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Standardise cwl tools output names #71

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tonyyzy opened this issue Feb 19, 2019 · 3 comments
Open
1 task

Standardise cwl tools output names #71

tonyyzy opened this issue Feb 19, 2019 · 3 comments
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@FilipeJesus @tonyyzy @ajle96
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Essential Essential functions need implementation
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End of week 7

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tonyyzy commented Feb 19, 2019 •
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  • change all scripts file input as input_script no matter R or python script
@tonyyzy tonyyzy added the Essential Essential functions need implementation label Feb 19, 2019
@tonyyzy tonyyzy added this to the End of week 7 milestone Feb 19, 2019
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tonyyzy commented Feb 19, 2019 •
edited by ajle96
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DESeq2

count_matrix: prev/gene_count

  • prepDE, salmon_count should output gene_count_matrix as gene_count

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tonyyzy commented Feb 19, 2019

DEXSeq

count_matrix: prev_folder/out

  • DEXSeq takes the foldered output from previous step

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tonyyzy commented Feb 21, 2019

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?

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@ajle96 ajle96

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@FilipeJesus @tonyyzy @ajle96