add new links

docs/assets/md/session2020/Workflow_Snakemake.html

@@ -152,7 +152,7 @@
 snakemake  -s exo5.smk -R all  fastqc
 </code></pre><p><em><strong><span>Observe the results</span></strong></em><br>
 <span>Does Snakemake do the job?</span></p><p><em><strong><span>Fastqc:  job or jobs?</span></strong></em><br>
-<span>Look at more precisely the fastqc job.  We have many input files but snakemake launched only one fastqc job:</span></p><p><img src="https://github.com/chernan/FAIR_bioinfo_docs/blob/master/03_workflow/images/FAIR_ex1_o5_smk.png" alt="image"></p><p><span>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.</span></p><h3 id="Objective-6-Running-n-individual-jobs" data-id="Objective-6-Running-n-individual-jobs"><a class="anchor hidden-xs" href="#Objective-6-Running-n-individual-jobs" title="Objective-6-Running-n-individual-jobs"><span class="octicon octicon-link"></span></a><span>Objective 6: Running n individual jobs</span></h3><p><span>Create snakemake file </span><em><span>exo6.smk</span></em><span>. 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.</span></p><hr><p><em><strong><span>HINT</span></strong></em><br>
+<span>Look at more precisely the fastqc job.  We have many input files but snakemake launched only one fastqc job:</span></p><p><img src="https://github.com/chernan/FAIR_bioinfo_docs/raw/master/03_workflow/images/FAIR_ex1_o5_smk.png" alt="image"></p><p><span>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.</span></p><h3 id="Objective-6-Running-n-individual-jobs" data-id="Objective-6-Running-n-individual-jobs"><a class="anchor hidden-xs" href="#Objective-6-Running-n-individual-jobs" title="Objective-6-Running-n-individual-jobs"><span class="octicon octicon-link"></span></a><span>Objective 6: Running n individual jobs</span></h3><p><span>Create snakemake file </span><em><span>exo6.smk</span></em><span>. 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.</span></p><hr><p><em><strong><span>HINT</span></strong></em><br>
 <span>Replace the expand()function with a wildcard for one filename in the fastqc rule.</span></p><hr><p><strong><span>Solution</span></strong></p><pre><code>SAMPLES = ["SRR3099585_chr18","SRR3099586_chr18","SRR3099587_chr18"]
 BIDX = ["1","2","3","4","rev.1","rev.2"]
 
@@ -178,7 +178,7 @@
 </code></pre><p><strong><span>Snakemake run</span></strong></p><pre><code>rm -Rf  FastQC/
 snakemake  -s exo6.smk -R all fastqc
 </code></pre><p><em><strong><span>Observe the results</span></strong></em><br>
-<span>Now Snakemake did many fastqc jobs:</span></p><p><img src="https://github.com/chernan/FAIR_bioinfo_docs/blob/master/03_workflow/images/FAIR_ex1_o6_smk.png" alt="image"></p><p><span>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.</span></p><h3 id="Objective-7-Adding-log-file" data-id="Objective-7-Adding-log-file"><a class="anchor hidden-xs" href="#Objective-7-Adding-log-file" title="Objective-7-Adding-log-file"><span class="octicon octicon-link"></span></a><span>Objective 7: Adding log file</span></h3><p><span>Create snakemake file </span><em><span>exo7.smk</span></em><span>. Improve previous code:</span><br>
+<span>Now Snakemake did many fastqc jobs:</span></p><p><img src="https://github.com/chernan/FAIR_bioinfo_docs/raw/master/03_workflow/images/FAIR_ex1_o6_smk.png" alt="image"></p><p><span>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.</span></p><h3 id="Objective-7-Adding-log-file" data-id="Objective-7-Adding-log-file"><a class="anchor hidden-xs" href="#Objective-7-Adding-log-file" title="Objective-7-Adding-log-file"><span class="octicon octicon-link"></span></a><span>Objective 7: Adding log file</span></h3><p><span>Create snakemake file </span><em><span>exo7.smk</span></em><span>. Improve previous code:</span><br>
 <span>In Unix systems, the output of a command is usually sent to two separate streams:  the normal output:  to Standard Out (stdout also “&gt;” in shell),and error messages:  to Standard Error (stderr, or “2&gt;” in shell).  To integrate stderr into the same log file as the stdout can be use “&amp;&gt;” instead of “&gt;”:</span><br>
 <span>shell:  … &amp;&gt; {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.</span></p><hr><p><em><strong><span>HINT</span></strong></em><br>
 <span>For the bowtie2-build and fastqc rules, add the log: directive with two variables (log1 and log2) to redirect each streams.</span></p><hr><p><strong><span>Solution</span></strong></p><pre><code>SAMPLES = ["SRR3099585_chr18","SRR3099586_chr18","SRR3099587_chr18"]

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.
 

docs/session2020.html

@@ -403,7 +403,7 @@ <h2 id="materiel">Matériels des participants</h2>
         <p>Outils collaboratif pour le md : <a href="https://hackmd.io/">HackMD</a>. Merci Clémence et Diane !</p> 
 
         <ul>
-            <li>Git / GitHub par Alexandra & Clothilde : <a href="./assets/md/session2020/" target="_blank">html</a> <a href="./assets/md/session2020/git-github.md" target="_blank">md</a></li>
+            <li>Git / GitHub par Alexandra & Clothilde : <a href="./assets/md/session2020/git-github.html" target="_blank">html</a> <a href="./assets/md/session2020/git-github.md" target="_blank">md</a></li>
             <li>Docker par Diane & Clémence : <a href="./assets/md/session2020/TPDocker.html" target="_blank">html</a> <a href="./assets/md/session2020/TPDocker.md" target="_blank">md</a></li>
             <li>Conda par Thomas & Krisley :  <ul>
                 <li>Cours : <a href="./assets/md/session2020/Conda cours.html" target="_blank">html</a> <a href="./assets/md/session2020/Conda_cours.md" target="_blank">md</a>