param file for runCommandline not working on trim_galore

[rfarouni]

Hi, I would like to do adapter trimming using trim_galore, but since it does not accept an output file name as an argument (only output directory), I am unable to run the runCommandline function from within R. I tried changing the value of outfile1 () to NA and also tried removing it but nothing worked. Is there a way to leave the value empty?

PairSet Name    Value
type    system  TRUE
modules     
software    NA  trim_galore
other   NA  --length 50 --phred64 
outfile1    -o  <FileName1>
outfile1    path    ./data/trimmed
reference   NA  NA
infile1 NA  <FileName1>
infile1 path    NA
infile2 NA  <FileName2>
infile2 path    NA

[tgirke]

Take a look at the tophat param file where the situation is similar: https://goo.gl/p15kQB. If it doesn't work for you then I can add a trim_galore sample *.param file later next week. Right now I have to focus on some internal deadlines. In the next major release of systemPipeR these param files will semi auto-generated so that the user doesn't have to deal with these details anymore.

[rfarouni]

Thanks @tgirke. I tried many configuration but nothing seemed to work. Here is my last attempt

PairSet Name    Value
type    system  TRUE
modules     
software    NA  trim_galore
other   NA  --length 50 --phred64 
outfile1    -o  <FileName1>
outfile1    path    ./results/trimmed/
outfile1    remove  NA
outfile1    append  .trimmed
outfile1    outextension    .trimmed/trimmed.fq.gz
reference   NA  NA
infile1 NA  <FileName1>
infile1 path    NA
infile2 NA  <FileName2>
infile2 path    NA

[tgirke]

Sorry for the delay. I didn't get to this before the holidays. - i have now added a trim_galor.param and a trim_galore_run.sh file to systemPipeRdata here. Please download both of them to your param directory on the same level where you have the data and results directories of your analysis project. In addition, I committed a small update to systemPipeR (version 1.9.2) to make things easier. After installing this version from GitHub (as shown here) or Bioc, you should be able to run git_galore from systemPipeR like this:

library(systemPipeR) # needs to be version >=1.9.2
args <- systemArgs(sysma="./param/trim_galore.param", mytargets="targets.txt") 
runCommandline(args, make_bam=FALSE)
writeTargetsout(x=args, file="targets_trim.txt") # generates targets file for trimmed FASTQ files

Please note the argument settings for trim_galore are defined in trim_galor_run.sh. If you don't use a module system then please also remove the module load commands at the beginning of this file.

The next upgrade should make those things much easier. I am optimistic to have a functional version of this upgrade committed to the developer branch by the end of Jan or early Feb.

Thomas

[rfarouni]

Thanks!

On Tue, Dec 27, 2016 at 9:07 PM Thomas Girke notifications@github.com wrote:

Sorry for the delay. I didn't get to this before the holidays. - i have now added a trim_galor.param and a trim_galore_run.sh file to systemPipeRdata here https://github.com/tgirke/systemPipeRdata/tree/master/inst/extdata/param. Please download both of them to your param directory on the same level where you have the data and results directories of your analysis project. In addition, I committed a small update to systemPipeR (version 1.9.2) to make things easier. After installing this version from GitHub (as shown here https://github.com/tgirke/systemPipeR) or Bioc, you should be able to run git_galore from systemPipeR like this:

library(systemPipeR) # needs to be version >=1.9.2 args <- systemArgs(sysma="./param/trim_galore.param", mytargets="targets.txt") runCommandline(args, make_bam=FALSE) writeTargetsout(x=args, file="targets_trim.txt") # generates targets file for trimmed FASTQ files

Please note the argument settings for trim_galore are defined in trim_galor_run.sh. If you don't use a module system then please also remove the module load commands at the beginning of this file.

The next upgrade should make those things much easier. I am optimistic to have a test version committed to the developer branch by the end of Jan or early Feb.

Thomas

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