From 0f70f3efa202ad4498bf1ee38a750a680dd56a9a Mon Sep 17 00:00:00 2001 From: apalleja Date: Mon, 25 Nov 2024 23:51:47 +0000 Subject: [PATCH] deploy: 188f5c0d392d12bb104e5e257f9feacc04560290 --- .doctrees/course_contents/Tutorial.doctree | Bin 56660 -> 56658 bytes .doctrees/environment.pickle | Bin 41542 -> 41542 bytes _sources/course_contents/Tutorial.md | 10 +++++----- course_contents/Tutorial.html | 10 +++++----- 4 files changed, 10 insertions(+), 10 deletions(-) diff --git a/.doctrees/course_contents/Tutorial.doctree b/.doctrees/course_contents/Tutorial.doctree index 423bb6ce437b58d43f99b3bcfefad80e0196bff6..552d7d5de124a49449d024c0341b927bebdde36b 100644 GIT binary patch delta 245 zcmcbzi}}(nW|julsqPzD{s(X?siYUBrj}&pr7KP53zR|TZ#E5_?aqs&K*4VEffG`b zzt1>;DZ2UI%y-<3(UZ?E)t~%#sR^8=ySaZ^rjiPZDGCUlZhmP=L1~FzNkxg$W|@=I h8G$Be<^e_G(=u~Xl{OzZ^?->2%{h#luUu&00RXOwU&H_a delta 260 zcmcb#i}}hfW|julsh%5I{s(ZYtE3mDrj}&prK?Zo3zR|TZ#E5_?aq&+K*3HyeRAVW zF-G;t-)0=dF0=XW%=g@kF_R6K=`-p~PFSYPk-;82B}1$SDzrIa*)$~;G(+KT(9JI` uDJU(`E2$_^-z;@ zd`uE2xk)ll@)?Ona*Je+WQ}BodG^a0KIrz9MGL^Ec$3m4<=QNM6>49)o0lyK^HZX2(o z1>d19wg6?$8mv&Wvy9Dy-&qb`R{>miW?_ZaoaI=dpHUa#sk02KT=`Jy$_5k0w_Ikd zZlh~2W(d1}fUj#UaH_TqY;FrYtnGsH^%ltSwZNL&jhW7QD!?~U2;a6Az`;5cmMWZy(J*y`OdR%e0b`ZK(2a()KZk@ujQi1*+C5${0* z5%0kzmq!X1ThPC6@Kbordx64g<3$FKn*vyZov;ZCy^b~Pp8lcP3pcQ~*lWuP>B z;R~M?erry`<5>mEvjR8bxu68|^(|i!LsOvt`}RCRp1#tu%&>BQL@#31I-tfYUOf0t z1w)gk2iovO0`u|P0)A=#T!40RSb(YXQvvt7mIMrSUlw5Qtu*lM4gI(H%EsWTcyjmj zO##D0;)z~)HX>H;_}c|k1kN&eqgBBs7Q@b<7jgo*x)O9UggkxoTv))7(K7<>g$@ZY zpAQO%Uyuc4z1J;ZeC!#6eUbtto)_Wy`(Ah^Sz&NI3BN~04Ob!^kU7cA0L9THR7Y%( z9Xf!c5`upsR{hDu9)^$$MU#KCS>5!(F@~XYs+GdV^azEQXEqtkD+>rRD&MX0&8n>G<4Zr9{sVZO{#yV5 delta 1595 zcmY+DUrbwd6vz1$v}J>=9XNrq?oT^cBO^Yzw)@l4ma)_nR>K(C_$LF(pqAbaT2wOH zWMDjjKj^qZ(0?AF1EXgW~O!5)QBFP<+Iqho~D^1e}6n%ZS(emZ~CwW3ezY!IV zk}CS&F9}D975(6C;V8MH_ghSSAALa4x111;KBDMndW4(fE;J$>9YfI{k%d#XaC`MS zS_mE8Wb6^x;FSoL~g%4da8rUt&~sD{HnFHAOD;T>NW zW~R66{GIT?Z-tdqHGJUrLL51iX#hvF7aU$IEH{tvvPG)Ou#UV34Me;LhlqF&juY`7 zoFw8s=qKVm7$c(6M5c&%ce6yiyLqIfT9%LoC-T#IdxVdH5f|011IcJKtYwasGcd+X zAjPY++bz{(wrk%X?-t+<3=6pXVv@n+1qqAs6s!dU;Ged^&ej4P2*$817LeKk@GxkD zpW6y>ztsU1i9=YX75J>prfr658G=ds=cOe9%k3)+79{C$^?IN$Zqp8*+RG43+F0kJ zfQr*=0yfXw5+HZS1Q>d62w3l17BJEe0xAaVI-aLx=tHscZ}_HwyXUS8h>kvf^vo-1 zvGQrOOTeC3l)?Qu2|HN_JK_PjmNRKm+|3ZSYwPE+5Ckm~BLX%OM+H<)#s%bFjR@HK zdcT0_sfP@w;Dj$p?9W(!kyW13j4C_4Bk5-;fOsAqjCUlh4yJb$YzFM zg7w6H?b-Qb+-NCP5m39B6|k1Wp5uF({Z0IPg5^sY=B3dImhmwSGCrdiXh4Idd^&?h zKAJ%TpG$m3Ly3VVGN_9va3=3(D!iTVNYm0%q;pG2Ne*XHxYI?htH?!)T(ro=id?+N zrT_1eYUR18H1Kjl(xl5l9Y0TRo}UK;-8l?&9t?EbFwj-QK=%v-od*N`E(Qf2z18ZZ hqR2dl%u~obgUl1ie80@M%Y3)YH_H)4o4)dG`F{;42ZsOv diff --git a/_sources/course_contents/Tutorial.md b/_sources/course_contents/Tutorial.md index 2a9c307..4420f8f 100644 --- a/_sources/course_contents/Tutorial.md +++ b/_sources/course_contents/Tutorial.md @@ -149,7 +149,7 @@ process sayHello { Changing the code to write the variable (containing our grreting) in the output file: ```bash -echo '$greeting' > output.txt +echo "$greeting" > output.txt ``` ### 3. Creating an input channel @@ -318,7 +318,7 @@ process sayHello { script: """ - echo '$greeting' > '${greeting}-output.txt' + echo "$greeting" > "${greeting}-output.txt" """ } ``` @@ -345,7 +345,7 @@ Finally last modification to our script. Usually workflows start from a sample f ```bash mkdir data cd data -echo "Hello,Bonjour,Hola,Hej," > greetings.csv +echo "Hello,Bonjour,Hola,Hej" > greetings.csv less greetings.csv cd .. ``` @@ -416,7 +416,7 @@ process sayHello { script: """ - echo '$greeting' > '$greeting-output.txt' + echo "$greeting" > "$greeting-output.txt" """ } @@ -437,7 +437,7 @@ process convertToUpper { // now we add the bash code to convert the greeting to uppercase script: """ - cat '$input_file' | tr '[a-z]' '[A-Z]' > UPPER-${input_file} + cat "$input_file" | tr '[a-z]' '[A-Z]' > UPPER-${input_file} """ } diff --git a/course_contents/Tutorial.html b/course_contents/Tutorial.html index 777c495..261a4a7 100644 --- a/course_contents/Tutorial.html +++ b/course_contents/Tutorial.html @@ -496,7 +496,7 @@

1. Input definition to the process block:

2. Editing the process command to use the input variable#

Changing the code to write the variable (containing our grreting) in the output file:

-
echo '$greeting' > output.txt
+
echo "$greeting" > output.txt
 

 

 
@@ -665,7 +665,7 @@ 
Let’s run the script on a batch of input values    script:
     """
-    echo '$greeting' > '${greeting}-output.txt'
+    echo "$greeting" > "${greeting}-output.txt"
     """
 }
@@ -688,7 +688,7 @@

Take a file source of input values (a sample file)Finally last modification to our script. Usually workflows start from a sample file. In Nextflow and in nf-core standards this is usually called samplesheet.csv. We will create a file called greetings.csv for our example pipeline and save it in a folder called data.

mkdir data
 cd data
-echo "Hello,Bonjour,Hola,Hej," > greetings.csv
+echo "Hello,Bonjour,Hola,Hej" > greetings.csv
 less greetings.csv
 cd ..
@@ -755,7 +755,7 @@

Full script script: """ - echo '$greeting' > '$greeting-output.txt' + echo "$greeting" > "$greeting-output.txt" """ } @@ -776,7 +776,7 @@

Full script // now we add the bash code to convert the greeting to uppercase script: """ - cat '$input_file' | tr '[a-z]' '[A-Z]' > UPPER-${input_file} + cat "$input_file" | tr '[a-z]' '[A-Z]' > UPPER-${input_file} """ }