From f0fdd6c21fc3cfeb054b50d9746d98e0faaff706 Mon Sep 17 00:00:00 2001 From: apalleja Date: Fri, 22 Nov 2024 10:20:13 +0000 Subject: [PATCH] deploy: 60718d06fa9540e1dde6ebf9a99d910e6757641e --- .doctrees/environment.pickle | Bin 41907 -> 41542 bytes .doctrees/index.doctree | Bin 11195 -> 12421 bytes _sources/index.md | 10 ++++++---- about.html | 2 +- index.html | 9 +++++---- searchindex.js | 2 +- 6 files changed, 13 insertions(+), 10 deletions(-) diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle index 28cbf5950d4cf958abfacfa398b83f3d5b788631..a8f95e181515ac6ec7b286de3d3929e5df858660 100644 GIT binary patch delta 5871 zcma)=eNa@_6~MWVkL6Ro0?6001T-dU0hLb?7ElQ8h!I;p91s!L;)?SUB-+%b?O$y&V@IQ{jx*^vopyT9eeAyL4uE-rQ{fFPcJ1__-(q5^uS-! zSC9?}%+Qf8NY2m_8?4V*u%Xl4%}qXyq8r8gD2|~xkHUiD0tzdNizs?fjG*X1@iB@n z6qixhu3XR1xSOAL)qb)66)%ReY8uZd8se-P&F>Tqkyg#cyNZTbtEMk~D;tMstL9Lh zq9NX@k(w0E#g~? zm0j>7ZLxuGjuw1!Lg%epM&$p{!3N3HB6mY^&NKK&ek}BC@PeA$@8Cy$0#xdcQ^fB4 zmtkJsPWX3T0tD@jg3t5xU|pR6QTb(%Mtgl^ehG&1_0W``K>N*y%7T}u$&~zD*h@!T zwMGy-)pEdnO-vaJ^b!vmHWuhiykmhb#5)$~jd;fby#?=Bpm*UNMnT?-ckC5*;2nE~ zb}+5^8~L0XNdf(Va5!5S<^LHz)uOoU0Z&WPLq2gfT%vcTt@0rJeRm`ofv5WUqeixh*xP-dD`h1AF5r7?N;MhAH zWD%P_#hTo3>F0_cR}TlnH*ffGeryo@C=vWHpzbik5@a?rf6moPX2r~{k|@r^JA#R~ z1rvLC6D;!_CNLZLJgC%{O2dkYrgCv6Lx|yWYQS^OoQgXhD@{09ArMd+$+Y%G!ouS|MFhxo4|VIPM1uMqSE-a|hK{ zoi5#0VKJMNIoO2gp7X4YqsVJG%>eJY0?60rj=VecN* z!h;<-WYUQ}DD%<3DPnK9gvAf_xi|IXi4&W(b0z2PV-fq%Wo*^1FcNyaRms4cyFxf> zkhhS50j$B5L>Oy`Bxw$6YGXJ@T`p3Sl?F8dvsk`ywOXq*s6C?D3Ud@|_V+Y6^@W~R zUv@{42K1!t0AH@(RHmX z4nCY|+NAAuDcpyBK+6sU!}+#F+*dplh?)O$3qqaCw;74OW-VNPJ5Ouxe4gV)wdU$~p=F2k7_h2yGIs7vB)$%RZQqO#g<^KGtutFE@Gbw^`^U9P5WCb<~9MagUFMK+*dyFeFQOYG=1J6w}- z;7$|`D4M8H{iBL4uz;RPv>0`DjSa2FhSnCl?2^NB4dPm;m~u4n1xNkp!x=p_^FgGe ztL-H=?qKAIy;fFSm(BEPtuvHVDRIrSDSwh)@W<&6d}&zDeSZRdaiMa11%J#UuEP@_ zp~GW7>)Eb-=B$s!0|RLov$b5L_#K>RTv06Y@!$3?;G6NF_R&PoiQ1_*#Q%MhJ~J9uprYK)D7b&@>5X3 zLX}N3La0{q3>88)L*~gCGxk14N8#umHcZv9+Nm0rJyk=Zs$ua_HLOCahUG}raK$?{ zlMViO@|sla3w`f>MaH1EFFxuzEh}Ju^^ko(^$M$Di9A7@O5~exrf)^)ZFWD&Bo@yS z`D^&0FS{~}-s6a)EDG${r`pa!NiP^mdck7>dchw~dcp58yOg2ew zVIJIrwo~!s9`v7z+l=qW!k89@v@oKD0WFMYVK@t;Ss2V>s!uk!nd%$RxqH;@{dW0( z?84e@?#(T&Q-&h?6RDx>{#d%H+|<8)UYNg|8;yfJM$O6*@O6KDSUhd2PmzTu9;X+O zh49+xq~s9#Tt-o!a>Oo2qZZ@PaICBV=(B~WEdFyE!TCt{t( zAL=y?(N5!cuWK6OoyK3B(X?G$TimBd>UB-SK{$<(e#XjY^PptYO914*$L*fw9qSEhqkx2i?%A%o!-eaYS*ln~83TJ-D zSoOJMU}@GTuqHPiLQCeriR^4h%Z`VV%_HI5ykRgcCmWjb;^An{B3Pdj4-vWZ;Vahn z(8gi#Ms7Bno%-C!mR1ho6X?Hx%$c9-9(TB}7h5jeiBJQlI`Dv$Oo zkdu=M|7D(b<%N^CpgV8Td_Mb=5Xomh6QB6(=i?Kf{kizWXTK7k`0TI7C!89(9-nw# zp>-{<-U9QiFUg0HlA8j13dcd+n!u1hVk;l~`+i_9OCQoVP|?etnA_*!c6PXLBKr1S%az;6p<1n6W5IuZ2{5ejv4(?iY;xZLZ0 z_@D-14;CptX&A1N15fjiQYU$Pn`9tl=^FgP^UYQRIt$ zP#An)D#AXK9KOQgdPx4J!5@zE-Le8gAZ2j@+}RigU2|p$QTR!M-s8Feh3>f-!TNlk z<+|Sf8|?3%2mTRyic%rT14wIHl#dLz^;|CcCWFM78a6Y1K2+=%onhSWo+kTuyVTnuxJYD z9RNEPrwHJS8b@Cj&Oa`om~(4?o=&a~&;phu3$!m}H$Rizyy7XSF%|iWpAlXuEr*_p zEFt9xlvQO2^YoL~$Qw&1DC0C_ZDqWG9E(U{EsR55SPMNmX)|XlFKEO;Rha^@KqAiK zPV2dJ#a~(o&+`hwrpIhMy)08%r`gP3K2@;UB-yk{qwq+qvdmJBaN@odGX-Fm1U%p^ zFrj*y(xbU}wt9*{ydV+JdQ1FkO_p*^Bd)F$1N{$)__?>lcABji0(gFnTRBbeQGxm< zF&XZAOPsxGxRR(5&#Vd)hzSyL4C>xY^~u$v6q80AV;wFKXG_HAQ5XKRC31SDY883{ zCiAbxz4G!+kEfM4itYO%lx+d<@ty_JZ+0^uiN0901UzQ-#l<46ezNi^lFH#?{RCk| zFG(Xh!pXY7T^jk}#rLCzNTp9BK5rW-5HCr@9?wL1fpj=ym9I5sPh+IOyulgzc&|Na zyj}JPB_NQGcTm#^fn$BoSwOOH|g!DfJq$Wqp)Dv`WO4T-Rs$K6Gyow+q*}uD5qd?JZLKdYm73QuF=0 zp49qI8xt`icZBlmK&UUuhl(}gHtCe);z`NHU!m?c!4C$WOt90D@}*`XV5_`A{kvr5 zQ_0LHq8Wbb(9JxUuHgxfI(P*K@q^cHwvT@Bv^6S>x3JR|Zo&_s5Dr=yc6yXmnFu|G zEia+qXBp%@^2DVXvH)qxfx9MgZx#?F?ad4t!_z>b;P93Nw#)0?Qou-IFly@& zvCDlaQ5IXJRncZv(sd{{Fkzv~nKUWX0^e>QwO|EP9JHFrU9^Tj*J85|rCeFbp18xj>VWBZBPr(IA!bu|)wt)CcOy>C`bTCLA6yCx8W%Fwz&zXw%3YU4N=C+7A z|ACyPeHcVfM}Az0*uRF{L=wB*db=@6$oQ`~OW5gN*WmhccvXWx{8RLI#gIYJ+m2AH zYmxvBV(0#{bOCDQ6~dp#BXmo97D?`h2JSWq&?Ff;!E5Mq9r*cap1#sCL4cOZ&?2v) zcnoeDfDVOwrQrhDCWF^_4IaNQoOJbr9s9-#&;v3Qctx-<=i11oUf%L?2numVHL3N3p4f^Ugxx4RT-!|O_V2ZB4} z$Q?-PjH$r+ad4)CBORRR;6MlGIXKS2X$}r^*lUtaKK2?bhcUNXR2mb41+RDcHrN{b z4IS?s%M5+g8AVdzo6Z$arLk`8H%{MSW@!ePyW)oDvZ|UCDzzN!N+1RByRK)FQ&~Gj tQIoPmrPEQH;nwh7ssUJA0cr&hd1x(JaC-ltQ^fx@!fIYWU3BEG;r|Vz6Ttug diff --git a/.doctrees/index.doctree b/.doctrees/index.doctree index 66f26ad75e52090636d346f04f59312637addbde..301e14089a4cef9fc7a2078a370b2da259a3a24f 100644 GIT binary patch literal 12421 zcmeHN%a0sK8DBqUz3;W1#CdG&RFs6Qo!!|eL0k zPA!X#r0oUkteyG}r-iu}vn1lK@A{pLMq=RMtLTPtckKUGmhX8q3e8_cTqV9<8@i;~!em8vVPX8Kn(y)4IaeFlq zZTga`BMI-&r%cYuQx^}&lj@}<8T7PEDxnEuwxw5@lM1;S>xsPFCG{fxe&8W92K*1nk*7&%v+v#ft`&+-X4iK^^zE$ z!YFW3+tr`1x{+{L&_=WCuYqr1Jxiou>rx2s1$Grb69A>dT%3*MNo~CAxydHuzQY7Y z(g(p4-pZTN-Im<*gx{gjx`*4QtuUMqTNBYHv+=8)dW^S%G-0bkgl6>^oMds(PS&Y2 z(cBY>h+@4O#>T)|++^niJ>fd{6P5(b6Fl;n1f=k?9=S=yh=tm|J+YwYiEZu?lUV46 zf*=vUkfZLzCk)*;h8AK85HAsk<;i7viX=}y0&$a%LdGA%-xK(I5`U*5O7bbW2oXY8 zxlqG?GuKJ7as4kq`E9kT8r7)?=2&gkP-dKo-0pT%g}#LqLfZc%(f6k^&;!3q7$> z5`u;7D2QXW#v?aKVUNY>-f&_1R+=LM<57TMXGX@u9a*RFt? z#BMg5Xbd9urAy~dHzC~MT)`Ro<666htm3X&43(R&v~STaa=kCP4}HdL*wN z_d6;0obRN`E^Q_<@E6$S1@K9YDQfYhb~=Xm%jE_Ns^$*cHr>dLS#=G&?-q z)KWMvPsq^gRAW@3B7@- z7L3$~=&t5=kvRcm6FoRvb6XKvHK>AK>XV&qrSQE--pJtgAWI}q^d2W@;gRFsgkGy# zcTz_E+KPLdTCo||13FH^iQy!$xi*8Bp#43qsd{|1a31Ok5=s@*kiIbX6Uw)~ZZ5y_ z#Q!q~Dm;C4c!fh|@5q4Jn>1$6_|ivBgSx*2k~vT22js|V*ZIWm->c09!*7n<+VNs@ z9u0#wEWv*L^U#Xdga^37UktRZ)O%qtmile`UIT4Rv?(Ts6Uc-6W=k>=@JG*IeHDu1 zMK_33037C*U|%+BuTqEz_%FkaZJp}c5?5=yiAfXer{>W99GjW zB7vqGELBGD`k_x)NqDHKa;I6zk0JBXR?qTO$>Pw>OkG>^wD@{vtwr4E{U%k9vQiWNC?8P=EiQqR?bp* zRpAd-p^&L&$4z9~BK++fnd-o-DU+UenxuNwM`)D?Yji@n$ia`r@AL4W*%jNRLt&7% zgq&n8v+EQzR^2g*;&9AsVoW4|FGQ@X9 zPrhTTG>U=0bfGq9PU!+$A#a)-`u$quLh}- zQJk=r!1*A;PIy#C{1V%W7jXaxx05D&g-(*fb;;L?p3rpqis2kx7=_$MWPyNzkk$?; z$jMb;k|sd{75Py}qi}(Oo29FmjPz~6xgrcJP-A*E*=1a^Xy1sfTowp~t`#BRzU-lx zoF+E&)((=Ojo6NC*2)#}x`;TqpW}aDR?p`&QyM8EIU>kg(-v$328oY#kawAES}AAd1U)OilOUs-~fTTvwX%?b1bQ zXx(G?+Mm>i?XGL(d+K?kWbaCQl}dQJP{Mk@S_yxXSnx3`wjmffWzK^xz6?M6 z8!NW{dT6#@y9>4sqeS;$_`!v`Y2OVvV@3rVTC0YN&OZ!I=av1TvrmujL1RN(z9Eiv zG`9kVNb_2e_`%R5er111tQnF$2>klTYh#As?3gh_hPPEi#od1l&D~3P&s}4s`fb@B z%zezq5Y#6bv zy<)}Ozr%{x_JI{U*!VrT5Kxr+-!%UvXJntczH^jf%x=8rsIUDk1%IJ-} zW52y5N&~s(y&{W_G6(I^e zli)eJ-;DF<^$Rr*(@D~%vs&HFsMddezcm!SI)H&1ists9%HV3xJ{8h#46L#z(jFg% zVI`Q36<{)iYzLG1GCY`yIZH5&qbvdWvH(Q{wcDWlwp5NFFCW-Q^wn>Qif_9mAmyBD z=;S-901$&luFm~0tA@Uc$llJlg5zy_sUzC1r$2VLz(cOadVIqXVIs4O2T?(QyFs8h zL%l)A3tHKh8kMf&pnBrAnl2_N8n)D!pOOd&C%ZVJCUmhx9QfWQMopjyquK}3qun>? z#3(y@>f$|euDgNP!HlY!E$CicN3lRCqKpqDS-WdA%UsS!Gh5o~uA|w+Z#k#BU)$ES zYgz=`c^kdE@8E&Tk7f199l{0hb6L&p(8>7Py2FDzbjUqbd=}kr<*RjnN=yHY9zVxJ zbia+~#e?1N;6HV|@TO{)KUw#?__Edg9-gnpWD8gdlvomvB9xBxN5rNslkr@ zj!fU#{06+}{+1rUqsQ;@=s%#@;(*MKhdiC`FKN0z;xTY4kKRgl(s5cuI@MKiA9sJSj@9a+*E8-UCL}n zk$~d$VvdPg;%JH@jJ{<~mCMwVGUb|3Tc{72S2Ky&c&5uYER=7+F+}+pGBL8&AV|Hb za<*NH%C>C`g<87GYV@V+~w=axd56MIWuw zQ=FANpl0keqWTG|EJd3#EmVgBO*j^dgl=R}k9VvrutR!@u0x$njlRY`ct@q7Q=_;e zNBK#%EN20)jzEP4$Bijw8i!8k*di>?_hQ(}kpiUCE<-LjfOJ{f5<%cEKuvZfQr(3P(ZbqwVx;3CRy(%5ursD>k2 zX$Q;AplpopgVBR(e9$tEBeMmOMEi4n@XSK4BA|?VrpD8xz4+Nh)COhh;r@@7h@v2} z=q}ZR71ebouAO9RHs^e8mWG}M388^615Th?%067IGXGiH3T>L|SN$o1rds zY6ejU5_KQ-)Ehug3)N+Y(|^iLPXP%*7DZA`S0rt{ z1{A^)CF8KzI0`KxMGpCzW9lU2t!I_OSrTCBEDe0fqwywUq76&B9qHi@_&rSb{h6AI zdr0?Kucx|l;I_I)zvr(OUBc!bt~!ZoPD+W3D3>>IS+fwMSJMznP(85rTMIR?1@r_q zd0VAkI8KTpPFn-r+#agOuolmSk*af7Ge8Cou>%R-#12r5nqZClZ1h^SbnIrKavA27 zYIJX_V@2&Tuv!%aprSef~p#gGA_m*C&rt4y)*O<25yuOn} zH*X7%g5cad{gt&1XN6t?-iL*@2cGu2k6T6mr@c8Y# zec#M{GjC@ua$lTwKIdHjXn(%Vg$u)uR>cpe3O_cvF@ss$fgQMW4tJ3~XujT$yJisXBxy8#g27(8 znTz9ATz65upgsf8h7xz;F?iLMi}QGZ>Vq*Ahu{~1-w^ypVrmXYu}8;)ml@oMJBnYT zuk42zJXy9nmy2^%5e@+YI9Ni^{Fx|T+jR?h8GOu)gS*L3b)f?cK4sQcN2l>R4Rio2 z9<2WrOe}g(%PLgrmDkfbn1YU`?dqpwpH)AFr?&cn1aK3f`N_&F= zuxfQ`ew-{e{_BZzS$>I4XR>nYX*MGg&V3Zw=}wTW1xk zKa-jE^E;(_oIKXmutTa>yCOr3;6yfC&5lfJ*>?NAMvZTeeM^mRq5bwXUP9YeR=wli#~T z5k?4DUaD5`qY0$OTBDk+Z`|OXkDkKYi?j-pn&|q9%L$Y9L$h`eIw`*vas** zd{j6>BhVX_7c;^nJX*Vr;*m26S>pNdio`81^ODM0T9|N%qA=7pZIoKu^XB5h1gJ}_ z;X2xPg`;Lwzox6$+Q6S<@VaoEq_FMyn}35(i83}j4IToSjE;Fk3x=RpUp+00J99o#uf z^_FHV#6ejLBkeUXQkf7p9Tzqk`K7l|X5~xg-%7@s1EQirp_r15}$?aC-|)TqRI(+xd9j~^)n`cQ~`7U)M2 zax>63WjO{DsW$&P=p8h>X&pIX%++X8@fdlq{~i=AKHJ}5xBr8RYlBgQ#){X1H|%Fd z?j6$xWf(pjbghp!z(Uk+vt>;zl;9Q5N=90Oc|nxJbd`m##HNeF2pppx=HledNXrAG z@L2jXC}_B33RY!9M=BVC^S+iHv56RopkeZQq#aF>Pb0ymZy;mBbtafSR9@pV(> fnx

previous

-

Nextflow fundamentals training

+

Nextflow fundamentals training

 Contents
-

Nextflow fundamentals training#

+

Nextflow fundamentals training#

Is your code reusable? Are your results reproducible? Tired of reinventing the wheel? The thing is that reproducibility and even repeatability is challenging even if you are very careful about keeping the same software parameters and versions. Do you want to learn how to write reusable, reproducible, and scalable pipelines?

Nextflow is an advanced workflow management system designed to streamline data-driven processes, especially in the bioinformatics and computational biology fields. It allows users to develop, to execute, and to scale complex workflows across various environments (i.e local machine, Cloud - Azure, AWS, etc… - or HPC). This system is simple and flexible and supports different programming languages (i.e. Python, R, Bash) and containers (e.g Docker, Singularity, etc…).

Let us introduce you to Nextflow and unlock you a door to a vibrant community building and maintaining standardized reproducible bioinformatics analyses, trainings, hackathons and resources to make your data-driven analysis scalable an reproducible.

Nextflow training notes#

-

Welcome to the notes for the Nextflow training offered to the researchers of DTU - Biosustain and DTU - Bioengineering. This course is half dedicated to explain Nextflow fundamentals and half dedicated to practice Nextflow. The materials are based mostly on Nextflow trainings portal.

-

Please visit About to know about the course, the Data Science platform and what the course covers, go to Course Information to figure out about the details (instructions, location and timing). Please visit Instructions first before starting the hands-on part. Once you have started your Codespace, please follow course along in the Course contents. To keep learning Nextflow and nf-core pipelines please visit Resources.

-

And remember to ask questions during the course or after the course, you can contact us at Data Science platform email.

+

Welcome to the notes for the Nextflow training offered to the researchers of DTU - Biosustain and DTU - Bioengineering. This course is half dedicated to explain Nextflow fundamentals and half dedicated to practice Nextflow. The materials are adapted from the Nextflow trainings portal.

+

Please visit About to know about the course, the Data Science platform and what the course covers, go to Course Information to figure out about the (instructions, location and timing). Please visit Instructions first before starting the hands-on part. Once you have started your Codespace, please follow the tutotial in the Course contents. Running a Real Workflow and the use of Seqera Platform is going to be more like a demo than hands-on but you are welcome to try to follow along with the instructors.

+

To keep learning Nextflow and nf-core pipelines please visit Resources.

+

And remember to ask questions during the course or after the course, you can always contact us at Data Science platform email.

diff --git a/searchindex.js b/searchindex.js index 48c8386..ce1dd90 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"1. Input definition to the process block:": [[4, "input-definition-to-the-process-block"]], "2. Editing the process command to use the input variable": [[4, "editing-the-process-command-to-use-the-input-variable"]], "3. Creating an input channel": [[4, "creating-an-input-channel"]], "4. Adding the channel as input to the process call": [[4, "adding-the-channel-as-input-to-the-process-call"]], "About": [[0, null]], "Add in variable inputs using a channel": [[4, "add-in-variable-inputs-using-a-channel"]], "Asking for help, following specific developements": [[9, "asking-for-help-following-specific-developements"]], "Citations": [[9, "citations"]], "Contents": [[1, null]], "Data Science platform": [[0, "data-science-platform"]], "Docker": [[5, "docker"]], "Download and install Nextflow": [[5, "download-and-install-nextflow"]], "Find the output and logs in the work directory": [[4, "find-the-output-and-logs-in-the-work-directory"]], "Full script": [[4, "full-script"]], "Initial checks": [[5, "initial-checks"]], "Instructions": [[5, null]], "Let\u2019s add a second process to our pipeline": [[4, "let-s-add-a-second-process-to-our-pipeline"]], "Let\u2019s run the script on a batch of input values": [[4, "let-s-run-the-script-on-a-batch-of-input-values"]], "Local installation": [[5, "local-installation"], [9, "local-installation"]], "Location": [[6, null]], "Nextflow events": [[9, "nextflow-events"]], "Nextflow fundamentals training": [[8, null]], "Nextflow fundamentals tutorial": [[4, null]], "Nextflow in Windows": [[5, "nextflow-in-windows"]], "Nextflow training notes": [[8, "nextflow-training-notes"]], "Objectives": [[0, "objectives"]], "Opening the Nextflow environment": [[5, "opening-the-nextflow-environment"]], "RNA-Seq workflow": [[2, null]], "Relaunch a pipeline without repeating steps": [[4, "relaunch-a-pipeline-without-repeating-steps"]], "Requirements": [[5, "requirements"]], "Resources": [[9, null]], "Run Nextflow CLI with Seqera Platform visualizing and capturing logs": [[3, null]], "Run hello.nf script and follow the run in Seqera platform": [[3, "run-hello-nf-script-and-follow-the-run-in-seqera-platform"]], "Running our first script": [[4, "running-our-first-script"]], "Send the output to a file and save it on an specific folder": [[4, "send-the-output-to-a-file-and-save-it-on-an-specific-folder"]], "Seqera platform": [[3, "seqera-platform"], [9, "seqera-platform"]], "Summary": [[4, "summary"]], "Take a file source of input values (a sample file)": [[4, "take-a-file-source-of-input-values-a-sample-file"]], "The course": [[0, "the-course"]], "Timing": [[7, null]], "Training material": [[9, "training-material"]], "Use command line interface (CLI) parameters for inputs": [[4, "use-command-line-interface-cli-parameters-for-inputs"]]}, "docnames": ["about", "course_contents/Contents", "course_contents/RunningRealWorkflow", "course_contents/SeqeraPlatform", "course_contents/Tutorial", "course_information/Instructions", "course_information/Location", "course_information/Timing", "index", "resources"], "envversion": {"sphinx": 64, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2}, "filenames": ["about.md", "course_contents/Contents.md", "course_contents/RunningRealWorkflow.md", "course_contents/SeqeraPlatform.md", "course_contents/Tutorial.md", "course_information/Instructions.md", "course_information/Location.md", "course_information/Timing.md", "index.md", "resources.md"], "indexentries": {}, "objects": {}, "objnames": {}, "objtypes": {}, "terms": {"": [2, 3, 5], "0": 4, "00": 7, "011": 6, "02_local": 9, "10": [4, 7, 9], "1038": 9, "113": 0, "12": 7, "20": 7, "2017": 9, "2024": [6, 7], "208": 6, "21": 5, "27th": [6, 7], "316": 9, "319": 9, "35": 9, "3820": 9, "4": 2, "7": 2, "A": 4, "And": [2, 4, 8], "As": [0, 4], "At": 0, "But": 4, "By": 4, "For": [0, 2, 4], "If": [1, 4, 5], "In": [0, 2, 4], "It": [0, 2, 4, 8], "One": 4, "The": [3, 4, 5, 8], "Then": [2, 4], "There": [2, 4, 5], "These": 4, "To": [0, 1, 2, 4, 5, 8], "_": 4, "abil": 4, "abl": 2, "about": [4, 5, 8], "academia": 0, "acceler": [0, 3], "accept": 4, "access": [0, 3, 4, 5], "accomod": 4, "accordingli": 4, "account": 3, "accumul": 4, "achiev": 4, "across": [0, 8], "actual": 4, "ad": 5, "adapt": 4, "add": 2, "addit": [3, 5], "advanc": [2, 8], "affect": 4, "after": [2, 8], "again": 4, "aggreg": 2, "aim": 0, "al": 9, "alc2": 6, "all": [2, 4, 5], "allow": [0, 3, 4, 5, 8], "along": 8, "alreadi": 4, "also": [0, 4, 9], "an": [0, 1, 2, 3, 8], "analis": 2, "analys": 8, "analysi": [0, 2, 3, 4, 8], "analyt": 0, "ani": 4, "ansi": 4, "appli": 4, "approach": 0, "ar": [0, 2, 4, 5, 8, 9], "argument": 4, "arrai": 4, "arriv": 7, "ask": [5, 8], "autom": 0, "automat": 4, "avoid": [2, 4], "aw": 8, "azur": [0, 5, 8], "b": 4, "back": 4, "base": [0, 2, 5, 8], "bash": [4, 5, 8], "basic": 4, "batch": 5, "becom": 0, "been": [0, 4], "befor": 8, "begin": 4, "between": 4, "bgin": 4, "bin": [4, 5], "binari": 5, "bioengin": [0, 8], "bioinformat": [0, 2, 8], "biologi": [0, 8], "biosustain": [0, 8], "biotechnologi": 9, "bonjour": 4, "both": [0, 4], "broken": 2, "build": [0, 4, 5, 6, 8], "built": [0, 4, 5], "bulk": 4, "button": 5, "cach": 4, "cake": 7, "campu": 6, "can": [0, 1, 2, 3, 4, 5, 8], "care": 8, "case": [2, 4], "cat": 4, "catalog": 3, "cd": [2, 4], "central": 0, "centric": 0, "challeng": 8, "chang": 4, "channel": [0, 9], "characterist": 0, "check": [2, 4], "checkifexist": 4, "chmod": 5, "choic": 0, "click": [1, 4, 5], "clone": 2, "closer": 4, "cloud": [0, 8], "club": 0, "cluster": 0, "co": 9, "code": [2, 4, 5, 8], "codespac": [4, 5, 8], "coffe": 7, "collabor": [0, 3], "colleagu": 3, "collect": 2, "colloect": 2, "com": [2, 9], "comma": 4, "command": [3, 5], "comment": 4, "commonli": 2, "commun": [0, 8, 9], "compat": [2, 5], "compil": [2, 4], "complet": [4, 5], "complex": 8, "complianc": 3, "compon": 4, "comput": [0, 3, 8, 9], "concept": 0, "config": [0, 2], "configur": 5, "congratul": 4, "connect": 4, "construct": 4, "contact": [0, 8], "contain": [2, 4, 8], "container": 5, "content": [4, 8, 9], "context": 4, "control": 2, "convert": 4, "converttoupp": 4, "coomonli": 2, "coorgan": 0, "copi": 4, "copyandpastetokenfromthesqeraplatformher": 3, "core": [0, 2, 4, 8, 9], "corner": 2, "correspond": 4, "cost": 3, "could": [4, 5], "cours": [5, 6, 7, 8, 9], "cover": [2, 8], "creat": [0, 2, 3, 5], "credenti": 5, "csv": 4, "curl": 5, "current": [4, 5], "custom": 5, "dansk": 4, "data": [1, 2, 4, 8], "dataflow": 4, "declar": 4, "dedic": 8, "default": 4, "defin": 4, "depend": 5, "deploi": 0, "describ": 4, "design": [0, 8], "desir": 4, "detail": [2, 8], "dev": 0, "devcontain": 5, "develop": [0, 4, 5, 8], "di": 9, "did": 4, "differ": [2, 4, 5, 8, 9], "diffrent": 2, "direct": 4, "directli": 5, "directori": [0, 2], "displai": 4, "do": [4, 5, 8], "doc": 9, "docker": [0, 2, 8], "dockerfil": 5, "document": 9, "doe": 4, "doi": 9, "done": 4, "door": 8, "doubl": 4, "download": 1, "driven": 8, "dsp": 0, "dtu": [0, 6, 8], "duplic": 4, "dure": 8, "dynam": 4, "e": [0, 4, 5, 8], "each": [0, 4], "earli": 3, "earlier": 4, "easi": [0, 2, 4], "easili": 4, "echo": 4, "edit": [6, 7], "editor": 5, "educ": 0, "effect": 3, "element": 4, "email": [0, 8], "emit": 4, "enabl": [2, 5, 9], "end": 0, "enjoi": 2, "ensur": [3, 4, 5], "entir": [0, 4], "env": 4, "environ": [0, 2, 3, 8], "envsetup": 9, "err": 4, "error": 4, "especi": 8, "essenti": [0, 4], "et": 9, "etc": [5, 8], "even": 8, "everyth": 5, "evolv": 0, "exampl": [0, 4], "execut": [0, 3, 4, 5, 8], "exist": 0, "exit": 4, "exitcod": 4, "expand": 4, "expect": 4, "explain": 8, "export": 3, "extens": [2, 4, 5], "factori": 4, "fals": 4, "fastq": 4, "fastqc": [2, 4], "featur": [0, 4, 5], "feed": 4, "feel": 4, "fellow": 0, "ferri": 4, "few": [2, 4], "field": [0, 8], "figur": 8, "file": [0, 2, 5], "final": [2, 4, 5], "find": 2, "first": [0, 1, 2, 3, 5, 8], "flatmap": 4, "flatten": 4, "flexibl": [4, 8], "focus": 0, "folder": 2, "follow": [0, 1, 2, 4, 5, 8], "format": 4, "forum": 9, "four": 0, "fq": 4, "framework": 3, "from": [2, 4], "fromfilepair": 4, "frompath": 4, "fulli": 5, "function": [4, 5], "fundament": 2, "furthermor": 4, "g": [0, 4, 8], "gain": 0, "gene": 4, "gener": [0, 2, 3, 4, 5], "genom": 4, "get": [2, 4, 5, 9], "git": [2, 5], "github": [2, 5], "give": 3, "given": 2, "go": [1, 2, 4, 5, 8], "gone": 9, "good": [4, 5, 9], "great": 2, "greet": 4, "greeting_ch": 4, "groovi": 0, "grrete": 4, "gz": 4, "ha": [0, 4], "hackathon": 8, "half": 8, "hand": [1, 4, 7, 8], "handl": [4, 5], "hang": 4, "happen": 4, "happi": 4, "have": [2, 4, 5, 8, 9], "hej": 4, "hello": [2, 4], "help": 3, "here": [1, 2, 4, 5, 9], "hexadecim": 4, "high": [0, 2], "hola": 4, "how": [4, 8], "hpc": 8, "html": [2, 9], "http": [2, 5, 9], "hyphen": 4, "i": [0, 2, 3, 4, 5, 6, 7, 8], "icon": [2, 4], "idea": 4, "ident": 5, "identifi": 4, "igen": 4, "imag": 0, "implement": 0, "includ": 0, "inclus": 0, "index": [2, 9], "indic": 4, "individu": 4, "industri": 0, "info": [4, 5], "inform": [2, 8], "infrastructur": 0, "ingreet": 4, "inmagin": 4, "innov": 0, "input_fil": 4, "insid": 4, "insight": 0, "inspir": 9, "instal": [0, 2], "instead": 4, "instruct": [1, 8], "integr": 0, "interest": 2, "interpret": 4, "introduc": [0, 4, 8], "introduct": [1, 7], "involv": [0, 4], "io": [2, 5, 9], "issu": 5, "iter": 4, "its": 5, "java": 5, "jave": 2, "join": 9, "json": 5, "just": 4, "keep": [0, 2, 8, 9], "know": [4, 8], "knowledg": 9, "l": [2, 4], "languag": [0, 4, 8, 9], "larg": 0, "last": [2, 4], "later": 3, "latest": [4, 9], "launch": 3, "lean": 9, "learn": [0, 2, 4, 5, 8, 9], "less": 4, "let": [2, 3, 5, 8], "level": [0, 9], "lifecycl": 0, "like": [0, 5], "line": 2, "link": [1, 5], "linux": 5, "list": 4, "live": 2, "local": [0, 8], "locat": [7, 8], "log": [1, 2], "logic": 4, "look": [2, 4], "machin": [0, 5, 8], "maco": 5, "mai": [2, 4, 5], "main": [2, 4], "maintain": [0, 8], "make": [0, 4, 5, 8], "manag": [0, 4, 5, 8], "mani": [2, 5], "match": 5, "materi": [2, 8], "meant": 4, "mention": 2, "messag": 4, "metadata": 4, "method": 0, "mind": 0, "minim": [2, 4], "minut": [2, 4], "mkdir": 4, "mode": 4, "modif": 4, "modifi": 4, "modular": 0, "monitor": [0, 3], "more": [0, 4, 5], "mostli": 8, "move": 2, "multidisciplinari": 0, "multipl": [0, 4], "multiqc": 2, "multiqc_report": 2, "mv": 5, "name": 4, "nativ": 5, "natur": 9, "nbt": 9, "need": [0, 2, 3, 4, 5], "network": [5, 7], "new": [0, 4, 9], "newli": 4, "next": 5, "nextflow": [0, 1, 2, 7], "nf": [0, 2, 4, 8, 9], "notic": [4, 5], "novemb": [6, 7], "now": [4, 5], "o": 5, "offer": 8, "ok": 4, "onc": [8, 9], "one": [0, 4], "ones": 4, "ongo": 0, "onli": 4, "open": [0, 4], "oper": [0, 4, 5], "optim": [0, 3, 5], "option": [2, 4], "orchestr": 0, "order": 2, "organ": [0, 3], "other": 4, "our": [0, 2, 3, 5, 9], "out": [4, 8], "output": 0, "outputfil": 4, "own": 9, "p": 9, "packag": 4, "parallel": 0, "param": 4, "paramet": 8, "pars": 4, "part": [2, 8], "pass": 4, "past": 4, "path": [4, 5], "pdf": 1, "per": 4, "perform": [0, 4], "piec": [0, 2, 4], "pillar": 0, "pipelin": [0, 1, 2, 3, 8, 9], "place": 2, "platform": [1, 8], "pleas": [4, 5, 8, 9], "plug": 4, "point": 4, "portabl": 0, "portal": [8, 9], "possibl": 5, "powerpoint": 1, "practic": 8, "pre": 0, "prefer": 1, "prepar": [0, 9], "preview": 2, "primari": 5, "print": 4, "process": [0, 1, 8], "produc": 4, "product": 0, "program": [0, 4, 8], "project": 0, "projectdir": 4, "promot": [0, 3], "properli": 5, "provid": [0, 3, 4, 5], "publish": 4, "publishdir": 4, "pursu": 0, "put": 4, "python": 8, "p\u00e5": 4, "qo": 5, "qualifi": 4, "qualiti": 2, "quantif": 2, "question": 8, "quit": [2, 4], "r": 8, "random": 4, "rather": 0, "rdm": 5, "re": [4, 9], "read": 4, "read_pairs_ch": 4, "readi": [4, 5], "recommend": [2, 5], "recov": 4, "reduc": 3, "reentranc": [0, 4], "refresh": 9, "regular": 4, "reinvent": 8, "relat": [4, 5], "reliabl": 3, "rememb": [2, 8], "rememeb": 5, "repeat": 8, "replac": 4, "report": 2, "repositori": [0, 2, 5], "reproduc": [0, 3, 8, 9], "requir": [0, 4], "research": [0, 3, 8], "resolv": 5, "resourc": [0, 3, 8], "result": [0, 1, 2, 3, 4, 8], "resum": 4, "reusabl": [0, 8], "right": 2, "rna": 1, "rnaseq": [0, 2], "room": 6, "rsearch": 0, "run": [0, 1, 2, 5], "runtim": 5, "sai": 4, "salmon": 2, "same": [2, 4, 8], "samplesheet": 4, "sayhello": 4, "scalabl": [0, 8], "scale": 8, "scheme": 4, "scienc": 8, "scrip7": 2, "script": [0, 1, 2, 5], "script7": 2, "search": 2, "seat": 5, "secur": 3, "see": [2, 4], "seem": 5, "separ": 4, "seq": 1, "seqera": [0, 1], "sequenc": [2, 4], "session": 7, "set": [2, 4], "sh": 4, "share": [3, 9], "shared_invit": 9, "short": 0, "should": [2, 4, 5], "show": 2, "simpl": 8, "singl": 4, "singular": 8, "slack": 9, "small": 2, "smooth": 5, "snack": 7, "so": 4, "softwar": [0, 2, 4, 8], "some": [2, 4, 5, 9], "someth": [4, 9], "sourc": 0, "space": 4, "specif": 5, "specifi": [2, 4], "spend": 4, "splitcsv": 4, "standard": [0, 3, 4, 8], "start": [4, 8], "statist": [0, 2], "stderr": 4, "stdout": 4, "step": 2, "storag": [3, 5], "store": 4, "strategi": 0, "streamlin": 8, "strong": 0, "structur": 4, "subdirectori": 4, "subsequ": 4, "subsystem": 5, "succesfulli": 2, "success": 4, "sudo": 5, "summar": 2, "summit": 9, "support": [0, 5, 8], "sure": 5, "system": [0, 3, 4, 5, 8], "tab": 5, "taht": 4, "task": 4, "teach": 0, "team": [0, 5], "technologi": 0, "tell": 4, "termin": [4, 5], "test": 5, "text": 4, "than": [0, 4], "thei": [4, 9], "them": 4, "theoret": 2, "thi": [0, 1, 2, 4, 5, 6, 7, 8], "thing": [4, 8], "think": 4, "through": [1, 2, 9], "throughput": 2, "time": [0, 2, 4, 8], "tire": 8, "todai": [2, 5], "togeth": [4, 5], "token": 3, "tommaso": 9, "tool": [0, 2, 5], "top": 2, "tosortedlist": 4, "tower": 3, "tower_access_token": 3, "tr": 4, "train": [0, 2], "transcript": 2, "transcriptom": 2, "transform": 4, "tree": [2, 4], "true": [2, 4], "try": [1, 4], "turn": 4, "tutori": [1, 2], "two": 4, "txt": 4, "type": 4, "typic": 4, "u": [0, 3, 4, 8], "ubuntu": 5, "uniqu": 4, "unix": 5, "unlock": 8, "until": 4, "up": [4, 5], "upcom": 9, "updat": 9, "upgrad": 4, "upper": 4, "uppercas": 4, "us": [0, 2, 5], "usag": 0, "user": [4, 8], "usr": [4, 5], "usual": [2, 4], "util": 4, "v": 5, "val": 4, "variou": [4, 8], "ve": 4, "verden": 4, "veri": 8, "verifi": 5, "version": [0, 2, 5, 8], "via": 4, "vibrant": 8, "view": 4, "virtual": 5, "visit": [8, 9], "viw": 2, "vscode": [2, 4, 5], "wa": 4, "wai": 4, "want": [2, 4, 5, 8], "we": [0, 2, 4, 5, 9], "websit": 5, "welcom": 8, "well": [4, 5], "went": 5, "were": 4, "wget": 5, "what": [0, 4, 8], "wheel": 8, "when": 4, "where": [2, 3, 4, 5], "wherea": 4, "which": [0, 4], "while": [0, 4, 5, 9], "why": 0, "word": 4, "work": [0, 2], "workflow": [0, 4, 5, 8, 9], "workshop": 0, "world": 4, "would": 0, "write": [0, 4, 5, 8], "written": 4, "wrote": 4, "wsl": 5, "www": 9, "x": 5, "you": [0, 1, 2, 3, 4, 5, 8], "your": [0, 1, 2, 3, 4, 5, 8], "z": 4}, "titles": ["About", "Contents", "RNA-Seq workflow", "Run Nextflow CLI with Seqera Platform visualizing and capturing logs", "Nextflow fundamentals tutorial", "Instructions", "Location", "Timing", "Nextflow fundamentals training", "Resources"], "titleterms": {"": 4, "1": 4, "2": 4, "3": 4, "4": 4, "The": 0, "about": 0, "ad": 4, "add": 4, "an": 4, "ask": 9, "batch": 4, "block": 4, "call": 4, "captur": 3, "channel": 4, "check": 5, "citat": 9, "cli": [3, 4], "command": 4, "content": 1, "cours": 0, "creat": 4, "data": 0, "definit": 4, "develop": 9, "directori": 4, "docker": 5, "download": 5, "edit": 4, "environ": 5, "event": 9, "file": 4, "find": 4, "first": 4, "folder": 4, "follow": [3, 9], "full": 4, "fundament": [4, 8], "hello": 3, "help": 9, "initi": 5, "input": 4, "instal": [5, 9], "instruct": 5, "interfac": 4, "let": 4, "line": 4, "local": [5, 9], "locat": 6, "log": [3, 4], "materi": 9, "nextflow": [3, 4, 5, 8, 9], "nf": 3, "note": 8, "object": 0, "open": 5, "our": 4, "output": 4, "paramet": 4, "pipelin": 4, "platform": [0, 3, 9], "process": 4, "relaunch": 4, "repeat": 4, "requir": 5, "resourc": 9, "rna": 2, "run": [3, 4], "sampl": 4, "save": 4, "scienc": 0, "script": [3, 4], "second": 4, "send": 4, "seq": 2, "seqera": [3, 9], "sourc": 4, "specif": [4, 9], "step": 4, "summari": 4, "take": 4, "time": 7, "train": [8, 9], "tutori": 4, "us": 4, "valu": 4, "variabl": 4, "visual": 3, "window": 5, "without": 4, "work": 4, "workflow": 2}}) \ No newline at end of file +Search.setIndex({"alltitles": {"1. Input definition to the process block:": [[4, "input-definition-to-the-process-block"]], "2. Editing the process command to use the input variable": [[4, "editing-the-process-command-to-use-the-input-variable"]], "3. Creating an input channel": [[4, "creating-an-input-channel"]], "4. Adding the channel as input to the process call": [[4, "adding-the-channel-as-input-to-the-process-call"]], "About": [[0, null]], "Add in variable inputs using a channel": [[4, "add-in-variable-inputs-using-a-channel"]], "Asking for help, following specific developements": [[9, "asking-for-help-following-specific-developements"]], "Citations": [[9, "citations"]], "Contents": [[1, null]], "Data Science platform": [[0, "data-science-platform"]], "Docker": [[5, "docker"]], "Download and install Nextflow": [[5, "download-and-install-nextflow"]], "Find the output and logs in the work directory": [[4, "find-the-output-and-logs-in-the-work-directory"]], "Full script": [[4, "full-script"]], "Initial checks": [[5, "initial-checks"]], "Instructions": [[5, null]], "Let\u2019s add a second process to our pipeline": [[4, "let-s-add-a-second-process-to-our-pipeline"]], "Let\u2019s run the script on a batch of input values": [[4, "let-s-run-the-script-on-a-batch-of-input-values"]], "Local installation": [[5, "local-installation"], [9, "local-installation"]], "Location": [[6, null]], "Nextflow events": [[9, "nextflow-events"]], "Nextflow fundamentals training": [[8, null]], "Nextflow fundamentals tutorial": [[4, null]], "Nextflow in Windows": [[5, "nextflow-in-windows"]], "Nextflow training notes": [[8, "nextflow-training-notes"]], "Objectives": [[0, "objectives"]], "Opening the Nextflow environment": [[5, "opening-the-nextflow-environment"]], "RNA-Seq workflow": [[2, null]], "Relaunch a pipeline without repeating steps": [[4, "relaunch-a-pipeline-without-repeating-steps"]], "Requirements": [[5, "requirements"]], "Resources": [[9, null]], "Run Nextflow CLI with Seqera Platform visualizing and capturing logs": [[3, null]], "Run hello.nf script and follow the run in Seqera platform": [[3, "run-hello-nf-script-and-follow-the-run-in-seqera-platform"]], "Running our first script": [[4, "running-our-first-script"]], "Send the output to a file and save it on an specific folder": [[4, "send-the-output-to-a-file-and-save-it-on-an-specific-folder"]], "Seqera platform": [[3, "seqera-platform"], [9, "seqera-platform"]], "Summary": [[4, "summary"]], "Take a file source of input values (a sample file)": [[4, "take-a-file-source-of-input-values-a-sample-file"]], "The course": [[0, "the-course"]], "Timing": [[7, null]], "Training material": [[9, "training-material"]], "Use command line interface (CLI) parameters for inputs": [[4, "use-command-line-interface-cli-parameters-for-inputs"]]}, "docnames": ["about", "course_contents/Contents", "course_contents/RunningRealWorkflow", "course_contents/SeqeraPlatform", "course_contents/Tutorial", "course_information/Instructions", "course_information/Location", "course_information/Timing", "index", "resources"], "envversion": {"sphinx": 64, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2}, "filenames": ["about.md", "course_contents/Contents.md", "course_contents/RunningRealWorkflow.md", "course_contents/SeqeraPlatform.md", "course_contents/Tutorial.md", "course_information/Instructions.md", "course_information/Location.md", "course_information/Timing.md", "index.md", "resources.md"], "indexentries": {}, "objects": {}, "objnames": {}, "objtypes": {}, "terms": {"": [2, 3, 5], "0": 4, "00": 7, "011": 6, "02_local": 9, "10": [4, 7, 9], "1038": 9, "113": 0, "12": 7, "20": 7, "2017": 9, "2024": [6, 7], "208": 6, "21": 5, "27th": [6, 7], "316": 9, "319": 9, "35": 9, "3820": 9, "4": 2, "7": 2, "A": 4, "And": [2, 4, 8], "As": [0, 4], "At": 0, "But": 4, "By": 4, "For": [0, 2, 4], "If": [1, 4, 5], "In": [0, 2, 4], "It": [0, 2, 4, 8], "One": 4, "The": [3, 4, 5, 8], "Then": [2, 4], "There": [2, 4, 5], "These": 4, "To": [0, 1, 2, 4, 5, 8], "_": 4, "abil": 4, "abl": 2, "about": [4, 5, 8], "academia": 0, "acceler": [0, 3], "accept": 4, "access": [0, 3, 4, 5], "accomod": 4, "accordingli": 4, "account": 3, "accumul": 4, "achiev": 4, "across": [0, 8], "actual": 4, "ad": 5, "adapt": [4, 8], "add": 2, "addit": [3, 5], "advanc": [2, 8], "affect": 4, "after": [2, 8], "again": 4, "aggreg": 2, "aim": 0, "al": 9, "alc2": 6, "all": [2, 4, 5], "allow": [0, 3, 4, 5, 8], "along": 8, "alreadi": 4, "also": [0, 4, 9], "alwai": 8, "an": [0, 1, 2, 3, 8], "analis": 2, "analys": 8, "analysi": [0, 2, 3, 4, 8], "analyt": 0, "ani": 4, "ansi": 4, "appli": 4, "approach": 0, "ar": [0, 2, 4, 5, 8, 9], "argument": 4, "arrai": 4, "arriv": 7, "ask": [5, 8], "autom": 0, "automat": 4, "avoid": [2, 4], "aw": 8, "azur": [0, 5, 8], "b": 4, "back": 4, "base": [0, 2, 5], "bash": [4, 5, 8], "basic": 4, "batch": 5, "becom": 0, "been": [0, 4], "befor": 8, "begin": 4, "between": 4, "bgin": 4, "bin": [4, 5], "binari": 5, "bioengin": [0, 8], "bioinformat": [0, 2, 8], "biologi": [0, 8], "biosustain": [0, 8], "biotechnologi": 9, "bonjour": 4, "both": [0, 4], "broken": 2, "build": [0, 4, 5, 6, 8], "built": [0, 4, 5], "bulk": 4, "button": 5, "cach": 4, "cake": 7, "campu": 6, "can": [0, 1, 2, 3, 4, 5, 8], "care": 8, "case": [2, 4], "cat": 4, "catalog": 3, "cd": [2, 4], "central": 0, "centric": 0, "challeng": 8, "chang": 4, "channel": [0, 9], "characterist": 0, "check": [2, 4], "checkifexist": 4, "chmod": 5, "choic": 0, "click": [1, 4, 5], "clone": 2, "closer": 4, "cloud": [0, 8], "club": 0, "cluster": 0, "co": 9, "code": [2, 4, 5, 8], "codespac": [4, 5, 8], "coffe": 7, "collabor": [0, 3], "colleagu": 3, "collect": 2, "colloect": 2, "com": [2, 9], "comma": 4, "command": [3, 5], "comment": 4, "commonli": 2, "commun": [0, 8, 9], "compat": [2, 5], "compil": [2, 4], "complet": [4, 5], "complex": 8, "complianc": 3, "compon": 4, "comput": [0, 3, 8, 9], "concept": 0, "config": [0, 2], "configur": 5, "congratul": 4, "connect": 4, "construct": 4, "contact": [0, 8], "contain": [2, 4, 8], "container": 5, "content": [4, 8, 9], "context": 4, "control": 2, "convert": 4, "converttoupp": 4, "coomonli": 2, "coorgan": 0, "copi": 4, "copyandpastetokenfromthesqeraplatformher": 3, "core": [0, 2, 4, 8, 9], "corner": 2, "correspond": 4, "cost": 3, "could": [4, 5], "cours": [5, 6, 7, 8, 9], "cover": [2, 8], "creat": [0, 2, 3, 5], "credenti": 5, "csv": 4, "curl": 5, "current": [4, 5], "custom": 5, "dansk": 4, "data": [1, 2, 4, 8], "dataflow": 4, "declar": 4, "dedic": 8, "default": 4, "defin": 4, "demo": 8, "depend": 5, "deploi": 0, "describ": 4, "design": [0, 8], "desir": 4, "detail": 2, "dev": 0, "devcontain": 5, "develop": [0, 4, 5, 8], "di": 9, "did": 4, "differ": [2, 4, 5, 8, 9], "diffrent": 2, "direct": 4, "directli": 5, "directori": [0, 2], "displai": 4, "do": [4, 5, 8], "doc": 9, "docker": [0, 2, 8], "dockerfil": 5, "document": 9, "doe": 4, "doi": 9, "done": 4, "door": 8, "doubl": 4, "download": 1, "driven": 8, "dsp": 0, "dtu": [0, 6, 8], "duplic": 4, "dure": 8, "dynam": 4, "e": [0, 4, 5, 8], "each": [0, 4], "earli": 3, "earlier": 4, "easi": [0, 2, 4], "easili": 4, "echo": 4, "edit": [6, 7], "editor": 5, "educ": 0, "effect": 3, "element": 4, "email": [0, 8], "emit": 4, "enabl": [2, 5, 9], "end": 0, "enjoi": 2, "ensur": [3, 4, 5], "entir": [0, 4], "env": 4, "environ": [0, 2, 3, 8], "envsetup": 9, "err": 4, "error": 4, "especi": 8, "essenti": [0, 4], "et": 9, "etc": [5, 8], "even": 8, "everyth": 5, "evolv": 0, "exampl": [0, 4], "execut": [0, 3, 4, 5, 8], "exist": 0, "exit": 4, "exitcod": 4, "expand": 4, "expect": 4, "explain": 8, "export": 3, "extens": [2, 4, 5], "factori": 4, "fals": 4, "fastq": 4, "fastqc": [2, 4], "featur": [0, 4, 5], "feed": 4, "feel": 4, "fellow": 0, "ferri": 4, "few": [2, 4], "field": [0, 8], "figur": 8, "file": [0, 2, 5], "final": [2, 4, 5], "find": 2, "first": [0, 1, 2, 3, 5, 8], "flatmap": 4, "flatten": 4, "flexibl": [4, 8], "focus": 0, "folder": 2, "follow": [0, 1, 2, 4, 5, 8], "format": 4, "forum": 9, "four": 0, "fq": 4, "framework": 3, "from": [2, 4, 8], "fromfilepair": 4, "frompath": 4, "fulli": 5, "function": [4, 5], "fundament": 2, "furthermor": 4, "g": [0, 4, 8], "gain": 0, "gene": 4, "gener": [0, 2, 3, 4, 5], "genom": 4, "get": [2, 4, 5, 9], "git": [2, 5], "github": [2, 5], "give": 3, "given": 2, "go": [1, 2, 4, 5, 8], "gone": 9, "good": [4, 5, 9], "great": 2, "greet": 4, "greeting_ch": 4, "groovi": 0, "grrete": 4, "gz": 4, "ha": [0, 4], "hackathon": 8, "half": 8, "hand": [1, 4, 7, 8], "handl": [4, 5], "hang": 4, "happen": 4, "happi": 4, "have": [2, 4, 5, 8, 9], "hej": 4, "hello": [2, 4], "help": 3, "here": [1, 2, 4, 5, 9], "hexadecim": 4, "high": [0, 2], "hola": 4, "how": [4, 8], "hpc": 8, "html": [2, 9], "http": [2, 5, 9], "hyphen": 4, "i": [0, 2, 3, 4, 5, 6, 7, 8], "icon": [2, 4], "idea": 4, "ident": 5, "identifi": 4, "igen": 4, "imag": 0, "implement": 0, "includ": 0, "inclus": 0, "index": [2, 9], "indic": 4, "individu": 4, "industri": 0, "info": [4, 5], "inform": [2, 8], "infrastructur": 0, "ingreet": 4, "inmagin": 4, "innov": 0, "input_fil": 4, "insid": 4, "insight": 0, "inspir": 9, "instal": [0, 2], "instead": 4, "instruct": [1, 8], "instructor": 8, "integr": 0, "interest": 2, "interpret": 4, "introduc": [0, 4, 8], "introduct": [1, 7], "involv": [0, 4], "io": [2, 5, 9], "issu": 5, "iter": 4, "its": 5, "java": 5, "jave": 2, "join": 9, "json": 5, "just": 4, "keep": [0, 2, 8, 9], "know": [4, 8], "knowledg": 9, "l": [2, 4], "languag": [0, 4, 8, 9], "larg": 0, "last": [2, 4], "later": 3, "latest": [4, 9], "launch": 3, "lean": 9, "learn": [0, 2, 4, 5, 8, 9], "less": 4, "let": [2, 3, 5, 8], "level": [0, 9], "lifecycl": 0, "like": [0, 5, 8], "line": 2, "link": [1, 5], "linux": 5, "list": 4, "live": 2, "local": [0, 8], "locat": [7, 8], "log": [1, 2], "logic": 4, "look": [2, 4], "machin": [0, 5, 8], "maco": 5, "mai": [2, 4, 5], "main": [2, 4], "maintain": [0, 8], "make": [0, 4, 5, 8], "manag": [0, 4, 5, 8], "mani": [2, 5], "match": 5, "materi": [2, 8], "meant": 4, "mention": 2, "messag": 4, "metadata": 4, "method": 0, "mind": 0, "minim": [2, 4], "minut": [2, 4], "mkdir": 4, "mode": 4, "modif": 4, "modifi": 4, "modular": 0, "monitor": [0, 3], "more": [0, 4, 5, 8], "move": 2, "multidisciplinari": 0, "multipl": [0, 4], "multiqc": 2, "multiqc_report": 2, "mv": 5, "name": 4, "nativ": 5, "natur": 9, "nbt": 9, "need": [0, 2, 3, 4, 5], "network": [5, 7], "new": [0, 4, 9], "newli": 4, "next": 5, "nextflow": [0, 1, 2, 7], "nf": [0, 2, 4, 8, 9], "notic": [4, 5], "novemb": [6, 7], "now": [4, 5], "o": 5, "offer": 8, "ok": 4, "onc": [8, 9], "one": [0, 4], "ones": 4, "ongo": 0, "onli": 4, "open": [0, 4], "oper": [0, 4, 5], "optim": [0, 3, 5], "option": [2, 4], "orchestr": 0, "order": 2, "organ": [0, 3], "other": 4, "our": [0, 2, 3, 5, 9], "out": [4, 8], "output": 0, "outputfil": 4, "own": 9, "p": 9, "packag": 4, "parallel": 0, "param": 4, "paramet": 8, "pars": 4, "part": [2, 8], "pass": 4, "past": 4, "path": [4, 5], "pdf": 1, "per": 4, "perform": [0, 4], "piec": [0, 2, 4], "pillar": 0, "pipelin": [0, 1, 2, 3, 8, 9], "place": 2, "platform": [1, 8], "pleas": [4, 5, 8, 9], "plug": 4, "point": 4, "portabl": 0, "portal": [8, 9], "possibl": 5, "powerpoint": 1, "practic": 8, "pre": 0, "prefer": 1, "prepar": [0, 9], "preview": 2, "primari": 5, "print": 4, "process": [0, 1, 8], "produc": 4, "product": 0, "program": [0, 4, 8], "project": 0, "projectdir": 4, "promot": [0, 3], "properli": 5, "provid": [0, 3, 4, 5], "publish": 4, "publishdir": 4, "pursu": 0, "put": 4, "python": 8, "p\u00e5": 4, "qo": 5, "qualifi": 4, "qualiti": 2, "quantif": 2, "question": 8, "quit": [2, 4], "r": 8, "random": 4, "rather": 0, "rdm": 5, "re": [4, 9], "read": 4, "read_pairs_ch": 4, "readi": [4, 5], "real": 8, "recommend": [2, 5], "recov": 4, "reduc": 3, "reentranc": [0, 4], "refresh": 9, "regular": 4, "reinvent": 8, "relat": [4, 5], "reliabl": 3, "rememb": [2, 8], "rememeb": 5, "repeat": 8, "replac": 4, "report": 2, "repositori": [0, 2, 5], "reproduc": [0, 3, 8, 9], "requir": [0, 4], "research": [0, 3, 8], "resolv": 5, "resourc": [0, 3, 8], "result": [0, 1, 2, 3, 4, 8], "resum": 4, "reusabl": [0, 8], "right": 2, "rna": 1, "rnaseq": [0, 2], "room": 6, "rsearch": 0, "run": [0, 1, 2, 5, 8], "runtim": 5, "sai": 4, "salmon": 2, "same": [2, 4, 8], "samplesheet": 4, "sayhello": 4, "scalabl": [0, 8], "scale": 8, "scheme": 4, "scienc": 8, "scrip7": 2, "script": [0, 1, 2, 5], "script7": 2, "search": 2, "seat": 5, "secur": 3, "see": [2, 4], "seem": 5, "separ": 4, "seq": 1, "seqera": [0, 1, 8], "sequenc": [2, 4], "session": 7, "set": [2, 4], "sh": 4, "share": [3, 9], "shared_invit": 9, "short": 0, "should": [2, 4, 5], "show": 2, "simpl": 8, "singl": 4, "singular": 8, "slack": 9, "small": 2, "smooth": 5, "snack": 7, "so": 4, "softwar": [0, 2, 4, 8], "some": [2, 4, 5, 9], "someth": [4, 9], "sourc": 0, "space": 4, "specif": 5, "specifi": [2, 4], "spend": 4, "splitcsv": 4, "standard": [0, 3, 4, 8], "start": [4, 8], "statist": [0, 2], "stderr": 4, "stdout": 4, "step": 2, "storag": [3, 5], "store": 4, "strategi": 0, "streamlin": 8, "strong": 0, "structur": 4, "subdirectori": 4, "subsequ": 4, "subsystem": 5, "succesfulli": 2, "success": 4, "sudo": 5, "summar": 2, "summit": 9, "support": [0, 5, 8], "sure": 5, "system": [0, 3, 4, 5, 8], "tab": 5, "taht": 4, "task": 4, "teach": 0, "team": [0, 5], "technologi": 0, "tell": 4, "termin": [4, 5], "test": 5, "text": 4, "than": [0, 4, 8], "thei": [4, 9], "them": 4, "theoret": 2, "thi": [0, 1, 2, 4, 5, 6, 7, 8], "thing": [4, 8], "think": 4, "through": [1, 2, 9], "throughput": 2, "time": [0, 2, 4, 8], "tire": 8, "todai": [2, 5], "togeth": [4, 5], "token": 3, "tommaso": 9, "tool": [0, 2, 5], "top": 2, "tosortedlist": 4, "tower": 3, "tower_access_token": 3, "tr": 4, "train": [0, 2], "transcript": 2, "transcriptom": 2, "transform": 4, "tree": [2, 4], "true": [2, 4], "try": [1, 4, 8], "turn": 4, "tutori": [1, 2], "tutoti": 8, "two": 4, "txt": 4, "type": 4, "typic": 4, "u": [0, 3, 4, 8], "ubuntu": 5, "uniqu": 4, "unix": 5, "unlock": 8, "until": 4, "up": [4, 5], "upcom": 9, "updat": 9, "upgrad": 4, "upper": 4, "uppercas": 4, "us": [0, 2, 5, 8], "usag": 0, "user": [4, 8], "usr": [4, 5], "usual": [2, 4], "util": 4, "v": 5, "val": 4, "variou": [4, 8], "ve": 4, "verden": 4, "veri": 8, "verifi": 5, "version": [0, 2, 5, 8], "via": 4, "vibrant": 8, "view": 4, "virtual": 5, "visit": [8, 9], "viw": 2, "vscode": [2, 4, 5], "wa": 4, "wai": 4, "want": [2, 4, 5, 8], "we": [0, 2, 4, 5, 9], "websit": 5, "welcom": 8, "well": [4, 5], "went": 5, "were": 4, "wget": 5, "what": [0, 4, 8], "wheel": 8, "when": 4, "where": [2, 3, 4, 5], "wherea": 4, "which": [0, 4], "while": [0, 4, 5, 9], "why": 0, "word": 4, "work": [0, 2], "workflow": [0, 4, 5, 8, 9], "workshop": 0, "world": 4, "would": 0, "write": [0, 4, 5, 8], "written": 4, "wrote": 4, "wsl": 5, "www": 9, "x": 5, "you": [0, 1, 2, 3, 4, 5, 8], "your": [0, 1, 2, 3, 4, 5, 8], "z": 4}, "titles": ["About", "Contents", "RNA-Seq workflow", "Run Nextflow CLI with Seqera Platform visualizing and capturing logs", "Nextflow fundamentals tutorial", "Instructions", "Location", "Timing", "Nextflow fundamentals training", "Resources"], "titleterms": {"": 4, "1": 4, "2": 4, "3": 4, "4": 4, "The": 0, "about": 0, "ad": 4, "add": 4, "an": 4, "ask": 9, "batch": 4, "block": 4, "call": 4, "captur": 3, "channel": 4, "check": 5, "citat": 9, "cli": [3, 4], "command": 4, "content": 1, "cours": 0, "creat": 4, "data": 0, "definit": 4, "develop": 9, "directori": 4, "docker": 5, "download": 5, "edit": 4, "environ": 5, "event": 9, "file": 4, "find": 4, "first": 4, "folder": 4, "follow": [3, 9], "full": 4, "fundament": [4, 8], "hello": 3, "help": 9, "initi": 5, "input": 4, "instal": [5, 9], "instruct": 5, "interfac": 4, "let": 4, "line": 4, "local": [5, 9], "locat": 6, "log": [3, 4], "materi": 9, "nextflow": [3, 4, 5, 8, 9], "nf": 3, "note": 8, "object": 0, "open": 5, "our": 4, "output": 4, "paramet": 4, "pipelin": 4, "platform": [0, 3, 9], "process": 4, "relaunch": 4, "repeat": 4, "requir": 5, "resourc": 9, "rna": 2, "run": [3, 4], "sampl": 4, "save": 4, "scienc": 0, "script": [3, 4], "second": 4, "send": 4, "seq": 2, "seqera": [3, 9], "sourc": 4, "specif": [4, 9], "step": 4, "summari": 4, "take": 4, "time": 7, "train": [8, 9], "tutori": 4, "us": 4, "valu": 4, "variabl": 4, "visual": 3, "window": 5, "without": 4, "work": 4, "workflow": 2}}) \ No newline at end of file