new module: trimmomatic

[alyssa-ab]

Is there an existing module for this?

• [X] I have searched for the existing module

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• [X] I have searched for existing PRs

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[alyssa-ab]

Creating module for trimmomatic Using cutadapt as a reference module for a similar process.

[alyssa-ab]

Script main.nf Test main.nf

[alyssa-ab]

Test fails [Command exit status: 1]

.command.err output

           Usage:                                                                                    
                  PE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog                   
         <trimLogFile>] [-summary <statsSummaryFile>] [-quiet] [-validatePairs]                      
         [-basein <inputBase> | <inputFile1> <inputFile2>] [-baseout <outputBase> |                  
         <outputFile1P> <outputFile1U> <outputFile2P> <outputFile2U>] <trimmer1>...                  
              or:                                                                                    
                  SE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog                   
         <trimLogFile>] [-summary <statsSummaryFile>] [-quiet] <inputFile>                           
         <outputFile> <trimmer1>...                                                                  
              or:                                                                                    
                  -version                       

.command.sh

trimmomatic \
    --cores 2 \
     \
    -o test.trim.fastq.gz \
    test_1.fastq.gz \
    > test.trimmomatic.log
cat <<-END_VERSIONS > versions.yml
"test_trimmomatic_single_end:TRIMMOMATIC":
    trimmomatic: $(trimmomatic --version)
END_VERSIONS```

[edmundmiller]

Ah, the issue is that trimmomatic handles the PE and SE differently than cutadapt:

def trimmed  = meta.single_end ? "SE ${prefix}.trim.fastq.gz" : "PE ${prefix}_1.trim.fastq.gz ${prefix}_2.trim.fastq.gz"

Or actually

def trimmed  = meta.single_end ? "SE ${reads}" : "PE ${reads}"

might work.