name: "trimgalore"
version: "add_biobase_modules"
argument_groups:
- name: "Input"
  arguments:
  - type: "file"
    name: "--input"
    description: "Input files. Note that paired-end files need to be supplied in a\
      \ pairwise fashion, e.g. file1_1.fq file1_2.fq SRR2_1.fq.gz SRR2_2.fq.gz"
    info: null
    example:
    - "sample1_r1.fq;sample1_r2.fq;sample2_r1.fq;sample2_r2.fq"
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: true
    multiple_sep: ";"
- name: "Trimming options"
  arguments:
  - type: "integer"
    name: "--quality"
    alternatives:
    - "-q"
    description: "Trim low-quality ends (below the specified Phred score) from reads\
      \ in addition to adapter removal. For RRBS samples, quality trimming will be\
      \ performed first, and adapter trimming is carried in a second round. Other\
      \ files are quality and adapter trimmed in a single pass. The algorithm is the\
      \ same as the one used by BWA (Subtract INT from all qualities; compute partial\
      \ sums from all indices to the end of the sequence; cut sequence at the index\
      \ at which the sum is minimal)."
    info: null
    example:
    - 20
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--phred33"
    description: "Instructs Cutadapt to use ASCII+33 quality scores as Phred scores\
      \ (Sanger/Illumina 1.9+ encoding) for quality trimming."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--phred64"
    description: "Instructs Cutadapt to use ASCII+64 quality scores as Phred scores\
      \ (Illumina 1.5 encoding) for quality trimming."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--fastqc"
    description: "Run FastQC in the default mode on the FastQ file once trimming is\
      \ complete."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--fastqc_args"
    description: "Passes extra arguments to FastQC. If more than one argument is to\
      \ be passed to FastQC they must be in the form \"arg1 arg2 ...\". Passing extra\
      \ arguments will automatically invoke FastQC, so --fastqc does not have to be\
      \ specified separately."
    info: null
    example:
    - "--nogroup --outdir /home/"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--adapter"
    alternatives:
    - "-a"
    description: "Adapter sequence to be trimmed. If not specified explicitly, Trim\
      \ Galore will try to auto-detect whether the Illumina universal, Nextera transposase\
      \ or Illumina small RNA adapter sequence was used. A single base may also be\
      \ given as e.g. -a A{10}, to be expanded to -a AAAAAAAAAA. \nAt a special request,\
      \ multiple adapters can also be specified like so: \n  -a  \" AGCTCCCG -a TTTCATTATAT\
      \ -a TTTATTCGGATTTAT\" -a2 \" AGCTAGCG -a TCTCTTATAT -a TTTCGGATTTAT\", \nor\
      \ so:\n  -a \"file:../multiple_adapters.fa\" -a2 \"file:../different_adapters.fa\"\
      \nPotentially in conjucntion with the parameter \"-n 3\" to trim all adapters.\
      \ \n      example: 20\n"
    info: null
    example:
    - "AGCTCCCG"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--adapter2"
    alternatives:
    - "-a2"
    description: "Optional adapter sequence to be trimmed off read 2 of paired-end\
      \ files. This option requires '--paired' to be specified as well. If the libraries\
      \ to be trimmed are smallRNA then a2 will be set to the Illumina small RNA 5'\
      \ adapter automatically (GATCGTCGGACT). A single base may also be given as e.g.\
      \ -a2 A{10}, to be expanded to -a2 AAAAAAAAAA."
    info: null
    example:
    - "AGCTCCCG"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--illumina"
    description: "Adapter sequence to be trimmed is the first 13bp of the Illumina\
      \ universal adapter 'AGATCGGAAGAGC' instead of the default auto-detection of\
      \ adapter sequence."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--stranded_illumina"
    description: "Adapter sequence to be trimmed is the first 13bp of the Illumina\
      \ stranded mRNA or Total RNA adapter 'ACTGTCTCTTATA' instead of the default\
      \ auto-detection of adapter sequence."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--nextera"
    description: "Adapter sequence to be trimmed is the first 12bp of the Nextera\
      \ adapter 'CTGTCTCTTATA' instead of the default auto-detection of adapter sequence."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--small_rna"
    description: "Adapter sequence to be trimmed is the first 12bp of the Illumina\
      \ Small RNA 3' Adapter 'TGGAATTCTCGG' instead of the default auto-detection\
      \ of adapter sequence. Selecting to trim smallRNA adapters will also lower the\
      \ --length value to 18bp. If the smallRNA libraries are paired-end then a automatically\
      \ (GATCGTCGGACT) unless -a 2 had been defined explicitly."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--consider_already_trimmed"
    description: "During adapter auto-detection, the limit set by this argument allows\
      \ the user to set a threshold up to which the file is considered already adapter-trimmed.\
      \ If no adapter sequence exceeds this threshold, no additional adapter trimming\
      \ will be performed (technically, the adapter is set to '-a X'). Quality trimming\
      \ is still performed as usual."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--max_length"
    description: "Discard reads that are longer than the specified value after trimming.\
      \ This is only advised for smallRNA sequencing to remove non-small RNA sequences."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--stringency"
    description: "Overlap with adapter sequence required to trim a sequence. Defaults\
      \ to a very stringent setting of 1, i.e. even a single bp of overlapping sequence\
      \ will be trimmed off from the 3' end of any read."
    info: null
    example:
    - 1
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "double"
    name: "--error_rate"
    alternatives:
    - "-e"
    description: "Maximum allowed error rate (no. of errors divided by the length\
      \ of the matching region)"
    info: null
    example:
    - 0.1
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--gzip"
    description: "Compress the output file with GZIP. If the input files are GZIP-compressed\
      \ the output files will automatically be GZIP compressed as well. As of v0.2.8\
      \ the compression will take place on the fly."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--dont_gzip"
    description: "Output files won't be compressed with GZIP. This option overrides\
      \ --gzip."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--length"
    description: "Discard reads that became shorter than the specified length because\
      \ of either quality or adapter trimming. A value of '0' effectively disables\
      \ this behaviour. For paired-end files, both reads of a read-pair need to be\
      \ longer than the specified length to be printed out to validated paired-end\
      \ files. If only one read became too short there is the possibility of keeping\
      \ such unpaired single-end reads using the --retain_unpaired option."
    info: null
    example:
    - 20
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--max_n"
    description: "The total number of Ns a read may contain before it will be removed\
      \ altogether.In a paired-end setting, either read exceeding this limit will\
      \ result in the entire pair being removed from the trimmed output files. If\
      \ COUNT is a number between 0 and 1, it is interpreted as a fraction of the\
      \ read length."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--trim_n"
    description: "Removes Ns from either side of the read. This option does currently\
      \ not work in RRBS mode."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--no_report_file"
    description: "If specified no report file will be generated."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--suppress_warn"
    description: "If specified any output to STDOUT or STDERR will be suppressed."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--clip_R1"
    description: "Instructs TrimGalore to remove given number of bp from the 5' end\
      \ of read 1 (or single-end reads). This may be useful if the qualities were\
      \ very poor, or if there is some sort of unwanted bias at the 5' end."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--clip_R2"
    description: "Instructs TrimGalore to remove given number bp from the 5' end of\
      \ read 2 (paired-end reads only). This may be useful if the qualities were very\
      \ poor, or if there is some sort of unwanted bias at the 5' end. For paired-end\
      \ BS-Seq, it is recommended to remove the first few bp because the end-repair\
      \ reaction may introduce a bias towards low methylation."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--three_prime_clip_R1"
    description: "Instructs Trim Galore to remove spacified number of bp from the\
      \ 3' end of read 1 (or single-end reads) AFTER adapter/quality trimming has\
      \ been performed. This may remove some  bias from the 3' end that is not directly\
      \ related to adapter sequence or basecall quality."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--three_prime_clip_R2"
    description: "Instructs Trim Galore to remove <int> bp from the 3' end of read\
      \ 2 AFTER adapter/quality trimming has been performed. This may remove some\
      \ unwanted bias from the 3' end that is not directly related to adapter sequence\
      \ or basecall quality."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--nextseq"
    description: "This enables the option '--nextseq-trim=3'CUTOFF' within Cutadapt,\
      \ which will set a quality cutoff (that is normally given with -q instead),\
      \ but qualities of G bases are ignored. This trimming is in common for the NextSeq-\
      \ and NovaSeq-platforms, where basecalls without any signal are called as high-quality\
      \ G bases. This is mutually exlusive with '-q INT'."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--basename"
    description: "Use specified name (PREFERRED_NAME) as the basename for output files,\
      \ instead of deriving the filenames from the input files. Single-end data would\
      \ be called PREFERRED_NAME_trimmed.fq(.gz), or PREFERRED_NAME_val_1.fq(.gz)\
      \ and PREFERRED_NAME_val_2.fq(.gz) for paired-end data. --basename only works\
      \ when 1 file (single-end) or 2 files (paired-end) are specified, but not for\
      \ longer lists."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--cores"
    alternatives:
    - "-j"
    description: "Number of cores to be used for trimming"
    info: null
    example:
    - 1
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Specific trimming options without adapter/quality trimming"
  arguments:
  - type: "integer"
    name: "--hardtrim5"
    description: "Instead of performing adapter-/quality trimming, this option will\
      \ simply hard-trim sequences to <int> bp at the 5'-end. Once hard-trimming of\
      \ files is complete, Trim Galore will exit. Hard-trimmed output files will end\
      \ in .<int>_5prime.fq(.gz)."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--hardtrim3"
    description: "Instead of performing adapter-/quality trimming, this option will\
      \ simply hard-trim sequences to <int> bp at the 3'-end. Once hard-trimming of\
      \ files is complete, Trim Galore will exit. Hard-trimmed output files will end\
      \ in .<int>_3prime.fq(.gz)."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--clock"
    description: "In this mode, reads are trimmed in a specific way that is currently\
      \ used for the Mouse Epigenetic Clock."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--polyA"
    description: "This is a new, still experimental, trimming mode to identify and\
      \ remove poly-A tails from sequences. When --polyA is selected, Trim Galore\
      \ attempts to identify from the first supplied sample whether sequences contain\
      \ more often a stretch of either 'AAAAAAAAAA' or 'TTTTTTTTTT'. This determines\
      \ if Read 1 of a paired-end end file, or single-end files, are trimmed for PolyA\
      \ or PolyT. In case of paired-end sequencing, Read2 is trimmed for the complementary\
      \ base from the start of the reads. The auto-detection uses a default of A{20}\
      \ for Read1 (3'-end trimming) and T{150} for Read2 (5'-end trimming). These\
      \ values may be changed manually using the options -a and -a2. In addition to\
      \ trimming the sequences, white spaces are replaced with _ and it records in\
      \ the read ID how many bases were trimmed so it can later be used to identify\
      \ PolyA trimmed sequences. This is currently done by writing tags to both the\
      \ start (\"32:A:\") and end (\"_PolyA:32\") of the reads. The poly-A trimming\
      \ mode expects that sequences were both adapter and quality  before looking\
      \ for Poly-A tails, and it is the user's responsibility to carry out an initial\
      \ round of trimming."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--implicon"
    description: "This is a special mode of operation for paired-end data, such as\
      \ required for the IMPLICON method, where a UMI sequence is getting transferred\
      \ from the start of Read 2 to the readID of both reads. Following this, Trim\
      \ Galore will exit. In it's current implementation, the UMI carrying reads come\
      \ in the following format\n  Read 1  5' FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\
      \ 3'\n  Read 2  3' UUUUUUUUFFFFFFFFFFFFFFFFFFFFFFFFFFFF 5'\nWhere UUUUUUUU is\
      \ a random 8-mer unique molecular identifier (UMI) and FFFFFFF... is the actual\
      \ fragment to be sequenced. The UMI of Read 2 (R2) is written into the read\
      \ ID of both reads and removed from the actual sequence.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "RRBS-specific options"
  arguments:
  - type: "boolean"
    name: "--rrbs"
    description: "Specifies that the input file was an MspI digested RRBS sample (recognition\
      \ site is CCGG). Single-end or Read 1 sequences (paired-end) which were adapter-trimmed\
      \ will have a further 2 bp removed from their 3' end. Sequences which were merely\
      \ trimmed because of poor quality will not be shortened further. Read 2 of paired-end\
      \ libraries will in addition have the first 2 bp removed from the 5' end (by\
      \ setting '--clip_r2 2'). This is to avoid using artificial methylation calls\
      \ from the filled-in cytosine positions close to the 3' MspI site in sequenced\
      \ fragments. This option is not recommended for users of the Tecan Ovation RRBS\
      \ Methyl-Seq with TrueMethyl oxBS 1-16 kit (see below)."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--non_directional"
    description: "Selecting this option for non-directional RRBS libraries will screen\
      \ quality-trimmed sequences for 'CAA' or 'CGA' at the start of the read and,\
      \ if found, removes the first two basepairs. Like with the option '--rrbs' this\
      \ avoids using cytosine positions that were filled-in during the end-repair\
      \ step. '--non_directional' requires '--rrbs' to be specified as well. Note\
      \ that this option does not set '--clip_r2 2' in paired-end mode."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--keep"
    description: "Keep the quality trimmed intermediate file."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Paired-end specific options"
  arguments:
  - type: "boolean"
    name: "--paired"
    description: "This option performs length trimming of quality/adapter/RRBS trimmed\
      \ reads for paired-end files. To pass the validation test, both sequences of\
      \ a sequence pair are required to have a certain minimum length which is governed\
      \ by the option --length (see above). If only one read passes this length threshold\
      \ the other read can be rescued (see option --retain_unpaired). Using this option\
      \ lets you discard too short read pairs without disturbing the sequence-by-sequence\
      \ order of FastQ files which is required by many aligners. Trim Galore expects\
      \ paired-end files to be supplied in a pairwise fashion, e.g. file1_1.fq file1_2.fq\
      \ SRR2_1.fq.gz SRR2_2.fq.gz ... ."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean"
    name: "--retain_unpaired"
    description: "If only one of the two paired-end reads became too short, the longer\
      \ read will be written to either '.unpaired_1.fq' or '.unpaired_2.fq' output\
      \ files. The length cutoff for unpaired single-end reads is governed by the\
      \ parameters -r1/--length_1 and -r2/--length_2."
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--length_1"
    alternatives:
    - "-r1"
    description: "Unpaired single-end read length cutoff needed for read 1 to be written\
      \ to '.unpaired_1.fq' output file. These reads may be mapped in single-end mode."
    info: null
    example:
    - 35
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--length_2"
    alternatives:
    - "-r2"
    description: "Unpaired single-end read length cutoff needed for read 2 to be written\
      \ to '.unpaired_2.fq' output file. These reads may be mapped in single-end mode."
    info: null
    example:
    - 35
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Output"
  arguments:
  - type: "file"
    name: "--output_dir"
    alternatives:
    - "-o"
    description: "If specified all output will be written to this directory instead\
      \ of the current directory."
    info: null
    default:
    - "trimmed_output"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--trimmed_r1"
    description: "Output file for read 1. Only works when 1 file (single-end) or 2\
      \ files (paired-end) are specified, but not for longer lists."
    info: null
    example:
    - "read_1.fastq"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--trimmed_r2"
    description: "Output file for read 2. Only works when 1 file (single-end) or 2\
      \ files (paired-end) are specified, but not for longer lists."
    info: null
    example:
    - "read_2.fastq"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--trimming_report_r1"
    description: "Trimming report for read 1. Only works when 1 file (single-end)\
      \ or 2 files (paired-end) are specified, but not for longer lists."
    info: null
    example:
    - "read_1.trimming_report.txt"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--trimming_report_r2"
    description: "Trimming report for read 1. Only works when 1 file (single-end)\
      \ or 2 files (paired-end) are specified, but not for longer lists."
    info: null
    example:
    - "read_2.trimming_report.txt"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--trimmed_fastqc_html_1"
    description: "FastQC report for trimmed (single-end) reads (or read 1 for paired-end).\
      \ Only works when 1 file (single-end) or 2 files (paired-end) are specified,\
      \ but not for longer lists."
    info: null
    example:
    - "read_1.fastqc.html"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--trimmed_fastqc_html_2"
    description: "FastQC report for trimmed reads (read2 for paired-end). Only works\
      \ when 1 file (single-end) or 2 files (paired-end) are specified, but not for\
      \ longer lists."
    info: null
    example:
    - "read_2.fastqc.html"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--trimmed_fastqc_zip_1"
    description: "FastQC results for trimmed (single-end) reads (or read 1 for paired-end).\
      \ Only works when 1 file (single-end) or 2 files (paired-end) are specified,\
      \ but not for longer lists."
    info: null
    example:
    - "read_1.fastqc.zip"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--trimmed_fastqc_zip_2"
    description: "FastQC results for trimmed reads (read2 for paired-end). Only works\
      \ when 1 file (single-end) or 2 files (paired-end) are specified, but not for\
      \ longer lists."
    info: null
    example:
    - "read_2.fastqc.zip"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--unpaired_r1"
    description: "Output file for unpired read 1. Only works when 1 file (single-end)\
      \ or 2 files (paired-end) are specified, but not for longer lists."
    info: null
    example:
    - "unpaired_read_1.fastq"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--unpaired_r2"
    description: "Output file for unpaired read 2. Only works when 1 file (single-end)\
      \ or 2 files (paired-end) are specified, but not for longer lists."
    info: null
    example:
    - "unpaired_read_2.fastq"
    must_exist: true
    create_parent: true
    required: false
    direction: "output"
    multiple: false
    multiple_sep: ";"
resources:
- type: "bash_script"
  path: "script.sh"
  is_executable: true
description: "A wrapper tool around Cutadapt and FastQC to consistently apply quality\
  \ and adapter trimming to FastQ files. \n"
test_resources:
- type: "bash_script"
  path: "test.sh"
  is_executable: true
info: null
status: "enabled"
requirements:
  commands:
  - "ps"
keywords:
- "trimming"
- "adapters"
license: "GPL-3.0"
links:
  repository: "https://github.com/FelixKrueger/TrimGalore"
  homepage: "https://github.com/FelixKrueger/TrimGalore"
  documentation: "https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md"
runners:
- type: "executable"
  id: "executable"
  docker_setup_strategy: "ifneedbepullelsecachedbuild"
- type: "nextflow"
  id: "nextflow"
  directives:
    tag: "$id"
  auto:
    simplifyInput: true
    simplifyOutput: false
    transcript: false
    publish: false
  config:
    labels:
      mem1gb: "memory = 1000000000.B"
      mem2gb: "memory = 2000000000.B"
      mem5gb: "memory = 5000000000.B"
      mem10gb: "memory = 10000000000.B"
      mem20gb: "memory = 20000000000.B"
      mem50gb: "memory = 50000000000.B"
      mem100gb: "memory = 100000000000.B"
      mem200gb: "memory = 200000000000.B"
      mem500gb: "memory = 500000000000.B"
      mem1tb: "memory = 1000000000000.B"
      mem2tb: "memory = 2000000000000.B"
      mem5tb: "memory = 5000000000000.B"
      mem10tb: "memory = 10000000000000.B"
      mem20tb: "memory = 20000000000000.B"
      mem50tb: "memory = 50000000000000.B"
      mem100tb: "memory = 100000000000000.B"
      mem200tb: "memory = 200000000000000.B"
      mem500tb: "memory = 500000000000000.B"
      mem1gib: "memory = 1073741824.B"
      mem2gib: "memory = 2147483648.B"
      mem4gib: "memory = 4294967296.B"
      mem8gib: "memory = 8589934592.B"
      mem16gib: "memory = 17179869184.B"
      mem32gib: "memory = 34359738368.B"
      mem64gib: "memory = 68719476736.B"
      mem128gib: "memory = 137438953472.B"
      mem256gib: "memory = 274877906944.B"
      mem512gib: "memory = 549755813888.B"
      mem1tib: "memory = 1099511627776.B"
      mem2tib: "memory = 2199023255552.B"
      mem4tib: "memory = 4398046511104.B"
      mem8tib: "memory = 8796093022208.B"
      mem16tib: "memory = 17592186044416.B"
      mem32tib: "memory = 35184372088832.B"
      mem64tib: "memory = 70368744177664.B"
      mem128tib: "memory = 140737488355328.B"
      mem256tib: "memory = 281474976710656.B"
      mem512tib: "memory = 562949953421312.B"
      cpu1: "cpus = 1"
      cpu2: "cpus = 2"
      cpu5: "cpus = 5"
      cpu10: "cpus = 10"
      cpu20: "cpus = 20"
      cpu50: "cpus = 50"
      cpu100: "cpus = 100"
      cpu200: "cpus = 200"
      cpu500: "cpus = 500"
      cpu1000: "cpus = 1000"
  debug: false
  container: "docker"
engines:
- type: "docker"
  id: "docker"
  image: "quay.io/biocontainers/trim-galore:0.6.9--hdfd78af_0"
  target_registry: "images.viash-hub.com"
  target_tag: "add_biobase_modules"
  namespace_separator: "/"
  setup:
  - type: "docker"
    run:
    - "echo \"TrimGalore: `trim_galore --version | sed -n 's/.*version\\s\\+\\([0-9]\\\
      +\\.[0-9]\\+\\.[0-9]\\+\\).*/\\1/p'`\" > /var/software_versions.txt\n"
  entrypoint: []
  cmd: null
- type: "native"
  id: "native"
build_info:
  config: "src/trimgalore/config.vsh.yaml"
  runner: "nextflow"
  engine: "docker|native"
  output: "target/nextflow/trimgalore"
  executable: "target/nextflow/trimgalore/main.nf"
  viash_version: "0.9.0"
  git_commit: "b0cbbf82c331a079e3d5ad6df5c8b56388349cac"
  git_remote: "https://github.com/viash-hub/rnaseq"
package_config:
  version: "add_biobase_modules"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
      dest: "testData"
  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
  - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
  - ".engines[.type == 'docker'].target_tag := 'add_biobase_modules'"
  organization: "vsh"
