snakepipes: Sample file in WGBS does not produces the appropriate groups

It appears as if names and conditions are all mixed up: Continuing from issue 589 Sample sheet is :

name	condition
109242	109242	wt_B73
109243	109243	wt_B73
109244	109244	wt_B73
109245	109245	mut_pht1_6
109246	109246	mut_pht1_6
109247	109247	mut_pht1_6

while running the metillene I found the following that is troublesome:

the following ids belong to group A (n=1): 0: column: 0, name:109242_wt_B73 the following ids belong to group B (n=1): 0: column: 1, name:109243_wt_B73

Group A should have been wt_B73 and GroupB mut_pht1_6

and same for dmrseq: params = list(NULL, 'dmrseq_BU16_minCoverage5', '/home/hthiele0/snakemake/BU16.txt', c('109242', '109243'), 300, 10, 0.1, 5, 0.1, "blacklist" = NULL, "odir" = 'dmrseq_BU16_minCoverage5', "sampleSheet" = '/home/hthiele0/snakemake/BU16.txt', "groups" = c('109242', '109243'), "maxDist" = 300, "minCpGs" = 10, "minMethDiff" = 0.1, "minCoverage" = 5, "FDR" = 0.1),

So I think that the outputs are not of the correct comparisons

just to add for metilene: from the header of

metilene_BU16_minCoverage5/metilene.IN.txt

chr pos 109242_wt_B73 109243_wt_B73 109244_wt_B73 109245_mut_pht1_6 109246_mut_pht1_6 109247_mut_pht1_6

and then: from header of

metilene_BU16_minCoverage5/DMRs.txt:

chrom start end q-value mean methylation difference nCpGs p (MWU) p (2D KS) mean_109242 mean_109243