Closed barrystokman closed 3 years ago
TC1:
(stage)[hiseq.clinical@thalamus 201111_A00621_0305_BHGJJKDSXY]$ demux sheet fetch -a nova -p -L HGJJKDSXY > /home/hiseq.clinical/STAGE/novaseq/runs/201111_A00621_0305_BHGJJKDSXY/TC1_samplesheet.csv
(stage)[hiseq.clinical@thalamus 201111_A00621_0305_BHGJJKDSXY]$ less TC1_samplesheet.csv | head
[Data]
FCID,Lane,SampleID,SampleRef,index,index2,SampleName,Control,Recipe,Operator,Project
HGJJKDSXY,1,ACC7198A3,hg19,CGTTAGAAAT,TTCAGGTCAC,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A16,hg19,GACCTGAAAT,TTGGTGAGAC,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A18,hg19,TCTCTACTAT,CGCGGTTCAC,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A7,hg19,GATTCTGCAT,GACGAGAGAC,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A20,hg19,CTCTCGTCAT,TATAACCTAC,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A9,hg19,TCGTAGTGAT,AGACTTGGAC,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A13,hg19,TAAGTGGTAT,CTTAAGCCAC,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A15,hg19,CGGACAACAT,TCCGGATTAC,300186,N,R1,script,300186
(stage)[hiseq.clinical@thalamus 201111_A00621_0305_BHGJJKDSXY]$ diff HGJJKDSXY_prod_samplesheet.csv TC1_samplesheet.csv
:heavy_check_mark:
TC2:
(stage)[hiseq.clinical@thalamus 201111_A00621_0305_BHGJJKDSXY]$ demux sheet fetch -a nova -p -L HGJJKDSXY > /home/hiseq.clinical/STAGE/novaseq/runs/201111_A00621_0305_BHGJJKDSXY/TC2_samplesheet.csv
(stage)[hiseq.clinical@thalamus 201111_A00621_0305_BHGJJKDSXY]$ less TC2_samplesheet.csv | head
[Data]
FCID,Lane,SampleID,SampleRef,index,index2,SampleName,Control,Recipe,Operator,Project
HGJJKDSXY,1,ACC7198A3,hg19,CGTTAGAAAT,TTCAGGTCAC,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A16,hg19,GACCTGAAAT,TTGGTGAGAC,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A18,hg19,TCTCTACTAT,CGCGGTTCAC,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A7,hg19,GATTCTGCAT,GACGAGAGAC,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A20,hg19,CTCTCGTCAT,TATAACCTAC,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A9,hg19,TCGTAGTGAT,AGACTTGGAC,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A13,hg19,TAAGTGGTAT,CTTAAGCCAC,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A15,hg19,CGGACAACAT,TCCGGATTAC,300186,N,R1,script,300186
(stage)[hiseq.clinical@thalamus 201111_A00621_0305_BHGJJKDSXY]$ diff HGJJKDSXY_prod_samplesheet.csv TC2_samplesheet.csv
:heavy_check_mark:
TC3:
(stage)[hiseq.clinical@thalamus 201111_A00621_0305_BHGJJKDSXY]$ demux sheet fetch -a nova -p -L HGJJKDSXY > /home/hiseq.clinical/STAGE/novaseq/runs/201111_A00621_0305_BHGJJKDSXY/TC3_samplesheet.csv
(stage)[hiseq.clinical@thalamus 201111_A00621_0305_BHGJJKDSXY]$ less TC3_samplesheet.csv | head
[Data]
FCID,Lane,SampleID,SampleRef,index,index2,SampleName,Control,Recipe,Operator,Project
HGJJKDSXY,1,ACC7198A3,hg19,CGTTAGAAAT,GACCTGAAGT,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A16,hg19,GACCTGAAAT,CTCACCAAGT,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A18,hg19,TCTCTACTAT,GAACCGCGGT,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A7,hg19,GATTCTGCAT,CTCTCGTCGT,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A20,hg19,CTCTCGTCAT,AGGTTATAGT,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A9,hg19,TCGTAGTGAT,CCAAGTCTGT,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A13,hg19,TAAGTGGTAT,GGCTTAAGGT,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A15,hg19,CGGACAACAT,AATCCGGAGT,300186,N,R1,script,300186
:heavy_check_mark:
TC4:
(stage)[hiseq.clinical@thalamus 201111_A00621_0305_BHGJJKDSXY]$ demux sheet fetch -a nova -p -L HGJJKDSXY > /home/hiseq.clinical/STAGE/novaseq/runs/201111_A00621_0305_BHGJJKDSXY/TC4_samplesheet.csv
(stage)[hiseq.clinical@thalamus 201111_A00621_0305_BHGJJKDSXY]$ less TC4_samplesheet.csv | head
[Data]
FCID,Lane,SampleID,SampleRef,index,index2,SampleName,Control,Recipe,Operator,Project
HGJJKDSXY,1,ACC7198A3,hg19,CGTTAGAA,GACCTGAA,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A16,hg19,GACCTGAA,CTCACCAA,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A18,hg19,TCTCTACT,GAACCGCG,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A7,hg19,GATTCTGC,CTCTCGTC,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A20,hg19,CTCTCGTC,AGGTTATA,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A9,hg19,TCGTAGTG,CCAAGTCT,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A13,hg19,TAAGTGGT,GGCTTAAG,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A15,hg19,CGGACAAC,AATCCGGA,300186,N,R1,script,300186
:heavy_check_mark:
TC5:
(stage)[hiseq.clinical@thalamus 201111_A00621_0305_BHGJJKDSXY]$ demux sheet fetch -a nova -L HGJJKDSXY
[Data]
FCID,Lane,SampleID,SampleRef,index,index2,SampleName,Control,Recipe,Operator,Project
HGJJKDSXY,1,ACC7198A3,hg19,CGTTAGAA,TTCAGGTC,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A16,hg19,GACCTGAA,TTGGTGAG,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A18,hg19,TCTCTACT,CGCGGTTC,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A7,hg19,GATTCTGC,GACGAGAG,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A20,hg19,CTCTCGTC,TATAACCT,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A9,hg19,TCGTAGTG,AGACTTGG,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A13,hg19,TAAGTGGT,CTTAAGCC,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A15,hg19,CGGACAAC,TCCGGATT,300186,N,R1,script,300186
:heavy_check_mark:
TC6:
(stage)[hiseq.clinical@thalamus 201111_A00621_0305_BHGJJKDSXY]$ demux sheet fetch -a nova -p HGJJKDSXY
Please specify an index length when using the pad option! Use --longest or --indexlength.
Aborted!
:heavy_check_mark:
TC7:
(stage)[hiseq.clinical@thalamus 201111_A00621_0305_BHGJJKDSXY]$ demux sheet fetch -a nova HGJJKDSXY
[Data]
FCID,Lane,SampleID,SampleRef,index,index2,SampleName,Control,Recipe,Operator,Project
HGJJKDSXY,1,ACC7198A3,hg19,CGTTAGAA,TTCAGGTC,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A16,hg19,GACCTGAA,TTGGTGAG,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A18,hg19,TCTCTACT,CGCGGTTC,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A7,hg19,GATTCTGC,GACGAGAG,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A20,hg19,CTCTCGTC,TATAACCT,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A9,hg19,TCGTAGTG,AGACTTGG,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A13,hg19,TAAGTGGT,CTTAAGCC,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A15,hg19,CGGACAAC,TCCGGATT,300186,N,R1,script,300186
:heavy_check_mark:
To be deployed together with https://github.com/Clinical-Genomics/servers/pull/461
Tests and test fixtures are WIP
RETESTS:
(stage)[hiseq.clinical@thalamus 201111_A00621_0305_BHGJJKDSXY]$ demux-stage sheet fetch -a nova -p -L HGJJKDSXY > TC1_samplesheet_RETEST.csv
(stage)[hiseq.clinical@thalamus 201111_A00621_0305_BHGJJKDSXY]$ less TC1_samplesheet_RETEST.csv | head
[Data]
FCID,Lane,SampleID,SampleRef,index,index2,SampleName,Control,Recipe,Operator,Project
HGJJKDSXY,1,ACC7198A3,hg19,CGTTAGAAAT,TTCAGGTCAC,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A16,hg19,GACCTGAAAT,TTGGTGAGAC,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A18,hg19,TCTCTACTAT,CGCGGTTCAC,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A7,hg19,GATTCTGCAT,GACGAGAGAC,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A20,hg19,CTCTCGTCAT,TATAACCTAC,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A9,hg19,TCGTAGTGAT,AGACTTGGAC,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A13,hg19,TAAGTGGTAT,CTTAAGCCAC,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A15,hg19,CGGACAACAT,TCCGGATTAC,300186,N,R1,script,300186
(stage)[hiseq.clinical@thalamus 201111_A00621_0305_BHGJJKDSXY]$ diff TC1_samplesheet.csv TC1_samplesheet_RETEST.csv
:heavy_check_mark:
(stage)[hiseq.clinical@thalamus 201111_A00621_0305_BHGJJKDSXY]$ demux-stage sheet fetch -a nova -p -L HGJJKDSXY > TC2_samplesheet_RETEST.csv
(stage)[hiseq.clinical@thalamus 201111_A00621_0305_BHGJJKDSXY]$ less TC2_samplesheet_RETEST.csv | head
[Data]
FCID,Lane,SampleID,SampleRef,index,index2,SampleName,Control,Recipe,Operator,Project
HGJJKDSXY,1,ACC7198A3,hg19,CGTTAGAAAT,TTCAGGTCAC,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A16,hg19,GACCTGAAAT,TTGGTGAGAC,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A18,hg19,TCTCTACTAT,CGCGGTTCAC,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A7,hg19,GATTCTGCAT,GACGAGAGAC,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A20,hg19,CTCTCGTCAT,TATAACCTAC,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A9,hg19,TCGTAGTGAT,AGACTTGGAC,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A13,hg19,TAAGTGGTAT,CTTAAGCCAC,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A15,hg19,CGGACAACAT,TCCGGATTAC,300186,N,R1,script,300186
(stage)[hiseq.clinical@thalamus 201111_A00621_0305_BHGJJKDSXY]$ diff TC2_samplesheet.csv TC2_samplesheet_RETEST.csv
:heavy_check_mark:
(stage)[hiseq.clinical@thalamus 201111_A00621_0305_BHGJJKDSXY]$ demux-stage sheet fetch -a nova -p -L HGJJKDSXY > TC3_samplesheet_RETEST.csv
(stage)[hiseq.clinical@thalamus 201111_A00621_0305_BHGJJKDSXY]$ less TC3_samplesheet_RETEST.csv | head
[Data]
FCID,Lane,SampleID,SampleRef,index,index2,SampleName,Control,Recipe,Operator,Project
HGJJKDSXY,1,ACC7198A3,hg19,CGTTAGAAAT,GACCTGAAGT,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A16,hg19,GACCTGAAAT,CTCACCAAGT,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A18,hg19,TCTCTACTAT,GAACCGCGGT,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A7,hg19,GATTCTGCAT,CTCTCGTCGT,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A20,hg19,CTCTCGTCAT,AGGTTATAGT,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A9,hg19,TCGTAGTGAT,CCAAGTCTGT,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A13,hg19,TAAGTGGTAT,GGCTTAAGGT,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A15,hg19,CGGACAACAT,AATCCGGAGT,300186,N,R1,script,300186
You have mail in /var/spool/mail/hiseq.clinical
(stage)[hiseq.clinical@thalamus 201111_A00621_0305_BHGJJKDSXY]$ diff TC3_samplesheet.csv TC3_samplesheet_RETEST.csv
:heavy_check_mark:
(stage)[hiseq.clinical@thalamus 201111_A00621_0305_BHGJJKDSXY]$ demux-stage sheet fetch -a nova -p -L HGJJKDSXY > TC4_samplesheet_RETEST.csv
(stage)[hiseq.clinical@thalamus 201111_A00621_0305_BHGJJKDSXY]$ less TC4_samplesheet_RETEST.csv | head
[Data]
FCID,Lane,SampleID,SampleRef,index,index2,SampleName,Control,Recipe,Operator,Project
HGJJKDSXY,1,ACC7198A3,hg19,CGTTAGAA,GACCTGAA,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A16,hg19,GACCTGAA,CTCACCAA,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A18,hg19,TCTCTACT,GAACCGCG,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A7,hg19,GATTCTGC,CTCTCGTC,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A20,hg19,CTCTCGTC,AGGTTATA,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A9,hg19,TCGTAGTG,CCAAGTCT,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A13,hg19,TAAGTGGT,GGCTTAAG,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A15,hg19,CGGACAAC,AATCCGGA,300186,N,R1,script,300186
(stage)[hiseq.clinical@thalamus 201111_A00621_0305_BHGJJKDSXY]$ diff TC4_samplesheet.csv TC4_samplesheet_RETEST.csv
(stage)[hiseq.clinical@thalamus 201111_A00621_0305_BHGJJKDSXY]$ demux-stage sheet fetch -a nova -L HGJJKDSXY > TC5_samplesheet_RETEST.csv
(stage)[hiseq.clinical@thalamus 201111_A00621_0305_BHGJJKDSXY]$ less TC5_samplesheet_RETEST.csv | head
[Data]
FCID,Lane,SampleID,SampleRef,index,index2,SampleName,Control,Recipe,Operator,Project
HGJJKDSXY,1,ACC7198A3,hg19,CGTTAGAA,TTCAGGTC,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A16,hg19,GACCTGAA,TTGGTGAG,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A18,hg19,TCTCTACT,CGCGGTTC,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A7,hg19,GATTCTGC,GACGAGAG,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A20,hg19,CTCTCGTC,TATAACCT,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A9,hg19,TCGTAGTG,AGACTTGG,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A13,hg19,TAAGTGGT,CTTAAGCC,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A15,hg19,CGGACAAC,TCCGGATT,300186,N,R1,script,300186
:heavy_check_mark:
(stage)[hiseq.clinical@thalamus 201111_A00621_0305_BHGJJKDSXY]$ demux-stage sheet fetch -a nova -p HGJJKDSXY
Please specify an index length when using the pad option! Use --longest or --index_length.
Aborted!
:heavy_check_mark:
(stage)[hiseq.clinical@thalamus 201111_A00621_0305_BHGJJKDSXY]$ demux-stage sheet fetch -a nova HGJJKDSXY > TC7_samplesheet_RETEST.csv
(stage)[hiseq.clinical@thalamus 201111_A00621_0305_BHGJJKDSXY]$ less TC7_samplesheet_RETEST.csv
(stage)[hiseq.clinical@thalamus 201111_A00621_0305_BHGJJKDSXY]$ less TC7_samplesheet_RETEST.csv | head
[Data]
FCID,Lane,SampleID,SampleRef,index,index2,SampleName,Control,Recipe,Operator,Project
HGJJKDSXY,1,ACC7198A3,hg19,CGTTAGAA,TTCAGGTC,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A16,hg19,GACCTGAA,TTGGTGAG,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A18,hg19,TCTCTACT,CGCGGTTC,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A7,hg19,GATTCTGC,GACGAGAG,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A20,hg19,CTCTCGTC,TATAACCT,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A9,hg19,TCGTAGTG,AGACTTGG,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A13,hg19,TAAGTGGT,CTTAAGCC,300186,N,R1,script,300186
HGJJKDSXY,1,ACC7198A15,hg19,CGGACAAC,TCCGGATT,300186,N,R1,script,300186
:heavy_check_mark:
Bumped:
Deployed on thalamus:
This PR adds constructing a novaseq samplesheet based on new run parameters: Novaseq Control Software version and reagent kit version
This PR solves issue https://github.com/Clinical-Genomics/demultiplexing/issues/111
How to prepare for test:
demux sheet fetch -p -L HGJJKDSXY > /home/hiseq.clinical/STAGE/novaseq/runs/201111_A00621_0305_BHGJJKDSXY/
bash servers/resources/clinical-preproc.scilifelab.se/update-demux-stage.sh feat/reverse-complement-index
bash servers/resources/clinical-preproc.scilifelab.se/update-servers-stage.sh feat/demux-novaseq-dirs
alias demux-stage='$HOME/miniconda2/envs/stage/bin/demux --config /home/hiseq.clinical/STAGE/servers/config/clinical-preproc.scilifelab.se/demux-stage.yaml'
How to test:
Preconditions:
/home/hiseq.clinical/STAGE/novaseq/runs/201111_A00621_0305_BHGJJKDSXY/
cp <run parameters file> RunParameters.xml
before running each testdemux sheet fetch -a nova -p -L <flowcell_id>
demux-stage sheet fetch -a nova -p -L HGJJKDSXY > /home/hiseq.clinical/STAGE/novaseq/runs/201111_A00621_0305_BHGJJKDSXY/HGJJKDSXY_prod_samplesheet.csv
Test Cases:
cp RunParameters_oldSCV.xml RunParameters.xml
:demux-stage sheet fetch -a nova -p -L HGJJKDSXY > TC1_samplesheet.csv
cp RunParameters_newSCV_oldkit.xml RunParameters.xml
:demux-stage sheet fetch -a nova -p -L HGJJKDSXY > /home/hiseq.clinical/STAGE/novaseq/runs/201111_A00621_0305_BHGJJKDSXY/TC2_samplesheet.csv
cp RunParameters_newSCV_newkit.xml RunParameters.xml
:demux-stage sheet fetch -a nova -p -L HGJJKDSXY > /home/hiseq.clinical/STAGE/novaseq/runs/201111_A00621_0305_BHGJJKDSXY/TC3_samplesheet.csv
cp RunParameters_fluffy.xml RunParameters.xml
:demux-stage sheet fetch -a nova -p -L HGJJKDSXY > /home/hiseq.clinical/STAGE/novaseq/runs/201111_A00621_0305_BHGJJKDSXY/TC4_samplesheet.csv
demux-stage sheet fetch -a nova -L HGJJKDSXY
demux-stage sheet fetch -a nova -p HGJJKDSXY
demux-stage sheet fetch -a nova HGJJKDSXY
Expected test outcome:
AT
, index2 ends withAC
, samplesheet is equal toHGJJKDSXY_prod_samplesheet.csv
HGJJKDSXY_prod_samplesheet.csv
Review:
This version is a: