flowcraft build -t 'trimmomatic fastqc spades pilon' -o my_nextflow_pipeline

$ nextflow run my_nextflow_pipeline.nf --help
N E X T F L O W  ~  version 0.32.0
Launching `my_nextflow_pipeline.nf` [jovial_swirles] - revision: b4473f5a12

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                F L O W C R A F T
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Built using flowcraft v1.4.0


Usage: 
    nextflow run my_nextflow_pipeline.nf

       --fastq                     Path expression to paired-end fastq files. (default: fastq/*_{1,2}.*) (default: 'fastq/*_{1,2}.*')
       
       Component 'INTEGRITY_COVERAGE_1_1'
       ----------------------------------
       --genomeSize_1_1            Genome size estimate for the samples in Mb. It is used to estimate the coverage and other assembly parameters andchecks (default: 1)
       --minCoverage_1_1           Minimum coverage for a sample to proceed. By default it's setto 0 to allow any coverage (default: 0)
       
       Component 'TRIMMOMATIC_1_2'
       ---------------------------
       --adapters_1_2              Path to adapters files, if any. (default: 'None')
       --trimSlidingWindow_1_2     Perform sliding window trimming, cutting once the average quality within the window falls below a threshold (default: '5:20')
       --trimLeading_1_2           Cut bases off the start of a read, if below a threshold quality (default: 3)
       --trimTrailing_1_2          Cut bases of the end of a read, if below a threshold quality (default: 3)
       --trimMinLength_1_2         Drop the read if it is below a specified length  (default: 55)
       --clearInput_1_2            Permanently removes temporary input files. This option is only useful to remove temporary files in large workflows and prevents nextflow's resume functionality. Use with caution. (default: false)
       
       Component 'FASTQC_1_3'
       ----------------------
       --adapters_1_3              Path to adapters files, if any. (default: 'None')
       
       Component 'SPADES_1_4'
       ----------------------
       --spadesMinCoverage_1_4     The minimum number of reads to consider an edge in the de Bruijn graph during the assembly (default: 2)
       --spadesMinKmerCoverage_1_4 Minimum contigs K-mer coverage. After assembly only keep contigs with reported k-mer coverage equal or above this value (default: 2)
       --spadesKmers_1_4           If 'auto' the SPAdes k-mer lengths will be determined from the maximum read length of each assembly. If 'default', SPAdes will use the default k-mer lengths.  (default: 'auto')
       --clearInput_1_4            Permanently removes temporary input files. This option is only useful to remove temporary files in large workflows and prevents nextflow's resume functionality. Use with caution. (default: false)
       --disableRR_1_4             disables repeat resolution stage of assembling. (default: false)
       
       Component 'ASSEMBLY_MAPPING_1_5'
       --------------------------------
       --minAssemblyCoverage_1_5   In auto, the default minimum coverage for each assembled contig is 1/3 of the assembly mean coverage or 10x, if the mean coverage is below 10x (default: 'auto')
       --AMaxContigs_1_5           A warning is issued if the number of contigs is overthis threshold. (default: 100)
       --genomeSize_1_5            Genome size estimate for the samples. It is used to check the ratio of contig number per genome MB (default: 2.1)
       
       Component 'PILON_1_6'
       ---------------------
       --clearInput_1_6            Permanently removes temporary input files. This option is only useful to remove temporary files in large workflows and prevents nextflow's resume functionality. Use with caution. (default: false)

flowcraft build -t 'reads_download (
    spades | skesa pilon (abricate | chewbbaca) | megahit | 
    fastqc_trimmomatic fastqc (spades pilon (
        mlst | prokka | chewbbaca) | skesa pilon abricate))'
     -o my_nextflow_pipeline