From 92e2180e4c6676c9a3ec991359e0e3ff164a9efd Mon Sep 17 00:00:00 2001 From: thomasdenecker Date: Wed, 2 Sep 2020 15:51:41 +0200 Subject: [PATCH] add new links --- docs/assets/md/session2020/Workflow_Snakemake.html | 4 ++-- docs/assets/md/session2020/workflow.md | 4 ++-- docs/session2020.html | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/assets/md/session2020/Workflow_Snakemake.html b/docs/assets/md/session2020/Workflow_Snakemake.html index 802a02e..9cda9aa 100644 --- a/docs/assets/md/session2020/Workflow_Snakemake.html +++ b/docs/assets/md/session2020/Workflow_Snakemake.html @@ -152,7 +152,7 @@ snakemake -s exo5.smk -R all fastqc

Observe the results
Does Snakemake do the job?

Fastqc: job or jobs?
-Look at more precisely the fastqc job. We have many input files but snakemake launched only one fastqc job:

image

It is because thefastqcrule is defined with a list of files and not for one unique file and because thefastqc tool accepts both a unique file as wellas a list of files.

Objective 6: Running n individual jobs

Create snakemake file exo6.smk. Improve previous code: Thank to the all rule, all expected files are designated. So we don’t need to give the fastqc rule a list anymore and we can replace it to manage only one file and all files one by one. We will gain in power in system shaving more than one core.

HINT
+Look at more precisely the fastqc job. We have many input files but snakemake launched only one fastqc job:

image

It is because thefastqcrule is defined with a list of files and not for one unique file and because thefastqc tool accepts both a unique file as wellas a list of files.

Objective 6: Running n individual jobs

Create snakemake file exo6.smk. Improve previous code: Thank to the all rule, all expected files are designated. So we don’t need to give the fastqc rule a list anymore and we can replace it to manage only one file and all files one by one. We will gain in power in system shaving more than one core.

HINT
Replace the expand()function with a wildcard for one filename in the fastqc rule.

Solution

SAMPLES = ["SRR3099585_chr18","SRR3099586_chr18","SRR3099587_chr18"]
 BIDX = ["1","2","3","4","rev.1","rev.2"]
 
@@ -178,7 +178,7 @@

Snakemake run

rm -Rf  FastQC/
 snakemake  -s exo6.smk -R all fastqc

Observe the results
-Now Snakemake did many fastqc jobs:

image

But what happens to the runtime displays on the screen? To correct this, we will move the displays to a log file specific for each rule and each input file.

Objective 7: Adding log file

Create snakemake file exo7.smk. Improve previous code:
+Now Snakemake did many fastqc jobs:

image

But what happens to the runtime displays on the screen? To correct this, we will move the displays to a log file specific for each rule and each input file.

Objective 7: Adding log file

Create snakemake file exo7.smk. Improve previous code:
In Unix systems, the output of a command is usually sent to two separate streams: the normal output: to Standard Out (stdout also “>” in shell),and error messages: to Standard Error (stderr, or “2>” in shell). To integrate stderr into the same log file as the stdout can be use “&>” instead of “>”:
shell: … &> {log}, but use with care when output files are printed tostdout (as often in shell comands). Redirect the stdout and stderr streams of the fastqc and bowtie2-build commands.

HINT
For the bowtie2-build and fastqc rules, add the log: directive with two variables (log1 and log2) to redirect each streams.

Solution

SAMPLES = ["SRR3099585_chr18","SRR3099586_chr18","SRR3099587_chr18"]
diff --git a/docs/assets/md/session2020/workflow.md b/docs/assets/md/session2020/workflow.md
index 03a3b9e..86406e9 100644
--- a/docs/assets/md/session2020/workflow.md
+++ b/docs/assets/md/session2020/workflow.md
@@ -242,7 +242,7 @@ Does Snakemake do the job?
 ***Fastqc:  job or jobs?***
 Look at more precisely the fastqc job.  We have many input files but snakemake launched only one fastqc job:
 
-![image](https://github.com/chernan/FAIR_bioinfo_docs/blob/master/03_workflow/images/FAIR_ex1_o5_smk.png)
+![image](https://github.com/chernan/FAIR_bioinfo_docs/raw/master/03_workflow/images/FAIR_ex1_o5_smk.png)
 
 It is because thefastqcrule is defined with a list of files and not for one unique file and because thefastqc tool accepts both a unique file as wellas a list of files.
 
@@ -294,7 +294,7 @@ snakemake  -s exo6.smk -R all fastqc
 ***Observe the results***
 Now Snakemake did many fastqc jobs:
 
-![image](https://github.com/chernan/FAIR_bioinfo_docs/blob/master/03_workflow/images/FAIR_ex1_o6_smk.png)
+![image](https://github.com/chernan/FAIR_bioinfo_docs/raw/master/03_workflow/images/FAIR_ex1_o6_smk.png)
 
 But what happens to the runtime displays on the screen? To correct this, we will move the displays to a log file specific for each rule and each input file.
 
diff --git a/docs/session2020.html b/docs/session2020.html
index 550d574..6cd1ad1 100644
--- a/docs/session2020.html
+++ b/docs/session2020.html
@@ -403,7 +403,7 @@ 
Matériels des participants

         
Outils collaboratif pour le md : HackMD. Merci Clémence et Diane !
 
 
         
    
-            
  • Git / GitHub par Alexandra & Clothilde : html md
    • 
+            
  • Git / GitHub par Alexandra & Clothilde : html md
    • 
             
  • Docker par Diane & Clémence : html md
    • 
             
  • Conda par Thomas & Krisley :