Modules/slms 3/1.0

[lkhilton]

This PR fixes a problem with Mutect2 VCF sample name replacement that occurred when the sample ID pulled from the BAM header contains a space (shockingly not uncommon). It also incorporates the full all input from each sub-module to ensure all the final 99-outputs directories are properly populated.

I've also rolled in a patch to all the Manta modules (version 2.0 or higher) that moves the augment_manta_vcf.py script from an input to a parameter to prevent re-running if the lcr-scripts directory moves or changes (see #166).

[rdmorin]

Wow. How does someone even put a space into the sample ID field in the bam header?

[rdmorin]

I don't see updates to the default.yaml config file for versions 2.1 and 2.2. Can you confirm that you've applied this bug fix retroactively and to both the config and smk file for each?

[lkhilton]

I can see it when I look at the files changed section...

[rdmorin]

I see them now. I guess you used version 1.0 and 1.1 of the script consistently with what version was used in the Manta version?

[lkhilton]

Right, I didn't change anything except how the script is called by the Snakemake rule and where it's specified in the config.

[rdmorin]

Seeing as there's active development of Manta on another branch, could you also drop in the changes Lakshay has made to this module (just in version 2.3) so he doesn't get another conflict later? You should be able to paste them right from his PR. I'm specifically thinking of the oncopipe version check and updates to symlinking.

[lkhilton]

I think this is going to result in a conflict for him anyway, but it will be trivial to fix. I can give him a heads up about it.

[rdmorin]

It will auto-merge when it can. I just thought if you add in his changes the auto-merge might happen. It's hard to know