tonyyzy / RNASeq

A framework for RNA-seq data analysis workflows

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Standardise cwl tools output names #71

Open tonyyzy opened 5 years ago

tonyyzy commented 5 years ago

[ ] change all scripts file input as input_script no matter R or python script

tonyyzy commented 5 years ago

DESeq2

count_matrix: prev/gene_count

[ ] prepDE, salmon_count should output gene_count_matrix as gene_count

tonyyzy commented 5 years ago

DEXSeq

count_matrix: prev_folder/out

[ ] DEXSeq takes the foldered output from previous step

tonyyzy commented 5 years ago

cufflinks

alignment_file: samtools_1/samtools_out cufflinks takes in bam file and samtools is the only one outputing bam files for now? maybe change samtools output name to bam?