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Some more AWS issues #473

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apeltzer opened this issue Jun 22, 2020 · 2 comments · Fixed by #500
Closed

Some more AWS issues #473

apeltzer opened this issue Jun 22, 2020 · 2 comments · Fixed by #500
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bug Something isn't working pending Addressed on branch waiting for related PR
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2.2 "Ulm"

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107[a3/57447f] Submitted process > endorSpy (JK2782)
108WARN: Directive 'validExitStatus' has been deprecated -- Check process 'nuclear_contamination'
109[94/330326] Submitted process > preseq (JK2782)
110Error executing process > 'sex_deterrmine'
111Caused by:
112  Can't stage file file:///NO_FILE -- file does not exist
113Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
@apeltzer apeltzer self-assigned this Jun 22, 2020
@apeltzer apeltzer mentioned this issue Jun 22, 2020
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jfy133 added a commit that referenced this issue Jun 23, 2020
@jfy133
Merge pull request #474 from nf-core/fix-indices-sexdet
b89163e 
Fix for #473
@jfy133 jfy133 added the bug Something isn't working label Jun 29, 2020
@jfy133 jfy133 mentioned this issue Jun 30, 2020
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jfy133 commented Jun 30, 2020

Should follow more the examples of e.g .viralrecon:

https://github.com/nf-core/viralrecon/blob/69326f97b1c1d1b8733a0df573cb1f3eff907e6d/main.nf#L163

and ch_fasta = file(params.fasta)

And then use proper

input:
    path fasta from ch_fasta

From the original issue report #472

@jfy133 jfy133 linked a pull request Jun 30, 2020 that will close this issue
Indices fix #477
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8 tasks
@jfy133 jfy133 added this to the V2.2 "Ulm" milestone Jun 30, 2020
@jfy133 jfy133 mentioned this issue Jun 30, 2020
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@jfy133 jfy133 linked a pull request Jul 15, 2020 that will close this issue
Adjusted fixes for AWS index handling #500
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8 tasks
@jfy133 jfy133 added the pending Addressed on branch waiting for related PR label Aug 3, 2020
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jfy133 commented Aug 3, 2020

Had a successful run the other day. Running few last checks

@jfy133 jfy133 closed this as completed Aug 3, 2020
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Adjusted fixes for AWS index handling nf-core/eager
Indices fix nf-core/eager
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