I'm creating a custom pipline for learning nextflow, and I want to use trimmomatic PE. But I get error from the process, but due to terrible trimmomatic error messages it can be known nothing, so I checked if all files are in nextfow working directory, if there are missspelings, if main.nf is good etc. And I'm 95% sure that it is trimmomatic problem not the nextflow's or docker's. From .command.sh I recive a it like this:
trimmomatic PE -phred33 Paris_stat1_R1_001.fastq Paris_stat1_R2_001.fastq stat1_1_trimmed.fastq stat1_drop1.fastq stat1_2_trimmed.fastq stat1_drop2.fastq ILLUMINACLIP:adaptors.fasta:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Is something wrong with this command build for trimmomatic?