{"id":98,"date":"2020-04-28T10:55:24","date_gmt":"2020-04-28T10:55:24","guid":{"rendered":"http:\/\/www.ebi.ac.uk\/training\/online\/courses\/nextflow\/getting-data-from-resource-name\/"},"modified":"2022-05-20T07:25:49","modified_gmt":"2022-05-20T07:25:49","slug":"rna-seq-example-pipeline-and-containers","status":"publish","type":"page","link":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/nextflow\/rna-seq-example-pipeline-and-containers\/","title":{"rendered":"RNA-Seq example pipeline and containers"},"content":{"rendered":"\n<p class=\"wp-block-paragraph\">This second video aims to demonstrate of writing a basic RNA-Seq example pipeline. <\/p>\n\n\n\n<p class=\"wp-block-paragraph\">A very important part of modern cloud-native development is containerisation, so it also covers popular containers (Docker\/Singularity\/Conda) too. The container helps to port the pipelines with dependencies irrespective of the environment, so researchers can move pipelines from one infrastructure to another infrastructure, easily.&nbsp; <\/p>\n\n\n\n<div style=\"text-align:center\"><iframe loading=\"lazy\" src=\"https:\/\/embl-ebi.cloud.panopto.eu\/Panopto\/Pages\/Embed.aspx?id=3511d55f-6d84-43e2-9fd9-ae7100d92d1d&amp;autoplay=false&amp;offerviewer=true&amp;showtitle=true&amp;showbrand=true&amp;captions=false&amp;interactivity=all\" style=\"border: 1px solid #464646;\" allowfullscreen=\"\" allow=\"autoplay\" width=\"720\" height=\"405\"><\/iframe><\/div>\n\n\n\n<p class=\"has-text-align-center wp-block-paragraph\"> This video is made available under a <a rel=\"noreferrer noopener\" href=\"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/\" target=\"_blank\">CC BY-NC-ND licence<\/a>\u00a0by\u00a0Seqera Labs.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Links mentioned in the recording:<\/p>\n\n\n\n<ol class=\"wp-block-list\"><li><a rel=\"noreferrer noopener\" href=\"https:\/\/github.com\/nextflow-io\/rnaseq-nf\" target=\"_blank\">RNA-Seq pipeline<\/a><\/li><li><a rel=\"noreferrer noopener\" href=\"https:\/\/www.nextflow.io\/docs\/latest\/singularity.html#how-it-works\" target=\"_blank\">Nextflow Singularity<\/a><\/li><li><a rel=\"noreferrer noopener\" href=\"https:\/\/www.nextflow.io\/docs\/latest\/executor.html#executors\" target=\"_blank\">Nextflow executors<\/a><\/li><li><a rel=\"noreferrer noopener\" href=\"https:\/\/www.nextflow.io\/blog\/2019\/demystifying-nextflow-resume.html\" target=\"_blank\">Demystifying Nextflow resume<\/a><\/li><\/ol>\n","protected":false},"excerpt":{"rendered":"<p>This second video aims to demonstrate of writing a basic RNA-Seq example pipeline. A very important part of modern cloud-native development is containerisation, so it also covers popular containers (Docker\/Singularity\/Conda) too. The container helps to port the pipelines with dependencies irrespective of the environment, so researchers can move pipelines from one infrastructure to another infrastructure,&#8230;<\/p>\n","protected":false},"author":30,"featured_media":0,"parent":0,"menu_order":3,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-98","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/nextflow\/wp-json\/wp\/v2\/pages\/98","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/nextflow\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/nextflow\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/nextflow\/wp-json\/wp\/v2\/users\/30"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/nextflow\/wp-json\/wp\/v2\/comments?post=98"}],"version-history":[{"count":10,"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/nextflow\/wp-json\/wp\/v2\/pages\/98\/revisions"}],"predecessor-version":[{"id":287,"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/nextflow\/wp-json\/wp\/v2\/pages\/98\/revisions\/287"}],"wp:attachment":[{"href":"https:\/\/www.ebi.ac.uk\/training\/online\/courses\/nextflow\/wp-json\/wp\/v2\/media?parent=98"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}