Readme formatting

olgabot-patch-2
Evan Floden 4 years ago
parent 8a9d3ad8a0
commit 87e8da61a4

@ -1,8 +1,11 @@
# nf-core/configs: Google Cloud Life Sciences Configuration
![Google Cloud](images/google-cloud-logo.png "https://cloud.google.com/life-sciences/docs/tutorials/nextflow")
To be used with the `google` profile by specifying the `-profile google` when running nf-core pipelines.
![Google Cloud](images/google-cloud-logo.svg "https://cloud.google.com/life-sciences/docs/tutorials/nextflow")
## Quick Start
```
GOOGLE_APPLICATION_CREDENTIALS=<your_key>.json
@ -10,21 +13,22 @@ NXF_MODE=google
nextflow run nf-core/rnaseq -profile google,test --google_bucket <gs://your_bucket/work>
```
## Required Parameters
### Required Parameters
#### `--google-bucket`
The Google Cloud Storage bucket location to be used as a Nextflow work directory. Can also be specified with (`-w gs://your_bucket/work`).
## Optional Parameters
### Optional Parameters
#### `--google-zone`
The Google zone where the computation is executed in Compute Engine VMs. Multiple zones can be provided separating them by a comma. Default (`europe-west2-c`).
#### `--google-preemptible`
Enables the usage of preemptible virtual machines with a retry error statergy for up to 5 retries. Default (`true`)
Enables the usage of preemptible virtual machines with a retry error statergy for up to 5 retries. Default (`true`).
#### `--google-debug`
Copies the /google debug directory from the VM to the task bucket directory. Useful for debugging. Default (`false`).
## Google Cloud Life Sciences Setup
## Cloud Life Sciences Setup
Please refer to the [Google Cloud](https://cloud.google.com/life-sciences/docs/tutorials/nextflow) and [Nextflow](https://www.nextflow.io/docs/latest/google.html#cloud-life-sciences) documentation which describe how to setup the Google Cloud environment.

Binary file not shown.

Before

Width:  |  Height:  |  Size: 13 KiB

@ -0,0 +1,96 @@
<?xml version="1.0" encoding="utf-8"?>
<!-- Generator: Adobe Illustrator 23.0.1, SVG Export Plug-In . SVG Version: 6.00 Build 0) -->
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd" [
<!ENTITY ns_extend "http://ns.adobe.com/Extensibility/1.0/">
<!ENTITY ns_ai "http://ns.adobe.com/AdobeIllustrator/10.0/">
<!ENTITY ns_graphs "http://ns.adobe.com/Graphs/1.0/">
<!ENTITY ns_vars "http://ns.adobe.com/Variables/1.0/">
<!ENTITY ns_imrep "http://ns.adobe.com/ImageReplacement/1.0/">
<!ENTITY ns_sfw "http://ns.adobe.com/SaveForWeb/1.0/">
<!ENTITY ns_custom "http://ns.adobe.com/GenericCustomNamespace/1.0/">
<!ENTITY ns_adobe_xpath "http://ns.adobe.com/XPath/1.0/">
]>
<svg version="1.1" id="Art" xmlns:x="&ns_extend;" xmlns:i="&ns_ai;" xmlns:graph="&ns_graphs;"
xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px" viewBox="0 0 8986.8 1407.9"
style="enable-background:new 0 0 8986.8 1407.9;" xml:space="preserve">
<style type="text/css">
.st0{fill:#EA4335;}
.st1{fill:#4285F4;}
.st2{fill:#34A853;}
.st3{fill:#FBBC05;}
.st4{fill:#5F6368;}
</style>
<metadata>
<sfw xmlns="&ns_sfw;">
<slices></slices>
<sliceSourceBounds bottomLeftOrigin="true" height="1407.9" width="8986.8" x="-4403.9" y="-689.9"></sliceSourceBounds>
</sfw>
</metadata>
<title>Cloud_Logo_Nav</title>
<g>
<g>
<path class="st0" d="M1057.1,369.2h50.8l144.8-144.8l7.1-61.5C990.3-75,579-49.3,341.1,220.2C275,295,227.1,384.1,200.9,480.5
c16.1-6.6,34-7.7,50.8-3l289.6-47.8c0,0,14.7-24.4,22.4-22.9c128.8-141.5,345.6-158,494.4-37.6L1057.1,369.2z"/>
<path class="st1" d="M1459,480.5c-33.3-122.6-101.6-232.8-196.6-317l-203.2,203.2c85.8,70.1,134.7,175.8,132.6,286.6v36.1
c99.9,0,180.9,81,180.9,180.9s-81,180.9-180.9,180.9H830l-36.1,36.6v217l36.1,36.1h361.8c259.8,2,472.1-207,474.1-466.8
C1667.1,716.3,1589.4,568.7,1459,480.5z"/>
<path class="st2" d="M467.7,1338.6h361.8V1049H467.7c-25.8,0-51.2-5.6-74.7-16.3l-50.8,15.8l-145.8,144.8l-12.7,50.8
C265.4,1305.9,365.2,1339.1,467.7,1338.6z"/>
<path class="st3" d="M467.7,399.2C207.8,400.7-1.5,612.6,0,872.5c0.9,145.1,68.6,281.7,183.7,370.1l209.8-209.8
c-91-41.1-131.5-148.3-90.4-239.3s148.3-131.5,239.3-90.4c40.1,18.1,72.2,50.3,90.4,90.4l209.8-209.8
C753.4,466.9,614.6,398.6,467.7,399.2z"/>
</g>
<g>
<g>
<path class="st4" d="M2629.1,1136.4c-125.9,1.6-246.9-48.1-335.3-137.7c-91.3-85.8-142.3-206-140.7-331.3
c-1.5-125.3,49.5-245.4,140.7-331.3c88-90.5,209.1-141.2,335.3-140.2c120.2-1.6,236.1,45.1,321.6,129.6l-90.4,92
c-61.9-59.9-145.1-92.7-231.2-91.5c-90.3-1.1-177,35.8-238.8,101.6c-64.2,63.7-99.6,150.9-98.1,241.3
c-0.8,89.4,34.6,175.3,98.1,238.3c130.8,130.4,341.7,132.9,475.6,5.6c39.9-43.6,64.3-99.2,69.6-158h-304.9V624.8H3062
c4.2,26.2,5.9,52.7,5.1,79.3c5.4,110.9-34.8,219.2-111.3,299.8C2870.7,1092.4,2751.9,1140.6,2629.1,1136.4z M3632.1,1050
c-120.3,115.3-310.1,115.3-430.4,0c-58.3-56.5-90.1-134.8-87.9-215.9c-2.2-81.1,29.7-159.4,87.9-215.9c120.4-115,310-115,430.4,0
c58.2,56.5,90.1,134.8,87.9,215.9c2.1,81.2-30,159.5-88.4,215.9H3632.1z M3296.7,965.2c62.1,66.4,166.3,69.8,232.7,7.6
c2.6-2.5,5.2-5,7.6-7.6c33.9-35.1,52.2-82.3,50.8-131.1c1.5-48.9-16.8-96.4-50.8-131.6c-63.9-66.6-169.7-68.9-236.4-5
c-1.7,1.6-3.4,3.3-5,5c-34,35.2-52.3,82.7-50.8,131.6c-1.3,48.8,17.2,96.1,51.3,131.1H3296.7z M4293.6,1050
c-120.3,115.3-310.1,115.3-430.4,0c-58.3-56.5-90.1-134.8-87.9-215.9c-2.2-81.1,29.7-159.4,87.9-215.9
c120.3-115.3,310.1-115.3,430.4,0c58.2,56.5,90.1,134.8,87.9,215.9C4383.8,915.2,4351.9,993.5,4293.6,1050z M3958.3,965.2
c62.1,66.4,166.3,69.8,232.7,7.6c2.6-2.5,5.2-5,7.6-7.6c33.9-35.1,52.2-82.3,50.8-131.1c1.5-48.9-16.8-96.4-50.8-131.6
c-63.9-66.6-169.7-68.9-236.3-5c-1.7,1.6-3.4,3.3-5,5c-34,35.2-52.3,82.7-50.8,131.6c-1.3,48.8,17.2,96.1,51.3,131.1H3958.3z
M4728.5,1407.7c-60.9,1.9-120.6-17.1-169.2-53.9c-43.1-32.4-77.1-75.5-98.6-125l115.8-48.3c12.6,29.6,32.3,55.6,57.4,75.7
c26.8,21.6,60.5,33,95,32c44.2,2.7,87.4-14,118.4-45.7c30.6-36.9,45.7-84.3,42.2-132.1v-43.7h-4.6c-39.3,46.6-98.2,72-159,68.6
c-77.1,0.2-150.8-31.8-203.2-88.4c-56.8-56.1-88.2-133-86.9-212.9c-1.4-80.3,30-157.7,86.9-214.4c52.3-56.8,126-89.1,203.2-88.9
c32.3-0.1,64.3,7.1,93.5,20.8c25.3,11,47.8,27.5,66.1,48.3h4.6v-48.3h126v541.1c6.7,86.5-22.5,172-80.8,236.3
C4879.8,1382,4805.3,1410.4,4728.5,1407.7z M4737.7,1017.5c43.9,1,86-17.7,114.8-50.8c31.3-35.9,47.9-82.4,46.2-130.1
c1.9-48.5-14.6-95.8-46.2-132.6c-28.8-33.2-70.9-51.8-114.8-50.8c-45.1-0.9-88.4,17.6-118.9,50.8
c-33.6,35.5-51.9,82.8-50.8,131.6c-1,48.4,17.2,95.2,50.8,130.1C4649.1,999.2,4692.4,1018.1,4737.7,1017.5z M5240.2,230v888.1
h-132.6V230L5240.2,230z M5604,1136.4c-80.3,2.1-157.8-29.4-213.9-86.9c-56.9-57-88-134.9-85.9-215.4
c-3-80.7,26.9-159.2,82.8-217.5c52.8-55.6,126.6-86.4,203.2-84.9c34.9-0.4,69.4,6.4,101.6,19.8c29,11.7,55.4,29,77.7,50.8
c19.2,18.5,36.2,39.1,50.8,61.5c11.8,18.9,21.8,38.8,30,59.4l13.7,34.6L5457.6,925c25.2,57.8,83.3,94.2,146.3,91.5
c60.9,0.2,117.4-31.7,148.9-83.8l101.6,68.6c-25.9,37.1-59.1,68.6-97.6,92.5C5711.2,1122.6,5658,1137.4,5604,1136.4z
M5434.3,824.9l270.3-112.3c-8.3-19.8-23.2-36.1-42.2-46.2c-21.2-12-45.2-18.1-69.6-17.8c-41.3,1.1-80.6,18.4-109.2,48.3
C5448.9,730.1,5430.8,777,5434.3,824.9z"/>
</g>
<g>
<path class="st4" d="M6558.7,1136.4c-231.2,4-421.8-180.2-425.8-411.4c-0.1-5.6-0.1-11.3,0.1-16.9
c-5.4-231.2,177.7-422.9,408.8-428.3c5.6-0.1,11.3-0.1,16.9-0.1c115.6-3.6,226.6,45.8,301.3,134.1l-73.2,71.1
c-54.9-69.1-139.5-107.8-227.6-104.2c-84.5-1.9-166.2,30.8-226.1,90.4c-62.3,62.7-95.6,148.5-92,236.8
c-3.7,88.3,29.7,174.1,92,236.8c59.9,59.7,141.6,92.3,226.1,90.4c98.4,1.1,191.9-42.7,254-118.9l73.2,73.2
c-38.3,45.8-86.4,82.4-140.7,107.2C6687.1,1123.8,6623.2,1137.4,6558.7,1136.4z"/>
<path class="st4" d="M7083,1118.1h-105.2V297.5H7083V1118.1z"/>
<path class="st4" d="M7254.8,624.2c114.7-113.9,299.9-113.9,414.6,0c54.4,57.5,83.7,134.3,81.3,213.4
c2.4,79.1-26.9,155.9-81.3,213.4c-114.7,113.9-299.9,113.9-414.6,0c-54.4-57.5-83.7-134.3-81.3-213.4
C7171.1,758.5,7200.3,681.7,7254.8,624.2z M7333,985c67.3,71.1,179.5,74.2,250.7,6.9c2.4-2.2,4.7-4.6,6.9-6.9
c37.1-39.8,56.7-92.9,54.4-147.3c2.4-54.4-17.2-107.5-54.4-147.3c-67.3-71.1-179.5-74.2-250.7-6.9c-2.4,2.2-4.7,4.6-6.9,6.9
c-37.1,39.8-56.7,92.9-54.4,147.3c-2.1,54.3,17.7,107.2,54.9,146.8L7333,985z"/>
<path class="st4" d="M8333.4,1118.1h-101.6v-77.7h-3c-18.1,29.5-43.7,53.7-74.2,70.1c-31.6,18.3-67.6,28-104.2,27.9
c-60.2,4.1-118.9-19.5-159.5-64c-38.5-48.7-57.8-109.8-54.4-171.7V557.2h105.2v326.2c0,104.7,46.2,157,138.7,157
c41.7,1.3,81.4-17.6,106.7-50.8c27.3-34.5,41.8-77.4,41.2-121.4v-311h105.2V1118.1z"/>
<path class="st4" d="M8690.6,1136.4c-72.2,0.2-140.9-31.1-188-85.9c-52.7-58.2-80.9-134.4-78.8-212.9
c-2.1-78.5,26.1-154.7,78.8-212.9c47.1-54.7,115.8-86.1,188-85.9c40-0.6,79.5,8.8,114.8,27.4c31.1,15.6,57.4,39.3,76.2,68.6h4.6
l-4.6-77.7V297.5h105.2v820.6h-101.6v-77.7h-4.6c-18.8,29.3-45.1,53-76.2,68.6C8769.4,1127.4,8730.3,1136.9,8690.6,1136.4z
M8707.9,1040.4c48.1,0.7,94.2-19.3,126.5-54.9c35.7-40.7,54-93.8,50.8-147.9c3.2-54-15.1-107.2-50.8-147.9
c-63.8-70.2-172.4-75.3-242.6-11.4c-4,3.6-7.8,7.5-11.4,11.4c-35.8,40.4-54.1,93.4-50.8,147.3c-3.3,53.9,15,106.9,50.8,147.3
C8612.8,1020.7,8659.3,1041.1,8707.9,1040.4z"/>
</g>
</g>
</g>
</svg>

After

Width:  |  Height:  |  Size: 7.2 KiB

Loading…
Cancel
Save