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rnaseq/target/executable/trimgalore/.config.vsh.yaml
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name: "trimgalore"
version: "main"
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.gz"
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.gz"
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"
repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
tag: "v0.1.0"
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: "main"
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: "executable"
engine: "docker|native"
output: "target/executable/trimgalore"
executable: "target/executable/trimgalore/trimgalore"
viash_version: "0.9.0"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_qP68SGVqiugFlLowIn73iXH8gzJeuD4MgS5A@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:
test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1"
dest: "testData"
repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
tag: "v0.1.0"
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 := 'main'"
organization: "vsh"
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