MTX_TO_H5AD module cannot take ch_star_index

[wzheng0520]

Description of the bug

Hi,

Thanks for upgrading this pipeline into newer version, I think here is a issue I meet after upgrading. I found it might cause by ch_star_index code is updated from ch_star_index = params.star_index ? file(params.star_index) : [] into ch_star_index = star_index ? [[id: star_index.baseName], star_index] : []. It causes the ch_star_index changed into linked list stared with star_index.baseName. However, in MTX_TO_H5AD module, their input still take path star_index.

From my understanding, path star_index cannot accept the new ch_star_index format and we might need to either change the input formate for star_index into acceptable way or we might can directly use star_index = params.star_index ? file(params.star_index, checkIfExists: true) : null as input for MTX_TO_H5AD.

like this:

MTX_CONVERSION (
        ch_mtx_matrices,
        ch_input,
        ch_txp2gene,
        star_index
    )

Command used and terminal output

Error executing process > 'NFCORE_SCRNASEQ:SCRNASEQ:MTX_CONVERSION:MTX_TO_H5AD (1)'

Caused by:
  Not a valid path value type: java.util.LinkedHashMap ([id:STARIndex])


Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

Relevant files

No response

System information

No response

[grst]

We are currently refactoring the matrix conversion code in #369. This should hopefully also fix the error you are encountering.

[wzheng0520]

Thanks so much!