Fixes #69 nanoplot error #70
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| @@ -23,7 +23,6 @@ process NANOPLOT { | |||
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| output: | |||
| tuple val(meta), path("*.html"), emit: html | |||
| tuple val(meta), path("*.png") , emit: png | |||
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One could also make that one optional ...? with optional: true ?
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I agree that optional output might be better, but thats just just a band aid here, so I think its fine.
The optimal solution might be to make NanoPlot output the png again? I mean it was sort of nice to look at them?!
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The issue is that static image generation is now dependent on having an internet connection, which cannot always be guaranteed. See: wdecoster/NanoPlot#281
The HTML reports are unaffected so still can visualise the plots. Making the pngs optional could be a pragmatic solution and doesn't cause the workflow to fail on occasions when internet access is unavailable.
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Thanks!
No, an internet connection may not be a prerequisite to run the pipeline.
So I am fine with the PR ;)
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The failing linting test below is only due to not having the template update 2.2 integrated yet.
LGTM!
Edit: Hm, I am not able to merge the PR due to missing rights it seems (I expect that not everybody can merge it due to the failing linting tests, but I was hoping to use admin power; which I lack obviously, maybe for the better).
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I thin this PR is not needed anymore. nf-core template v2.9 has been updated in #86 and Nanoplot has been implemented via nf-core/modules where the *.png requirement has been solved by adding |
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Indeed, thanks! |
This PR stops bacass v2.0.0 from failing on the nanoplot step and fixes #69.
The newer version of NanoPlot v1.38.0 doesn't generate png image by default anymore meaning that the NANOPLOT process will always fail as the png output requirement will never be satisfied.
Removing png output requirement in NANPLOT process.
PR checklist
nf-core lint).nextflow run . -profile test,docker).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).