Nils Homer

@anntzer I'll add it my list to make a PR for `definition_list`. Perhaps we can add to the docs that the description should be in RST. Are there other formats...

When I ran this with `4.5.0.0`, I get: ``` chr1 68896800 . G . . END=68896831 GT:DP:GQ:MIN_DP:PL 0/0:118:99:107:0,120,1800 chr1 68896832 . CTTTAGTTTT C, 1597.60 . BaseQRankSum=0.000;DP=122;ExcessHet=0.0000;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=439200,122;ReadPosRankSum=1.341 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:67,43,0:110:99:0|1:68896832_CTTTAGTTTT_C:1605,0,2683,1807,2813,4620:68896832:67,0,43,0 chr1 68896841...

@ldgauthier definitely `HaplotypeCaller` is doing the right thing. I did walk through the GenotypeGvcfs code, and it doesn't look at the PGT FORMAT tag at all, it just leads that...

@droazen @ldgauthier @eitanbanks @tfenne the issue with `GenotypeGvcfs` outputting the wrong phase will still exist, even if @tfenne makes the change to `HaplotypeCaller` (@tfenne: could you move further discussion of...

I would also add that I wouldn't mind having this!

CC: @tfenne @natproach

I think we're conflating a few things. 1. A sample sheet should list the meta data per-sample. For example, the sample name, identifier, sample barcode and so on. For demux...

Here's what I am thinking. sample_sheet.csv (aka "the per-flowcell actual samplesheet", `fqtk` needs TSV, but that's easily converted from the CSV) ``` sample_id,barcode s1,AAGCCCAATAAACCAC s2,TCTGACTGGCCGAATA s3,GGGATATAGGCAACGA s4,CATGTGCGGCGACCCT s5,TGCGACAGTGACGCTT s6,TCGCCGTTGCCTAAAC s7,CTATTTGAAGGAGTCT...

I disagree with @blajoie. The sample sheet describes samples and barcodes needed by a single demultiplexing invocation. The input to this pipeline is a manifest of independent invocations of the...

To be clear, here is the single metadata file that should be given as input to this pipeline: https://github.com/nf-core/demultiplex/blob/master/docs/usage.md#full-samplesheet  Then in that...