software:topical:lifescience:qc

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software:topical:lifescience:qc [2019/01/28 08:45]
meesters
software:topical:lifescience:qc [2019/01/28 15:44] (current)
meesters [The Wrapper Module on Mogon]
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 You can find a wrapper to ease your workflow, [[software:​topical:​lifescience:​qc#​the_wrapper_module_on_mogon|below]]. ​ You can find a wrapper to ease your workflow, [[software:​topical:​lifescience:​qc#​the_wrapper_module_on_mogon|below]]. ​
 +
 +<WRAP center round alert 80%>
 +As cutadapt is pretty slow, it is not supported by the wrapper module on Mogon II
 +</​WRAP>​
  
 ==== flexbar ==== ==== flexbar ====
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 It is available on Mogon as the module ''​bio/​flexbar''​ and you can find its [[https://​github.com/​seqan/​flexbar/​wiki|manual on the web]]. It is available on Mogon as the module ''​bio/​flexbar''​ and you can find its [[https://​github.com/​seqan/​flexbar/​wiki|manual on the web]].
 +
 +[[software:​topical:​lifescience:​qc#​the_wrapper_module_on_mogon|below]]. ​
  
 ==== Trimmomatic ==== ==== Trimmomatic ====
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 The figures are merely included for demonstration purposes, the important part is the access of the adaptor file, which would otherwise be searched for locally: ''​$EBROOTTRIMMOMATIC/​adaptors/​TruSeq3-PE.fa''​((Which adaptorfile you pick is, of course, project dependent.)) The figures are merely included for demonstration purposes, the important part is the access of the adaptor file, which would otherwise be searched for locally: ''​$EBROOTTRIMMOMATIC/​adaptors/​TruSeq3-PE.fa''​((Which adaptorfile you pick is, of course, project dependent.))
 +
 +[[software:​topical:​lifescience:​qc#​the_wrapper_module_on_mogon|below]]. ​
  
  
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 To leverage the task from 1 (or a few) samples to be trimmed to several in parallel, we provide a wrapper script, which is available as a module: To leverage the task from 1 (or a few) samples to be trimmed to several in parallel, we provide a wrapper script, which is available as a module:
  
-''​bio/​parallel_Trimmomatic''​+''​bio/​parallel_QCTools''​
  
  
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 The wrapper script will submit a job, it is not intended to be just within a SLURM environment,​ but rather creates one. The wrapper script will submit a job, it is not intended to be just within a SLURM environment,​ but rather creates one.
 </​WRAP>​ </​WRAP>​
-Calling ''​parallel_Trimmomatic ​-h''​ will display a help message with all the options, the script provides. Likewise, the call ''​parallel_Trimmomatic''​ will display credits and a version history.+Calling ''​QCWrapper ​-h''​ will display a help message with all the options, the script provides. Likewise, the call ''​QCWrapper''​ will display credits and a version history.
  
 The script, after loading the module, can then be run like: The script, after loading the module, can then be run like:
  
 <code bash> <code bash>
-parallel_Trimmomatic ​[options] <​readdir>​+QCWrapper ​[options] <​readdir>​
 </​code>​ </​code>​
  
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 The options: The options:
-  * ''​parallel_Trimmomatic''​ attempts to deduce your SLURM account. This may fail, in which case ''​-A, ​--account'' ​needs to be supplied. +  * ''​--executable'', ​mandatory argument ​to designate ​the executable 
-  * ''​-N,--nodes''​ allows ​to reserve more than 1 node (the default). This may speed up the screening; see the limitations above. + possible arguments: cutadaptflexbar, trimmomatic 
-  * ''​-d,--dependency''​, list of comma separated jobids, the job will wait for to finish+ check is case insensitive 
 + defaults to 'flexbar'
   * ''​-l,​--runlimit'',​ this defaults to 300 minutes.   * ''​-l,​--runlimit'',​ this defaults to 300 minutes.
-  * ''​-p,​--partition'',​ the default is ''​nodeshort''​ or ''​parallel''​ on Mogon2, ​no smp-partition should ​be choosen. +  * ''​-p,​--partition'',​ the default is ''​nodeshort''​ or ''​parallel''​ on Mogon2 
-  * ''​-t,​--threads'', ​Trimmomatic can work in parallel. Please consult ​the manualThe default is 2.+  * ''​-A,--account'',​ SLURM account 
 + - default is the last submit account 
 + - an error is triggered if none specified nor can be deduced 
 +  * ''​-t,​--threads'', ​number of threads ​the executable should use (defaults are application dependend) 
 + 
 +  * ''​-a,​--args'', ​      ​arguments otherwise not set by the wrapper 
 + - the defaults of the choosen executable apply for unset arguments 
 + - will superseed the defaults, e.g'​LEADING:​3 TRAILING:3 SLIDINGWINDOW:​4:​15 MINLEN:​36'​ for trimmomatic 
 +  * ''​-d,​--dependency'',​ list of comma separated jobids, the job will wait for to finish
   * ''​-o,​--outdir''​ output directory path (default is the current working directory)   * ''​-o,​--outdir''​ output directory path (default is the current working directory)
-  * ''​-a,​--adapter''​a selection of one of Trimmomatics pre-defined adapters, default to '​TruSeq3-PE.fa'​ +  * ''​-a,​--adapter''​,  ​a selection of one of Trimmomatics pre-defined adapters, default to '​TruSeq3-PE.fa'​ 
-  * ''​--options''​: a string of trimmomatic ​optionssuperseeds ​the defaults'LEADING:3 TRAILING:3 SLIDINGWINDOW:​4:​15 MINLEN:36+                      - a selection of one of Trimmomatics pre-defined adapters, defaults to ''​TruSeq3-PE.fa''​ else 
-  * ''​--constraint''​only on Mogon2, defaults to 'anyarch'+                      - an adaptor string specification according to the selected software. 
 +                      - defaults to '​TACACTCTTTCCCTACACGACGCTCTTCCGATCT'​ (adaptor 1 of TruSeq3-PE.fa) 
 +  * ''​--adapterp''​, adaptor for the mate pair 
 +                      - if the excecutable is trimmomatic, ​this argument is not necessara (it is contained in the global adaptor selection) 
 +                      - if the excecutable is cutadapt, this arguments ​defaults ​to 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'​ (the mate of TruSeq3-PE.fa) 
 +                      - if the excecutable is flexbar, this argument is not necessary (it is contained in the global adaptor selection) 
 +   
 +  * ''​--single'',​ if given, single end data will be assumed, otherwisepaired-end data are default 
 +  * flexbar specific  
 +      * ''​--qtrim'',​ see '​--qtrim'​ option of flexbar, default to '​WIN'​ 
 +      * ''​--qtrim-format'',​ see ''​-qf/​--qtrim-format''​ option of flexbar, default is 'i1.5
 +  * ''​--constraint''​only on Mogon2, defaults to 'broadwell'​ 
 +  * ''​--tag''​ a jobtag (default is decuced by naming scheme) 
 +  * ''​--credits''​ shows credits and version history 
 +  * ''​--version''​ shows the version number 
 +  * ''​-h,​--help'​' ​Prints help
  
 The output naming scheme: The output naming scheme:
  
 Within the specified (or default) output directory, you will find back your sample subdirectories (if any were present. The prefix of each sample is preserved. As the wrapper allows only certain designators to distinguish the mate pairs (see the limitations,​ above), these are also preserved. Trimmomatic splits it output in reads which are paired and unpaired (if any). The later are written in a subdirectory ''​unpaired''​ as of version ''​0.2''​. Within the specified (or default) output directory, you will find back your sample subdirectories (if any were present. The prefix of each sample is preserved. As the wrapper allows only certain designators to distinguish the mate pairs (see the limitations,​ above), these are also preserved. Trimmomatic splits it output in reads which are paired and unpaired (if any). The later are written in a subdirectory ''​unpaired''​ as of version ''​0.2''​.
 +
 +==== Selecting the Executable ====
 +
 +<WRAP center round todo 60%>
 +Note: The figure below is not the final evaluation - this is forthcoming. I assume that the assumption will hold, that flexbar outperform trimmomatic.
 +</​WRAP>​
 +
 +{{:​software:​topical:​lifescience:​speed_trimming.png?​direct&​400 |}} Selecting the executable should consider the following 3 minimum criteria:
 +  - Speed as indicated in the left figure
 +  - The memory footprint, which is negligible except for trimmomatic,​ where on Mogon II a higher reservation,​ than the default memory was necessary to implement.
 +  - Quality. Here, flexbar is the most feature rich, but also the most complex.
 +
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  • Last modified: 2019/01/28 08:45
  • by meesters