Add Trimmomatic support about multiqc

[ewels]

Hey @remiolsen,

Do you have any example reports that you could send to me for this? Preferably ok to publish in the public test data repo, but you can just e-mail me private reports otherwise.

Phil

[ewels]

No worries, found some..

[ewels]

@remiolsen: I have log file output from Trimmomatic in paired end mode, but not single end. Do you have an example single end log file output?

[ewels]

See example Trimmomatic command:

java -jar trimmomatic-0.35.jar \
    PE \
    -phred33 \
    input_forward.fq.gz \
    input_reverse.fq.gz \
    output_forward_paired.fq.gz \
    output_forward_unpaired.fq.gz \
    output_reverse_paired.fq.gz \
    output_reverse_unpaired.fq.gz \
    ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 \
    LEADING:3 \
    TRAILING:3 \
    SLIDINGWINDOW:4:15 \
    MINLEN:36

Single end is similar:

java -jar trimmomatic-0.35.jar \
    SE \
    -phred33 \
    input.fq.gz \
    output.fq.gz \
    ILLUMINACLIP:TruSeq3-SE:2:30:10 \
    LEADING:3 \
    TRAILING:3 \
    SLIDINGWINDOW:4:15 \
    MINLEN:36

The stdErr output contains the command that has been run in the first line, so we can get s_name from the first fastq filename found.

[remiolsen]

Makes sense. Sorry, I lost attention to this but I don't run this on single ends.

[ewels]

No problem! Ok, written at last! 7th september... it's been a while coming :)