From 5ea13d9fbd1457e97d4a2d2a168a04dd2eb22d5a Mon Sep 17 00:00:00 2001
From: Feiyu Du <fdu@wustl.edu>
Date: Wed, 2 Aug 2023 21:41:09 -0500
Subject: [PATCH] Use Repo for script path, launcher script update with
 151x19x10x151, QC metrics update with PCT_TARGET_BASES_GT_1250x

---
 MyeloseqHD.wdl                            |   2 +-
 MyeloseqHDAnalysis.wdl                    |   4 +-
 accessory_files/MyeloseqHD.QCMetrics.json |   2 +-
 dockerfiles/docker-myeloseq/QC_metrics.pl |   2 +-
 imports.zip                               | Bin 3347 -> 3340 bytes
 scripts/launcher.pl                       |  49 +++++++++++++---------
 6 files changed, 36 insertions(+), 23 deletions(-)

diff --git a/MyeloseqHD.wdl b/MyeloseqHD.wdl
index 274cfd4..5b7d3ee 100644
--- a/MyeloseqHD.wdl
+++ b/MyeloseqHD.wdl
@@ -51,7 +51,7 @@ workflow MyeloseqHD {
     String CustomAnnotationIndex = MyeloSeqHDRepo + "/accessory_files/MyeloseqHD.custom_annotations.vcf.gz.tbi"
     String CustomAnnotationParameters = "MYELOSEQ,vcf,exact,0,TCGA_AC,MDS_AC,BLACKLIST"
 
-    String QC_pl   = "/usr/local/bin/QC_metrics.pl"
+    String QC_pl   = MyeloSeqHDRepo + "/dockerfiles/docker-myeloseq/QC_metrics.pl"
     String xfer_pl = MyeloSeqHDRepo + "/scripts/data_transfer.pl"
 
     String DemuxFastqDir = "/storage1/fs1/gtac-mgi/Active/CLE/assay/myeloseqhd/demux_fastq"
diff --git a/MyeloseqHDAnalysis.wdl b/MyeloseqHDAnalysis.wdl
index 2c87cba..9850a17 100644
--- a/MyeloseqHDAnalysis.wdl
+++ b/MyeloseqHDAnalysis.wdl
@@ -106,6 +106,7 @@ workflow MyeloseqHDAnalysis {
                Vaf=MinVaf,
                Reads=MinReads,
                Name=Name,
+               MyeloSeqHDRepo=MyeloSeqHDRepo,
                queue=Queue,
                jobGroup=JobGroup
     }
@@ -313,6 +314,7 @@ task clean_variants {
 task combine_variants {
     input{
         Array[String] Vcfs
+        String MyeloSeqHDRepo
         String Cram
         String CramIndex
         String refFasta
@@ -328,7 +330,7 @@ task combine_variants {
      command {
          /usr/local/bin/bcftools merge -F x -m none --force-samples -Oz ${sep=" " Vcfs} | /usr/local/bin/bcftools sort -Oz -o combined.vcf.gz && \
          /usr/bin/tabix -p vcf combined.vcf.gz && \
-         /usr/bin/python3 /home/fdu/git/cle-myeloseqhd/dockerfiles/docker-myeloseq/filterHaloplex.py -r ${refFasta} --minreadsperfamily ${default='3' MinReadsPerFamily} -m ${default='5' Reads} -d ${default='0.02' Vaf} combined.vcf.gz ${Cram} ${Name} > ${Name}.combined_and_tagged.vcf
+         /usr/bin/python3 ${MyeloSeqHDRepo}/dockerfiles/docker-myeloseq/filterHaloplex.py -r ${refFasta} --minreadsperfamily ${default='3' MinReadsPerFamily} -m ${default='5' Reads} -d ${default='0.02' Vaf} combined.vcf.gz ${Cram} ${Name} > ${Name}.combined_and_tagged.vcf
      }
 
      runtime {
diff --git a/accessory_files/MyeloseqHD.QCMetrics.json b/accessory_files/MyeloseqHD.QCMetrics.json
index 566dca1..a0a0fe5 100644
--- a/accessory_files/MyeloseqHD.QCMetrics.json
+++ b/accessory_files/MyeloseqHD.QCMetrics.json
@@ -20,6 +20,6 @@
     "Failed hotspot": "0",
     "Haplotect sites": ",10",
     "Haplotect score": ",0.02",
-    "ASSAY VERSION": "2.2",
+    "ASSAY VERSION": "2.3",
     "DISCLAIMER": "This laboratory developed test (LDT) was developed and its performance characteristics determined by the CLIA Licensed Environment laboratory at the McDonnell Genome Institute at Washington University (MGI-CLE, CLIA #26D2092546, CAP #9047655), Dr. David H. Spencer MD, PhD, FCAP, Medical Director. 4444 Forest Park Avenue, Rm 4111 St. Louis, Missouri 63108 (314) 286-1460 Fax: (314) 286-1810. The MGI-CLE laboratory is regulated under CLIA as certified to perform high-complexity testing. Interpretation of sequencing results and case sign out is performed by Pathology and Immunology faculty in the Division of Anatomic and Molecular Pathology (WU-AMP Core Laboratory, CLIA #26D2013203, CAP #7233522) Dr. Fouad Boulos, MD, Medical Director. Pathology Consult Services, 425 S. Euclid Ave, Suite 4711, Mailstop 8024-14-4711, St. Louis, MO 63110 (314)-362-7784 Fax: (314) 362-4080. The AMP core laboratory is regulated under CLIA as certified to perform high-complexity testing. This test has not been cleared or approved by the FDA."
 }
diff --git a/dockerfiles/docker-myeloseq/QC_metrics.pl b/dockerfiles/docker-myeloseq/QC_metrics.pl
index 4dcccd5..2d22503 100644
--- a/dockerfiles/docker-myeloseq/QC_metrics.pl
+++ b/dockerfiles/docker-myeloseq/QC_metrics.pl
@@ -35,7 +35,7 @@
     PCT_MAPPED_READS   => 'MAPPING/ALIGNING SUMMARY: Mapped reads (%)',
     MEAN_INSERT_SIZE   => 'MAPPING/ALIGNING SUMMARY: Insert length: mean',
     PCT_TARGET_BASES_GT_250x  => 'COVERAGE SUMMARY: Target bases >250x (%)',
-    PCT_TARGET_BASES_GT_2000x => 'COVERAGE SUMMARY: Target bases >2000x (%)',
+    PCT_TARGET_BASES_GT_1250x => 'COVERAGE SUMMARY: Target bases >1250x (%)',
     PCT_TARGET_ALIGNED_READS  => 'COVERAGE SUMMARY: Aligned reads in target region (%)',
     AVG_ALIGN_TARGET_COVERAGE => 'COVERAGE SUMMARY: Average alignment coverage over target region',
     PCT_LOW_COVERAGE_AMPLICON => 'AMPLICON SUMMARY: Amplicons with low coverage (%)',
diff --git a/imports.zip b/imports.zip
index 70790f5abcc9ef332af71321230b029c16eb77f3..20ffd2f747e291326cb734ebb82056778125b804 100644
GIT binary patch
delta 3280
zcmV;>3@`JO8jKnpP)h>@6aWAK2mtb#0av33ZL3NQ008Yh000&M9Fxur8Gi`?11O-$
zWGJA?WOaB8009I(aSs3lhC&Yj-CKE68#xyLKc7P5r2@>NZre;!3`r-&5fXO8Kp>Tx
ztqkju+p^uz7u{`xL!8gPPf{OhNd`MyQ|l^lw~i<2>Al}OB#&v5dQpg4R`c1j%P2YT
z`_Uyjm{31T>BWcLt&sSW)PGCS^|NOPK3*7)vf_n(PO`)c2WXoFhNAtjN3YcK-GmHi
z_{HtdtT1-_g9KC?Hlh7Jl4b;{700ws6B@d7*K;$q@(Yb!;tr`+P7;rV+3vPB4rj;-
zW5_X$Bdz)aiTx;}ZnjN($WdCOf1-v>T$iS4luSB(&!?$fao8Fboqw$^?KM==TS4r5
zZWJ=g3zH^!=hR4gCmK`6@}DAIbpEts4F~HR#sNOL2Na&%l$9+yz^9$Ovvrn6p+5Oh
znnl4@7)BY%K!QPReqs=pQ|XYBOlpnYzBTxE>v&v7?{7RS>w342c|;OWf(%p^25ubu
z=iSG{lXsuifWjKRB7bhS)?E9%^M0$dwX=4xd&0i9KW^>(`{Vw}=Y}e?Z_#@SbSE*D
zHE}=8(18~oQ_@Sz!aYACy!Z?0YoZ?{p;|<Izhf%qY=LEHdVjdB7NxrW(<_(8nW6jf
z2sWc1i8pP2C!_AJm#C$OqYQA2RcJChq9Y9${uOoKC($TIqJQ~Re7UetbTOi^(YxD#
ziA5)lk(-P&PR@$8vM&FWyl~1VtxbtWPWhy@xnQ$(_?)%6vwYG{F?((9u1`tW84Kzu
zB57X2*R;Fc0m0Ij1>)iqi?+lA6F_xz2G<Vzr_~gg?Gz99y{ae#Xv#WW66muBqvXJ!
zMz%0kPVu0%kbi*Kk)D5Id9ztliltLNX>Ei+JL2n}S(l8$PVB+*{Z2v$%rDRwxC0R6
zNG!J8#K2D0O7K%@>S;}n>A;aJ(Y^BXZrtb&zIkycBVF%`>4x;0Gs&zR8WXL>^y6W4
z`j%~F6W15G;LIOhvxBY|(rR_4Wu#6@eek9_&|~Fm>3>tM8Q5U)GTLJR#%=YQhJSh!
z$!wmk8U_De)#G-af>m~eaW?1{*m0*Y=nL#*-K%lxuMYq^V;UQvMr=0|O?Bsuf;k7P
za>w5(9`v2j-Acz$c56SeyT;O6`&MqAMxd&CG(Z_abV7PY52rvo*gXq$1EwVuMH_{=
zLJ#Q%Nq_d^Mq6@sK`nzdog24{A5^e#)Tsrh4-X-XD{_STXreP9*^nk83ex!%B|WI@
zPMlK0tX>q(a*FmC5$9`d53FdE2~gHJU2B$l8BJ$5Wa4YY6N6}<{_T9WfSgmXXK|Dm
zWU}P3ycK3P&lZBaXfMQe4*Y555a5BG*0HdR@_(H2Nw;cpz~|K7ei|9dRE1MM-O(sM
zp<G0KKuH>;z?|(pa%8FD;*fU-0?#s%o-08VuPsu43eg2Je>{b!loep9mP;X)T2%$_
zN`*PrKa)8mm0y&Re$KYM9Jtr>65vre4$tZ|;D0`VpaeciK*An+{rYvaJN76|Y(E0c
zw12^2u`@DY9K>Vv;~Ka!g)eDgQ)FjB%o+`7&teVVKm*35DNEgXAl6oPm7(X)(O)x%
zNJ)@Ik)NWmM=ufn3=|5UP7&TgI6{qrD6=FDZP5A1dpzN#kb3^S>bT;9c;G&IF>4KZ
z{cj2rR?&BqGW7b6Mxl3sunSM*@*FMyVt@Z-+2|U@urC=}YOgJ|aO)MCF4y_wMkD4D
z8aTxk;Ks)J{J0kTJiWb-M1S61j5`Z8=9ataAsWAV^Cp)yFh!XcP)YkxFLKWT(Y*i=
zZ4))bYior?HffejtU>Bpm*7777VVAfVBld0W$Yl&MGkwL<MwKmaYSxB0xB)3B!8em
zluV$o{Tq5Om2<t>l+=fRK+8G<re>Rp!sW`PgA!sU9dS;vbmo#QSb8H*ZNoXHHe}l?
zH<Wf<qsezwX<Th}qnQ0PM?_O@#E6TWI&;tT5+f=e(}7YXa<dXv?uXf1w4Zw4lp-xv
zdkd(V0C;YAGy~pBN<ph>gkmqIeShNlOxPEKsDqF24oqO+$e1(*^|zxqvjw+t(`s8U
zx*Lp2JI}jdfni=~<pn>kdocLO&z$y)rr^{RWg`$^1h2k73cQfuBjP3R!rto5h*yl!
zuTL{p$HZsFya8f)9f){QImZZXmR`k2T37rY;iNt`l@_>O?mAQ)OBIdx$A3G+^^Ha@
zJW$)av36XI%w|%baY}n=Ikn&YvFm(o;@?kyeP!Fr^$ryVSIMFW!>x*CAP+CC_086t
z;MID0H}K+LGq8(sLBfxU4H|gJsl@9FH8f|+a4Krj*$dMl#hJkqEOl0zI@hgXmik_o
zOCz5fv${*yF#HtuwOEie>wo;1$|Tpq&tWSA9bqh)-Mz-tC$(uCk0up57j&Z~juLO^
zA{`G_LZzg7??J9+*^R|*#I+(M75H`CzAy&d=fj8J3c34!17en)!YBcEI>02HFoa%`
zQ4&ZkK%<8^4e0bnax6r)x7et;#C=xhy8H8_(*BSjs3yp3ewv9RWq(gi?(5CXGH*Tt
zP^5k<Nyy}@5YkhAD4<HNa-l=1t$A-!nbCi{KWD4%+|@n1n!k5MlRXl6{-km-*%|#?
zb{6on>KM>uKoQ<UAlL!uNC+>uA0;luDZ58P(_C3o8aoZt;B4i-+HLv`?oqyNy+zE(
zoPFX+HjKh`m{@&Jr+>CkC~*fvJmW%nY?0IZK>P?+c4fsA=5y811cS?%FlNU<gEJfI
z3vX(9eOcd(DPx?}=EX89{Is52-n5$SWwupQZH-I02b^n!WQ&WI9oWuJ9=w+h*WUwV
znvZ5vXE4JUvsFh+3P^~ktUP0ySFN?nV}g!;Ms#xnBb3ZO?tf7gJs?+Gdk+)dNxb*^
z=qp-U;d(YmfRPY1EdTc(%S=v7#!bJMx_Id#?5`rnfvD^B70QORx~;=MMe3v0zm)O(
zT9nvKMc)_b-6<0Gv&blb#r@xzbI>w+22Z!vNyn=B2i2y&(CD?^H%x<5ibn3RBvF{t
zPPLLO9amkcpMTOBga95PX5ANI1t^=%;tE!1e|dLgANiw!7p7Hhnz%L%QyO%A%-)%L
zayt`{jIT<WFvdJg#xW;^cB9J>aEr2}D(>^EpLNt84#r@pa5@RP5zGq%KLT`e$Xfek
z(1|_wTpPkuBno43PmdMrdOcm!iz`KCy`z5L_qhG!NPod>3AySJwhWe827fol5S}`i
zTl$|&Z0}*4g=BIt=Iov^ftw{k5J8QVgRMV1TYKoWVpW^1WdV#+6eZxoWJokzWv|6`
z$xePnvQ{RpOE!$#aX)Z!znWdmpzl3QPz^iPYQDfCPtdY{pFiR9cy53yK5Bp=AKV)I
zscbbm5P#~Czd6EQC}c1kYRw48P1o0Fc_ue!h0KwJ>;cR^&|(70PGrFRAMTwvjlZ%6
zTE0e0ZD*;?PGtB24L_Lqam~-Q-iTCT9Pyjyv$LU5OvAI@Io{wyoRKj>_|M?#<v?za
z&q$JIt%&bqpLFd3$<A?1+;fm={F~LXHmnwIZGYeaZTFk)ehZ)cv2}Fv;qWu&<5-MB
zc?F_Id%w&&^JJ=QO2Gdev0EAd+Aafml1xMkwkgvZl_0o4?IwJ8^KWv6do<357$7o_
zpHQm_AA|>BI()?83K}L-juup>%I(VJhgn>37Jsa>7K5rB!JGg*@^mck_W&u_QV%wp
z)_?lbr`d|TAF^UsS3V2}KGiJ{V;2w<&v@{oU$8JEKylY%9?gET>+wpZbR|NqD(^w4
z6$>7}-<)Y#Bq3tXeiY$LF$u0~hvM9R?lXKfKl1a51uiYaUU9dAB^JUmoacD}d4^Mw
zcbB#SN-m(J<i3J4PzACBjhNqCiVVDW;eQ<@g&!6zU6;}@74B9|2#n{^!5CTguU0;7
zcGfMuvR~k+Gk+Mj<8PGR%mpgHFq39IXtJ`ZqJ!a%+nn%FPf|*^+~!rdw|BkpGArc&
z%J!O*o}ym>D;wzal*tTK{37J5oYK^;nw}a%{@`51Jf<$X8_Pb0JYoo#vRQ*wd4EWW
zbN4Ki1AbHrkxr0eU=@r)@f8g{;@7?5$CWtsLhjrrK8qNg>Zg!O#SIqY?x#dD>?-lm
zxR?-!REDGF6!}?peu!j%Q?JC#vl?bTGJutEb;sK@cak0D*J@_bxfeNkLSdL?B>%rQ
zocpxp@9%_5Tdh_6hDAw={|``00Tu!t0~7!N00;o`nE_X$2W_iL3;+P_le!Er11O-$
OlkE&32AT{20000xEIM-l

delta 3277
zcmV;;3^MbK8j~6qP)h>@6aWAK2mqa1$X2Qus?<>o005+s7b1Vk0fJ<4F@j`ucnbgl
z1U_*O00f3Y4*=a;dsEvw7XQDWLO074xQpy0w0F3)Zih!{*)10eozC59*^J^SiNP;y
zCy>(gv+t4Qhb$?Olt(+88HlaNk#zJsPbp)Xq+S%FmeqXn<T6Um`+jtZ4kpx(QhM=j
zcPk|RB=u5s{p5cMf{z!*qpWygpOY-{!U5VQfuU$W?9nT=d^aHj8h&#7Gb@bU{vrX@
zhD~UHkE9tvYQ-__(}adD-Syl|t^7n|m$*Z!m6OCHVYa)ijl&so!WeQ)<4CK1M`Az9
zsGDum9&(h{=%1)z6W66_8YPoX-}7l|R~)v6MQ5u^dkue;^i~l2o*RXX^1`G^-Z?dr
z-igMPvHXWf7o9)sSi`~khH-!o?g51-H)Umu4)9?o?`)l=QK(OTlx9(|6^2npGC(lE
z<_89GIh776$)wiU?OTJdw~og#dVk|tS=YOD%p;P35M&^-FmU7GKX2Y2p1k?61{Bul
z6>+n*=GuS9owr+^t(~=l-4ph;{eElb-|zQNJ~mX$zD92;(4E9omc;!qLkC`XOi3>-
z3-|np@ZwLTuR%XZLbZtae#cbI*#gVZ<o<A5ElPFyr&lhGGeh^|5o|_35^vi4PDb5b
zFHuVmM;YibR-s{bL`Rxp_*c|@n?$1+iRM%B<-&hL(Zz_uM(=KePAocc9l6Ok<K(PZ
zE9>%4$qT1^(%O{T$SI$+HWzHR4xh7Dca~4uDQ2(D-SsI6J7YmTMI_Bj_?mXNI{++w
zSpXNOShOV`7y#ALnYwn^Kdq+F*-r6r->Zs3P)%8<O9FlNV3ZvA)5sRa$|)YS7Lp=%
zr00JhSl(>bl(2NlC#{VDv?IRmnRUr1?8F`{-|r-J!2AM@fjgjr9Eru2n;6*1S_ytC
zO+BsYF&#LPCAwFB-i;gG!B;QtWTfj|G1-t_b0(RELt~<~n0!2pOy9DtY~uO?7o7RS
zOLoxpLRziPw2ahAsSn;%2YRf0E`7>10~>!VUPgONfpJ^Crs+SuiDWiUSB=2GSMj)=
zr(l&GVVn)J1$Nvi4Em#CkV(Lp#s=jfHjsf$-Ag0X=2(30$~(n_&THLKbPQ#;_7nSM
zEWNdF<+y1Cs;WoZo)N?wq-XS53jGDUX93z_S_1moD9pKeNXJI92sc`Xy92chzjS|Y
z+zvmeU;(C63pXELDKM_cG3TQ}XF#$cO+;Ly^D9bvP}!Y0CBm#;6wY#U_81Z8b8Qc-
zXp{*xt8u#4EcG&)&Th!yYt$zOXrKOaURXfRDOjjDN(`7Rc`R>*na#67a2M%?Xw88?
ztsFu&u)Ml1EaNt(eA4Zd9Kt!Zw;zAj3}y1cDW9}9_2Av9zy3<Ni1>gK8l+I0?LBg2
z)NnZD-GRW9jHKsESj20KWS&BFfm|L>$|+@qvQ*2Zph>N&!f~a-9KD~(9Foc}%Gf<;
zTV4*_>v;+As2qpqX&Uf9A3#t7pClk*550W(vf3SclqR+xfn?g?u-F+HFb;p>G5UTD
zT$#d`w6H0%vmj=T2DE3fhOeLj<I<ER<2-=1m0e}%=~MJ&<`5|fvMBOXH1_Bv!XJS`
z!P6<iI|xUpQ4nR8q@fKuA9;_buoO~HpH>}LT!07eqvx~Mkk>y`n6Qezp_FN_Z)g;H
z7YMuXL@v+K@^AJR%SP8IhJAm@&{BJCsfAlF&~&-ZCpQ`~m(ai|wg5La&gc8J*yri(
zeI)wx_F~*ws4=(PRS(hl)vH%I*1!~HUO*-3L%qm72aWCppwTu_L%g<DSgev}$;29@
zu5}6Sqi@mP$PNY`hTy~w^6cWUw>fUFRyjoE#v`E8l1c&^M9BmS+s}W{TdADO&88$i
z`~y<f889*1R0J*;E?p@hX3`Po6iZMp$-vSZd1@QZF|{GvUb&&P;~GuAt4iZ)s~g4a
zr@2NnWjl;|kyB^xnO<VlipO-I6p3uBq$~Hs>^0g?y{}4<mVCWMshSk<-0IP+@K#a^
zQcWWidok@3&u3s?NJW1gyoYyS0#lBRNmCGiJBl+~a2q$Rw)MQb!Kk$JObQk{%nPl&
z;QMtC1|RvE(|+C*oSLF+1OP_x>ieU>3kg0VUh*dFt=_EhiZS~2X~yc9_^g;Ws90VH
z5HBj{7@^G)ruazfir*rf)W@dM0@ur3hl*pVqVe{4XSlx6$iaUDwY?i_$JNMeCiNMo
zw1<{c`^{gw&gUln^Yr%@w!K{MQ0d?*{qtaYt6~}8;SXzlvo)vkYW;CH<;A~d=q|<u
zNq<yq(3FRq9K5cyhUQEe&N)podto|uI5T*HrOZlG=dv}-Qs3)xH1fGItGjd!!%tyf
ziv>xu&JUhUxE6nY4qF+>2xH0Y?lq?VRGYT(XsFP+pc^f5ICw)B>A<f7m6E)@2VBjv
z8;jeBYXu~g^6R>NVGOv>hY!CNxchd4#w<I9Q3CFCfJr!E8hT0Al0a$!8a>2mK&Mxd
zV<Gal#YW8q_gS6m?$1v}`$H;0HRWCN(@Y#Gduq6^H#dJ{-kj7|P`{NVWb#>n^pvOh
zRpi$EGpWqzq1~T5Rd?U&zFW<sJEF-R2|RyNIg#vK{WZ(q|ERzPG#OBY_YgoA_oKw6
zIAwP}Xqt;*N@J&i8k}L=3%gBn!STsAq_>EHn6pnj$%aw5j_e^gEOsAcVBlpofCN`E
zU<;`cS0{hOb6IPP#N9jMN3h5%E1odNs-`k9_=O4McMLQ*zoEWxnU>d=_5FZOf!yZ#
zGAf+0o?PCvn(bw_TT^YhOSzky!(KADMavHCXeW=*ORwtJ&?L=AGn_M+VGPWw^CLwQ
zh|sG%NSar&wL4#ej(!kya|5F`nSG|C%6dSqw)TG>CWe!E@Ac7Vw6wxSZjb;YAu?G0
z??09qPD{p3zm;Nn=_2f}BFBNy>huN5hP1k5!#_oSqt?H~cz&BnY^Eam3-s<3S@~IH
z6y3$0+?jLG(sl-Sw$@2kTk{X9O?{!!YrSun2B#E_++j(gu$i4|C0RPIx>7%-GYElt
zgus7vU&Ia|Y&HuXSfTyt&5?cNj|N_tR<&v3+B8gQ(DgBUXX43CPCzogDrLeL^H><i
zoDkZLE<?~;lx0qFpWoQ5Ywh7+3^og=lb{>HyfE-1KqrT+wND0}*mKXdAv^_97>nz5
ztXP-p>6%_#2`cLy_4_{1Vsx0MV77!@bqIf321_4<Q=97$o*$SS{XY%1_pr?ZnOqrj
zcF&l=%}5YLP-Ep_>+jCi9(t)*)n;p1D8?y@67c0SBpR-=*W#9AC%@TPD-*XI8^-Op
zA9ZrSl3mT9?>$W93_I0oKF1;%(6auVKdbV1Zh#6OHHwf=XN~<-wi+D>^<3W^MlXL9
zH5g8=X2jg4Tj#SplbcgN=3qkh0A`<BF@UmT7cl>adnZogOV&Wk*J!EjEVbFO3qOV7
zr!U{H`Qg<okq?X`eqnre$}@^-c-A||8+?c}GA0QB9bEk}klW)klH{o=;``VqU3);X
za~u=*959WaSuJbBYT?!f9?*8b+3tV0@X23WM<?$NKVm+P#VC~b9BQ=p%hWQ@n98OE
z{NE9~iUCU7WlEkT6VZZg%Ctr$2rf{&3E$oPn_S@@jk6&J6`6-psMUlI!UHfJKH};M
z8YWUA7DT5?;L7BOSzK@yzpt|vgQy(AoIrWxIal8A0rIS+9BekN^`D<hD=vR{$bwzn
z>oA<^R98KWT>vPa@pMPOMPb$e#f6G_B>Sh`YF8?ydk<<=dD%g&Sn!Np`NfM;yGTyN
zoB%1pmtqoJ)(*wt{M-liYKlb8F)UrzmoU9CvB1$X>=hR%SYjb8!+D+ukY_j*$#rQP
zpyUEdO71Iq2C4u%(1`iHC1ii#y$kPv6n-MKbX}rhD%`Ca2#kl$!5CTg?^Zr-cAzc2
zvLDW<Gk+Mj;}=R{=77p?#iUsenyjp<+QD#<ZBF%2&qPXB+2$3v*LS_uGArc&%=Vg-
zo}%ACS2ob;DZ>m@{3h^KPHAdaO;3#>e{e2h9#a?Hjb)z#j~D``Y}S8ZRZ3Fg+&zPG
zz|TV=(g{)wtb$P}zM`Q={JJ;%xQJ74-Ohcivxw2De!-|z++Z>8eiT$o?bhR?aWNsT
zQkfntr^pYi^OGWjI`vAOc~;YzkF3B-b#=!pGk3y{@*^`dbnXQwKM@SGjO72<hI5~`
z{MnpvX{)u0pPnd5@&6hDP)h*<9s?8r000O8om<FOsu`-(Q49b8q?5A@Fayc~f|KS9
LAO@if00000h;~;T

diff --git a/scripts/launcher.pl b/scripts/launcher.pl
index d6f2a76..770b799 100755
--- a/scripts/launcher.pl
+++ b/scripts/launcher.pl
@@ -149,25 +149,6 @@
     $seq_id++;
 }
 
-## DRAGEN sample sheet
-my $dragen_ss  = File::Spec->join($out_dir, 'demux_sample_sheet.csv'); 
-my $ss_fh = IO::File->new(">$dragen_ss") or die "Fail to write to $dragen_ss";
-$ss_fh->print("[Settings]\n");
-$ss_fh->print("AdapterBehavior,trim\n");
-$ss_fh->print("AdapterRead1,AAGATCGGAAGAGCACACGTCTGAACTCC+CAGATCGGAAGAGCACACGTCTGAACTCC+GAGATCGGAAGAGCACACGTCTGAACTCC+TAGATCGGAAGAGCACACGTCTGAACTCC\n");
-$ss_fh->print("AdapterRead2,AAAGATCGGAAGAGCGTCGTGTAGGGAAA+CAAGATCGGAAGAGCGTCGTGTAGGGAAA+GAAGATCGGAAGAGCGTCGTGTAGGGAAA+TAAGATCGGAAGAGCGTCGTGTAGGGAAA\n");
-$ss_fh->print("OverrideCycles,N1Y150;I8N2;U10;N1Y150\n");
-$ss_fh->print("[Data]\n");
-$ss_fh->print("Lane,Sample_ID,Sample_Name,Sample_Project,index,index2\n");
-$ss_fh->print($ds_str);
-$ss_fh->close;
-
-## Sample Index
-my $si = File::Spec->join($out_dir, 'sample_index');
-my $si_fh = IO::File->new(">$si") or die "Fail to write to $si";
-$si_fh->print($si_str);
-$si_fh->close;
-
 ## Get RunInfoString
 my $run_xml = File::Spec->join($rundir, 'RunParameters.xml');
 unless (-s $run_xml) {
@@ -207,6 +188,36 @@
 }
 $xml_fh->close;
 
+## DRAGEN sample sheet
+my $num_N;
+if ($index1cycle == 19) {
+    $num_N = 11;
+}
+elsif ($index1cycle == 10) {
+    $num_N = 2;
+}
+else {
+    die "Invalid index1cycle $index1cycle";
+}
+
+my $dragen_ss  = File::Spec->join($out_dir, 'demux_sample_sheet.csv');
+my $ss_fh = IO::File->new(">$dragen_ss") or die "Fail to write to $dragen_ss";
+$ss_fh->print("[Settings]\n");
+$ss_fh->print("AdapterBehavior,trim\n");
+$ss_fh->print("AdapterRead1,AAGATCGGAAGAGCACACGTCTGAACTCC+CAGATCGGAAGAGCACACGTCTGAACTCC+GAGATCGGAAGAGCACACGTCTGAACTCC+TAGATCGGAAGAGCACACGTCTGAACTCC\n");
+$ss_fh->print("AdapterRead2,AAAGATCGGAAGAGCGTCGTGTAGGGAAA+CAAGATCGGAAGAGCGTCGTGTAGGGAAA+GAAGATCGGAAGAGCGTCGTGTAGGGAAA+TAAGATCGGAAGAGCGTCGTGTAGGGAAA\n");
+$ss_fh->print('OverrideCycles,N1Y150;I8N'.$num_N.";U10;N1Y150\n");
+$ss_fh->print("[Data]\n");
+$ss_fh->print("Lane,Sample_ID,Sample_Name,Sample_Project,index,index2\n");
+$ss_fh->print($ds_str);
+$ss_fh->close;
+
+## Sample Index
+my $si = File::Spec->join($out_dir, 'sample_index');
+my $si_fh = IO::File->new(">$si") or die "Fail to write to $si";
+$si_fh->print($si_str);
+$si_fh->close;
+
 my $run_info_str = join ',', $runid, $instr, $side, $fcmode, $wftype, $R1cycle, $index1cycle, $index2cycle, $R2cycle; 
 
 ## Input JSON