Anna

[annapamma]

There was an error with imputation, where it would say some rows are all NA.

This was happening because the R script running imputation was expecting a comma-separated file, but the protein fetching scripts produced tab-separated files.

In this PR, the R script has been updated to read in tab-separated files.

The updated Docker image has been built and pushed.

[sgosline]

I assigned @LifeWorks to review - Song if this solves your problem, then feel free to close and merge!

[LifeWorks]

I tried to run with:

cwltool --debug imputation-tool.cwl --input_f file-pro.tsv --use_missForest false

but got the error:

Error in DreamAI(data, k = 10, maxiter_MF = 10, ntree = 100, maxnodes = NULL, :
Some Rows Are Missing All Values !!
Execution halted
INFO [job imputation-tool] Max memory used: 1851MiB
ERROR [job imputation-tool] Job error:
("Error collecting output for parameter 'matrix':\nimputation-tool.cwl:35:13: Did not find output file with glob pattern: '['imputed_file.tsv']'", {})
WARNING [job imputation-tool] completed permanentFail
DEBUG [job imputation-tool] outputs {}
DEBUG [job imputation-tool] Removing input staging directory /private/tmp/docker_tmpgt7gu5q3
DEBUG [job imputation-tool] Removing temporary directory /private/tmp/docker_tmpna1pddyk
{}
WARNING Final process status is permanentFail