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software:topical:lifescience:qc [2019/01/28 09:40]
meesters [The Wrapper Module on Mogon]
software:topical:lifescience:qc [2019/01/28 14:16]
meesters [The Wrapper Module on Mogon]
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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''​.
software/topical/lifescience/qc.txt · Last modified: 2019/01/28 15:44 by meesters