Issue with calling trimmomatic

Here is the line of code I am using:

nextflow run hybpiper.nf -c hybpiper.config -entry assemble --illumina_reads_directory /projects/p31913/Amsonia-353/test --targetfile_dna Angiosperms353_targetSequences.fasta --use_trimmomatic --outdir trimmed

here is a snippet from the trace, I think its having problems finding trimmomatic

executor >  local (2)
[-        ] process > assemble:assemble_main:COMBINE_LANES_PAIRED_END       -
[-        ] process > assemble:assemble_main:COMBINE_LANES_SINGLE_END       -
[c1/115638] process > assemble:assemble_main:TRIMMOMATIC_PAIRED (1)         [100%] 2 of 2, failed: 2 ✘
[-        ] process > assemble:assemble_main:TRIMMOMATIC_SINGLE             -
[-        ] process > assemble:assemble_main:ASSEMBLE_PAIRED_AND_SINGLE_END -
[-        ] process > assemble:assemble_main:ASSEMBLE_PAIRED_END            -
[-        ] process > assemble:assemble_main:ASSEMBLE_SINGLE_END            -
[-        ] process > assemble:assemble_main:SUMMARY_STATS                  -
[-        ] process > assemble:assemble_main:VISUALISE                      -
[-        ] process > assemble:assemble_main:RETRIEVE_SEQUENCES             -
[-        ] process > assemble:assemble_main:PARALOG_RETRIEVER              -
Error executing process > 'assemble:assemble_main:TRIMMOMATIC_PAIRED (2)'

Caused by:
  Process `assemble:assemble_main:TRIMMOMATIC_PAIRED (2)` terminated with an error exit status (1)

Command executed:

  R1=A_arenaria_NM_S27_R1.fastq.gz
      R2=A_arenaria_NM_S27_R2.fastq.gz
      sampleID_R1=${R1%_R1*}
      sampleID_R2=${R2%_R2*}

      echo $R1
      echo $R2

      if [[ $R1 = *.gz ]]
        then 
          R1_filename_strip_gz="${R1%.gz}"
          fastq_extension="${R1_filename_strip_gz##*.}"

          output_forward_paired=${sampleID_R1}_R1_paired.fq.gz
          output_reverse_paired=${sampleID_R2}_R2_paired.fq.gz
          output_forward_unpaired=${sampleID_R1}_R1_unpaired.fq.gz
          output_reverse_unpaired=${sampleID_R2}_R2_unpaired.fq.gz
          output_both_unpaired=${sampleID_R1}_R1-R2_unpaired.fq.gz

        else
          fastq_extension="${R1##*.}"

          output_forward_paired=${sampleID_R1}_R1_paired.fq
          output_reverse_paired=${sampleID_R2}_R2_paired.fq
          output_forward_unpaired=${sampleID_R1}_R1_unpaired.fq
          output_reverse_unpaired=${sampleID_R2}_R2_unpaired.fq
          output_both_unpaired=${sampleID_R1}_R1-R2_unpaired.fq
      fi

      # Write adapters fasta file:
      echo -e ">PrefixPE/1
  TACACTCTTTCCCTACACGACGCTCTTCCGATCT
  >PrefixPE/2
  GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
  >PE1
  TACACTCTTTCCCTACACGACGCTCTTCCGATCT
  >PE1_rc
  AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA
  >PE2
  GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
  >PE2_rc
  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA" > TruSeq3-PE-2.fa

      # Run Trimmomtic:
      trimmomatic PE -phred33 -threads 2     A_arenaria_NM_S27_R1.fastq.gz A_arenaria_NM_S27_R2.fastq.gz ${output_forward_paired} ${output_forward_unpaired}     ${output_reverse_paired} ${output_reverse_unpaired}     ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10:1:true     LEADING:3     TRAILING:3     SLIDINGWINDOW:4:20     MINLEN:36 2>&1 | tee ${sampleID_R1}.log 
      cat ${output_forward_unpaired} ${output_reverse_unpaired} > ${output_both_unpaired}

Command exit status:
  1

Command output:
  A_arenaria_NM_S27_R1.fastq.gz
  A_arenaria_NM_S27_R2.fastq.gz
  .command.sh: line 46: trimmomatic: command not found

chrisjackson-pellicle / hybpiper-nf

Issue with calling trimmomatic #12