Update bgd to bw conversion in callpeak_macs2.bds

[florianduclot]

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The bedgraph to BigWig conversion step throws an error on my system for all my files: (...)pooled.tagAlign.fc.signal.srt.bedgraph is not case-sensitive sorted at line 1879. Please use "sort -k1,1 -k2,2n" with LC_COLLATE=C, or bedSort and try again. As mentioned in the error message and at https://gist.github.com/taoliu/2469050, using LC_COLLATE=C fixes the issue on my system when the command is ran separately (outside of chipseq.bds pipeline).

Would this addition cause conflict with the rest of the code?

Thanks,

[leepc12]

The funciton already has LC_COLLATE=C in line 67 of https://github.com/florianduclot/TF_chipseq_pipeline/blob/ca31df6fb4f484156eb7c098be3f938158141498/modules/callpeak_macs2.bds

But it was not exported so I modified it to export LC_COLLATE=C (in the commit 082c4a7d4e73f6ba7469e3d8a0f7d099dcc782cf).

[florianduclot]

Sorry I didn't notice this line before.

Thanks!