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Update more Docs #637
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Update more Docs #637
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alneberg
approved these changes
Sep 10, 2018
docs/USAGE.md
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| @@ -93,28 +93,33 @@ Choose an output directory | |||
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| ### --project `ProjectID` | |||
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| Specify a project number ID on a UPPMAX cluster. (optionnal if not on such a cluster) | |||
| Specify a project number ID on a UPPMAX cluster. | |||
| (optionnal if not on such a cluster) | |||
docs/USE_CASES.md
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| @@ -1,6 +1,9 @@ | |||
| # Use cases | |||
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| The workflow has three pre-processing options: `mapping`, `realign` and `recalibrate`. Using the `mapping` directive one will have a pair of mapped, deduplicated and recalibrated BAM files in the `Preprocessing/Recalibrated/` directory. Furthermore, during this process a deduplicated BAM file is created in the `Preprocessing/NonRealigned/` directory. This is the usual option you have to give when you are starting from raw FASTQ data: | |||
| The workflow has three pre-processing options: `mapping`, `realign` and `recalibrate`. | |||
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Realign should be removed here right?
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Good point, I'll update that as well
docs/USE_CASES.md
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| @@ -93,7 +112,8 @@ SUBJECT_ID XX 1 SAMPLEIDR 9 /samples/relapse9_1.fastq.gz /sample | |||
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| ## Starting from realignement | |||
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See if this paragraph and the one below should be removed?
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👍 👏 |
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So now, where can we find some beginners to help us with this USAGE.md docs? |
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I can give it a go. But it would need some careful proofreading for factual errors. |
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PR checklist
devbranch./scripts/test.sh -p docker -t ALL).CHANGELOG.mdis updatedREADME.mdis updated