--assembly flag of gridss module leads to empty bam files

[famosab]

Have you checked the docs?

• nf-core website: troubleshooting
• nf-core modules documentation

Description of the bug

GRIDSS allows to set a flag called --assembly which should report a bam file as a part of the structural variant calling algorithm that is implemented in the tool. This was also added to the nf-core module. While porting to nf-test I realised that the created files were always empty and the exact way to set the flag was unclear so I asked the tool developers: PapenfussLab/gridss#664. For now I suggest removing the flag from the module and add it later when the usage is better documented.

Command used and terminal output

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Relevant files

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System information

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