fixes to hello-nextflow after recent updates#401
fixes to hello-nextflow after recent updates#401FranBonath wants to merge 12 commits intonextflow-io:masterfrom
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to nf-test 0.9.0
change nf-test output and add note about what to do if there are file permission errors for files in the work dir
also corrected path and name of intervals.bed in section 2.3
also updated the nf-test output
also corrected dir and filename of intervals.bed and updated nf-test output
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Thanks Fran! Coincidentally I opened #400 around the same time you did, it looks like we both caught a few different things. I'll see if I can cherry-pick the bits you updated that I didn't; we're teaching it today so I'm very keen to get the fixes in. That being said we definitely can keep your PR open until your training so you can feel confident everything is working the way you expect. I have another PR with bigger changes to the GATK training module, which you may prefer not to take on at the last minute. Though it will have a lot more explanations for what's going on at the various steps, which may be of interest to you. I'm aiming to finalize that over the weekend since we'll be teaching it at the Summit. |
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Confirming we've addressed all the issues you picked up. Note that we've made significant updates in the meantime. Happy to give you a rundown in case you want to switch to the newer version for your training. |
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@FranBonath Do you mind if we close this now that we've moved on to v2 of Hello Nextflow? |
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sure, go ahead! :) |
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Recent updates made some changes that were not entirely followed through in the nf-test part of hello-nextflow. This PR fixes that.
Also, I updated the nf-test outputs to reflect the version used in the gitpod environement.
Feel free not to merge since @vdauwera will likely add similar fixes, but I would like to have the PR open until after the 5th of November, so I can use the build from this PR as page to use in my Nextflow training that will come up.
PS: Sorry about all the commits :/