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"planemo upload commit ff0d185541dc4b0a5839fca166f1beb459dee61c"
author gaelcge
date Tue, 02 Aug 2022 19:42:44 +0000
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1 # GenAP2 Galaxy implementation of CellRanger-ATAC
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2 Disclaimer: This wrapper for CellRanger-ATAC is not developed or supported by 10x Genomics. This wrapper was written by scientists at GenAP to help facilitate usage of CellRanger tools inside of Galaxy.
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3 Please find the full, official 10x Genomics licensing information at : https://support.10xgenomics.com/docs/license.
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5 What is CellRanger ATAC?
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7 https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac
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9 Naming convention of FASTQ files internally in Galaxy follows thes guidelines:
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10
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11 https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/using/fastq-input#rightname
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13 Installation:
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14 1) Install this wrapper via the Galaxy toolshed.
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15 2) CellRanger-ATAC (v2.0.0) is required for this wrapper and should be installed separately (see below).
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17 To use this tool, we assume that cellranger-atac (v.2.0.0) is available to Galaxy on the system, via the command cellranger-atac. Unfortunately at this point, we cannot include Cellranger-ATAC as part of this wrapper due to Licensing and distribution limitations. For more information on how to install CellRanger-ATAC on your system, please see :
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18 https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/installation