MuSiC-Deconvolution: Data generation | sc | metadata
1.0

Workflow Type: Galaxy

This workflow generates from only an EBI SCXA reference the metadata for creating an ESet object

Associated Tutorial

This workflows is part of the tutorial Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution, available in the GTN

Thanks to...

Workflow Author(s): Wendi Bacon, Mehmet Tekman

Tutorial Author(s): Wendi Bacon, Mehmet Tekman

Tutorial Contributor(s): Marisa Loach, Mehmet Tekman, Saskia Hiltemann, Wendi Bacon, Helena Rasche, Pablo Moreno, Julia Jakiela, Pavankumar Videm

gtn star logo followed by the word workflows

Steps

ID Name Description
0 EBI SCXA Data Retrieval toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.1+galaxy1
1 Cut Cut1
2 Add line to file toolshed.g2.bx.psu.edu/repos/bgruening/add_line_to_file/add_line_to_file/0.1.0
3 Reformatting metadata columns Adjust this step as necessary toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.2
4 Join two Datasets Experimental designs often include extra stuff (likely the barcodes not meeting the EBI pre-processing criteria), so this way we streamline down to only those barcodes in the barcodes file. join1
5 Advanced Cut Gets rid of the duplicated columns toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0

Outputs

ID Name Description Type
_anonymous_output_1 #main/_anonymous_output_1 n/a
  • File
_anonymous_output_2 #main/_anonymous_output_2 n/a
  • File
_anonymous_output_3 #main/_anonymous_output_3 n/a
  • File
_anonymous_output_4 #main/_anonymous_output_4 n/a
  • File
_anonymous_output_5 #main/_anonymous_output_5 n/a
  • File
_anonymous_output_6 #main/_anonymous_output_6 n/a
  • File
_anonymous_output_7 #main/_anonymous_output_7 n/a
  • File
_anonymous_output_8 #main/_anonymous_output_8 n/a
  • File
_anonymous_output_9 #main/_anonymous_output_9 n/a
  • File

Version History

1.0 (earliest) Created 2nd Jun 2025 at 10:58 by GTN Bot

Added/updated 4 files


Open master aba55c2
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Created: 2nd Jun 2025 at 10:58

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