Bubble up some more errors

[DLBPointon]

Last week I ran into a situation where it would be nice to have some extra error handling.

Essentially I was running nf-test on a number of subworkflows and modules for our internal modules repo, at some point the nf-core modules cache (the .git database) got corrupted, potentially me spamming too many runs over too short a period of time.

After this, the runner would stop at Installing nf-core modules.... at one point I left this overnight (prior to realising the cache was corrupted) and it was still at the same point. It wouldn't properly die until I exit the program.

Running later on with nf-core to install a module resulted in a an error that better led to the issue and I understand now, that many of these commands are actually wrappers for an underlying nf-core tools command. Which has taken me to where I think the error comes from...

Ignore the inlines pointing to specific lines, I was trying to link to the whole function.

nft-utils/src/main/java/nf_core/nf/test/utils/NfCoreUtils.java

Line 47 in 9a90921

@SuppressWarnings("unchecked")

nft-utils/src/main/java/nf_core/nf/test/utils/NfCoreUtils.java

Lines 111 to 121 in 9a90921

	// Spit out nf-core tools stderr if install fails
	if (result.exitCode != 0) {
	System.err.println("Error installing module " + name + ": exit code " + result.exitCode + "\n");
	System.out.println("Installation command: \n" + command.toString());
	System.err.println("nf-core tools output: \n");
	System.err.println(result.stderr);
	} else {
	System.out.println("Successfully installed module: " + name);
	// Write state file to mark module as installed
	writeModuleStateFile(stateFile);
	}

The error of nf-core crashing due to a corrupted nf-core-modules repo seems to fall outside of the current error catching.

I'll try and re-create the situation for more details.