Gene expression merge - combines RPKM gene expression from several experiments

Workflow: Gene expression merge - combines RPKM gene expression from several experiments

Fetched 2023-01-09 00:52:15 GMT

Verified with cwltool version 3.1.20221201130942

Gene expression merge - combines RPKM gene expression from several experiments =================================================================================== Workflows merges RPKM gene expression from several experiments based on the values from GeneId, Chrom, TxStart, TxEnd and Strand columns. Reported RPKM columns are renamed based on the experiments names.

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This workflow is Open Source and may be reused according to the terms of: Apache License 2.0

Note that the tools invoked by the workflow may have separate licenses.

Inputs

ID	Type	Title	Doc
alias	String	Experiment short name/Alias
rpkm_genes	File[] [TSV]	RNA-Seq experiments	CSV/TSV file with RPKM grouped by gene name
sample_names	String[]	RNA-Seq experiments	Aliases for RNA-Seq experiments to be used as the names for the reported columns in the merged file. Order corresponds to the rpkm_genes input

Steps

ID	Runs	Label	Doc
feature_merge	../tools/feature-merge.cwl (CommandLineTool)	Feature merge - merges feature files based on the specified columns	Tool merges input feature files based on the columns provided in --mergeby input. All input feature CSV/TSV files should have the header (case-sensitive) Format of the input files is identified based on file's extension .csv - CSV .tsv - TSV Otherwise used CSV by default The output file's rows order corresponds to the rows order of the first CSV/TSV feature file. Output is always saved in TSV format. Output file includes only rows intersected by column names set in --mergeby. Output file includes only columns set in --mergeby and --report parameters. Column set in the --report parameter is renamed based on the --aliases or basenames of the --features files.

Outputs

ID	Type	Label	Doc
merged_file	File [TSV]	Merged gene expression file	Merged by GeneId, Chrom, TxStart, TxEnd and Strand gene expression files with reported and renamed Rpkm columns.
feature_merge_stderr_log	File [Textual format]	Gene expression merge stderr log	Gene expression merge stderr log
feature_merge_stdout_log	File [Textual format]	Gene expression merge stdout log	Gene expression merge stdout log

Permalink: https://w3id.org/cwl/view/git/564156a9e1cc7c3679a926c479ba3ae133b1bfd4/workflows/feature-merge.cwl