Since 20140722 you can let GNU Parallel do the trimming of the file name:

s/_R..fastq.gz//; will remove _R1.fastq.gz or _R2.fastq.gz

$seen{$_}++ && $job->skip(); will skip the job if the trimmed name is already seen

--rpl  '{_} [...]' will replace {_} with [...].

So in total:

cat samplelist.txt |parallel --rpl  '{_} s/_R..fastq.gz//; $seen{$_}++ && $job->skip()' -j 6  --verbose --progress echo java -jar PE -threads 4 -phred33 {_}_R1.fastq.gz {_}_R2.fastq.gz {_}_R1.fq.gz {_}_U_R1.fq.gz {_}_R2.fq.gz {_}_U_R2.fq.gz ILLUMINACLIP:trimSeq.fasta:2:7:7 MINLEN:20

Here's my way.

Directory raw contains all paired-ends reads files, which are carefully named with same suffixes: _R1.fastq.gz for read 1 and _R2.fastq.gz for read 2.

$ ls raw | head -n 4
delta_G_9-30_R1.fastq.gz
delta_G_9-30_R2.fastq.gz
WT_9-30_R1.fastq.gz
WT_9-30_R2.fastq.gz
...

I use a python script cluster_files to cluster paired-end reads by samples:

$ cluster_files -p '(.+?)_R[12]\.fastq\.gz$' raw/ -o raw.cluster

$ tree
.
├── raw
│   ├── delta_G_9-30_R1.fastq.gz
│   ├── delta_G_9-30_R2.fastq.gz
│   ├── WT_9-30_R1.fastq.gz
│   └── WT_9-30_R2.fastq.gz
└── raw.cluster
    ├── delta_G_9-30
    │   ├── delta_G_9-30_R1.fastq.gz -> ../../raw/delta_G_9-30_R1.fastq.gz
    │   └── delta_G_9-30_R2.fastq.gz -> ../../raw/delta_G_9-30_R2.fastq.gz
    └── WT_9-30
        ├── WT_9-30_R1.fastq.gz -> ../../raw/WT_9-30_R1.fastq.gz
        └── WT_9-30_R2.fastq.gz -> ../../raw/WT_9-30_R2.fastq.gz

For every analysis step, I creat a new directory with same directory structure in which reads file are soft links. There are many benefits for this:

1. Safety. Previously produced files are independent from current working space, which would not be deleted by accident.
2. Clear file organization. Every process has its own working space.
3. Easy for parallelization using tools like GNU parallel and rush

Now let's clean the reads. (BTW, it should be ${TRIMMOMATIC} not $(TRIMMOMATIC)). Replacement string {/} represents the basename of input file path, here it's the sample name.

$ ls -d raw.cluster.clean/* | parallel -j 6 --dryrun \
    java -jar ${TRIMMOMATIC} PE -threads 4 -phred33 \
    {}/{/}_R1.fastq.gz {}/{/}_R2.fastq.gz \
    {}/{/}_R1.fq.gz {}/{/}_U_R1.fq.gz {}/{/}_R2.fq.gz {}/{/}_U_R2.fq.gz \
    ILLUMINACLIP:trimSeq.fasta:2:7:7 MINLEN:20

java -jar PE -threads 4 -phred33 raw.cluster.clean/delta_G_9-30/delta_G_9-30_R1.fastq.gz raw.cluster.clean/delta_G_9-30/delta_G_9-30_R2.fastq.gz raw.cluster.clean/delta_G_9-30/delta_G_9-30_R1.fq.gz raw.cluster.clean/delta_G_9-30/delta_G_9-30_U_R1.fq.gz raw.cluster.clean/delta_G_9-30/delta_G_9-30_R2.fq.gz raw.cluster.clean/delta_G_9-30/delta_G_9-30_U_R2.fq.gz ILLUMINACLIP:trimSeq.fasta:2:7:7 MINLEN:20

java -jar PE -threads 4 -phred33 raw.cluster.clean/WT_9-30/WT_9-30_R1.fastq.gz raw.cluster.clean/WT_9-30/WT_9-30_R2.fastq.gz raw.cluster.clean/WT_9-30/WT_9-30_R1.fq.gz raw.cluster.clean/WT_9-30/WT_9-30_U_R1.fq.gz raw.cluster.clean/WT_9-30/WT_9-30_R2.fq.gz raw.cluster.clean/WT_9-30/WT_9-30_U_R2.fq.gz ILLUMINACLIP:trimSeq.fasta:2:7:7 MINLEN:20

Next step, results of trimmomatic are clustered for further analyis, e.g., assembly.

$ cluster_files -p '(.+?)_\d.*\.fq\.gz$' raw.cluster.clean -o raw.cluster.clean.assembly

$ tree raw.cluster.clean.assembly
raw.cluster.clean.assembly
├── delta_G
│   ├── delta_G_9-30_R1.fq.gz -> ../../raw.cluster.clean/delta_G_9-30/delta_G_9-30_R1.fq.gz
│   ├── delta_G_9-30_R2.fq.gz -> ../../raw.cluster.clean/delta_G_9-30/delta_G_9-30_R2.fq.gz
│   ├── delta_G_9-30_U_R1.fq.gz -> ../../raw.cluster.clean/delta_G_9-30/delta_G_9-30_U_R1.fq.gz
│   └── delta_G_9-30_U_R2.fq.gz -> ../../raw.cluster.clean/delta_G_9-30/delta_G_9-30_U_R2.fq.gz
└── WT
    ├── WT_9-30_R1.fq.gz -> ../../raw.cluster.clean/WT_9-30/WT_9-30_R1.fq.gz
    ├── WT_9-30_R2.fq.gz -> ../../raw.cluster.clean/WT_9-30/WT_9-30_R2.fq.gz
    ├── WT_9-30_U_R1.fq.gz -> ../../raw.cluster.clean/WT_9-30/WT_9-30_U_R1.fq.gz
    └── WT_9-30_U_R2.fq.gz -> ../../raw.cluster.clean/WT_9-30/WT_9-30_U_R2.fq.gz

# assemble with spades:
ls -d raw.cluster.clean.assembly/* | parallel spades.py -k 21,33,47,55,63,77 -t 4 -m 10 --careful -o {}/spades -1 {}/{/}_1.fq.gz -2 {}/{/}_2.fq.gz -s {}/{/}_1.unpaired.fq.gz -s {}/{/}_2.unpaired.fq.gz'

Some times I want to assembly using another tool, so I can create another working space by:

$ cluster_files -p '(.+?)_\d.*\.fq\.gz$' raw.cluster.clean -o raw.cluster.clean.assembly_with_xxx

Here's one project of mine:

raw
raw.fastqc
raw.kaiju
raw.cluster
raw.cluster.clean
raw.cluster.clean.mapping
raw.cluster.clean.mapping.pilon
raw.cluster.clean.mapping.breseq
raw.cluster.clean.spades.plasmid
raw.cluster.clean.spades.result