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BIMSBbioinfo / pigx_bsseq

bisulfite sequencing pipeline from fastq to methylation reports
https://bioinformatics.mdc-berlin.de/pigx/
GNU General Public License v3.0
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Put the rules in order #117

Closed Blosberg closed 6 years ago

Blosberg commented 6 years ago

A make file should have rules shown in their hierarchical order for readability

D: requires C

C: requires B

B: requires A

so that can read A->B->C->D from bottom up. Things like this in the code, however, make this impossible 

rule final_report: 
    input:  
        rules.bam_methCall.output,
        rules.methseg.output,                                                                                 
        lambda wc: finalReportDiff

This forces bam_methCall to be defined as a rule before (i.e. higher in the script than) final_report. It makes the whole script harder to read, and at some point we should rearrange it so that bam_methCall has its output refer to the inputs of final_report.

Blosberg commented 6 years ago

This was done in the dedupe_patch merge, here: https://github.com/BIMSBbioinfo/pigx_bsseq/pull/124