>

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-- The Wellcome Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

Answer 6 · 2022-10-20T21:27:53.000Z

Ok, I will try that. The documentation presents nextflow as the more streamlined option. This implied to me that it was ready to go.

Answer 7 · 2022-10-20T21:33:38.000Z

have others successfully implemented the nextflow for this?