Closed yumisims closed 1 month ago
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit a6edc93
+| ✅ 130 tests passed |+
#| ❔ 19 tests were ignored |#
!| ❗ 3 tests had warnings |!
@yumisims Was this version of the pipeline tested on a big dataset with hic_aligner: minimap2
?
@ksenia-krasheninnikova not necessary to test on a bigger genome. I encountered an image downloading problem, have you seen this before?
@yumisims what image exactly threw the error? Can't see it in the current CI run.
As I understand the purpose of adding minimap2 option is to be able to run the pipeline on big genomes.
@muffato do you know the reason why Container library: 'quay.io' is not valid? thanks
@yumisims : there was a problem on the dev
in the first place. The python containers were not properly defined. https://github.com/sanger-tol/genomeassembly/commit/d72047aca168d6326d345583545aae8c9bbdc347 shows how it should be done (and no need to edit the nf-core download
command)
Will try when I get back.
From: Matthieu Muffato @.> Reply to: sanger-tol/genomeassembly @.> Date: Wednesday 29 May 2024 at 09:56 To: sanger-tol/genomeassembly @.> Cc: Ying Sims @.>, Mention @.***> Subject: Re: [sanger-tol/genomeassembly] add hic minimap2 (PR #44) [EXT]
@muffato commented on this pull request.
In modules/local/get_calcuts_params.nf [github.com]https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_sanger-2Dtol_genomeassembly_pull_44-23discussion-5Fr1618492295&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=X9VPYUGy4ibZarh9Rup1XaZ62i2u-I0xOZXEy11dXDM&m=Y32RMvJHKs6Pzr27gyOwNcQBsI2Vf-sOG8ZEHvHsjsCIwxLzkOSzWinPJtGARGtG&s=6xYTGhENyr96qK19lXcCOBrc_WgrRHpnPexEF--ElJ8&e=:
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'docker.io/python:3.9' }"
Oki. I'll let you try that
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PR checklist
nf-core lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).docs/usage.md
is updated.docs/output.md
is updated.CHANGELOG.md
is updated.README.md
is updated (including new tool citations and authors/contributors).