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broadinstitute / PANOPLY

Repository for the Broad Institute Proteogenomic Data Analysis Center (PGDAC) established by the NIH Clinical Proteomics Tumor Analysis Consortium (CPTAC)
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(Document update) panoply_cna_setup and panoply_cna_correlation #36

Closed hsiaoyi0504 closed 2 years ago

hsiaoyi0504 commented 2 years ago

It seems to me that the document of panoply_cna_setup module doesn't mention subgroups.txt is generated.

Also, relatively minor. In the document of panoply_cna_correlation, it doesn't mention these two files but looks like it's required in the process (run-pipeline.sh, around 603 to 607 lines).

groups=`cat subgroups.txt`
g=($groups)
# iterate through groups and execute cna-analysis.r for each
for i in `seq 1 "${#g[@]}"`; do
 line_i=`sed -n "${i}p" file_table.tsv`

Hope this helps other developers. Thanks.

drmani commented 2 years ago

Thanks for catching this. The panoply_cna_correlation should always be run using the tar file output from panoply_cna_setup as its input. In such a set up, the subgroups.txt and file_table.tsv files are internal to the workflow. We will update the documentation to reflect this.