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nextflow.config
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nextflow.config
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////
//// nextflow parameters ////
////
params.scratch_dir = "/lab/weng_scratch/tmp/" //Just for testing, not for general release
process.executor = "local" //Just for testing, not for general release
executor.queueSize = 2000
executor.exitReadTimeout = "120 sec"
report.enabled = true
trace.enabled = true
dag.enabled = true
dag.file = "dag.html"
process.errorStrategy = "retry"
process.maxRetries = 1
params.assembly_CPUs = 18 //In cores. Used for Trinity, rnaSPAdes, kallisto non-parallelized phases
params.assembly_MEM = 200 //In gigabases. Used for Trinity and rnaSPAdes high memory phases
////
//// transXpress parameters ////
////
params.storeDB = "/tmp/transXpress_db/" //All the used bioinformatic databases (e.g. pfam, swissprot) will be downloaded to this location
//Needs ~10 GB of space, and should be on a shared filesystem to enable all forked transXpress processes to access the files.
//By default, transXpress will add a prefix to your transcriptome assembly in the form <date>_<metadata>_<assembler>
//You may disable all these additions if you do not like them.
//For the <metadata> parameter, we suggest you put the "Genus species" of the main species your dataset describes
//but, you are free to disable the metadata parameter or use it to record non-genus-species metadata e.g. sample identifier
params.prefix_add_date = true //Set to false to disable
params.prefix_add_date_formatting = "yyMMdd" //See https://docs.oracle.com/javase/8/docs/api/java/text/SimpleDateFormat.html to change this formatting
params.prefix_add_metadata_file = "./species.txt" //Expects to find a text file with the content within separated by spaces. Set to "" to disable
params.prefix_add_assembler = true //Will add Trinity or rnaSPAdes to the prefix, depending on which assembler is used
//Paths to the Raw fastq reads used by transXpress are specified in this file. See the documentation for instructions on creating this file
params.samples = "samples.tsv"
params.trimmomatic_adapter_file = "./adapters.fasta" //This file contains many types of sequencing adapters for automated removal with trimmomatic
params.TRIMMOMATIC_PARAMS = "ILLUMINACLIP:adapters.fasta:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25" //transXpress will automatically rename the params.trimmomatic_adapters file to ./adapters.fasta internally
params.TRINITY_PARAMS = " --seqType fq"
params.RNASPADES_PARAMS = ""
params.SIGNALP_ORGANISMS = "euk"
//// See below for the profiles that choose which HPC system to use, and whether or you want to do a stranded or unstranded assembly
profiles {
notStrandSpecific_local {
process.executor = "local"
// Used for both trinity and kallisto jobs!
params.STRAND_SPECIFIC_TRINITY = "" // --SS_lib_type=RF
params.STRAND_SPECIFIC_RNASPADES = "" // --ss-rf
params.TRINITY_PARAMS += " --min_glue 2"
params.TRINITY_PARAMS += " --min_kmer_cov 2"
params.TRINITY_PARAMS += " --no_normalize_reads"
}
strandSpecific_local {
process.executor = "local"
// Used for both trinity and kallisto jobs!
params.STRAND_SPECIFIC_TRINITY = "--SS_lib_type=RF"
params.STRAND_SPECIFIC_RNASPADES = "--ss-rf"
params.TRINITY_PARAMS += " --min_glue 2"
params.TRINITY_PARAMS += " --min_kmer_cov 2"
params.TRINITY_PARAMS += " --no_normalize_reads"
}
notStrandSpecific_LSF {
// Used for both trinity and kallisto jobs!
params.STRAND_SPECIFIC_TRINITY = "--SS_lib_type=RF"
params.STRAND_SPECIFIC_RNASPADES = "--ss-rf"
params.TRINITY_PARAMS += " --min_glue 2"
params.TRINITY_PARAMS += " --min_kmer_cov 2"
params.TRINITY_PARAMS += " --no_normalize_reads"
}
strandSpecific_LSF {
process.executor = "lsf"
process.queue = "18" //Just for testing, not for general release
// Used for both trinity and kallisto jobs!
params.STRAND_SPECIFIC_TRINITY = "--SS_lib_type=RF"
params.STRAND_SPECIFIC_RNASPADES = "--ss-rf"
params.TRINITY_PARAMS += " --min_glue 2"
params.TRINITY_PARAMS += " --min_kmer_cov 2"
params.TRINITY_PARAMS += " --no_normalize_reads"
}
test_notStrandSpecific_local {
process.executor = "local"
params.assembly_CPUs = 4 //In cores. Used for Trinity and rnaSPAdes non-parallelized phases
params.assembly_MEM = 8 //In gigabases. Used for Trinity and rnaSPAdes high memory phases
params.storeDB = "./transXpress_db/"
process.maxForks = 2 //if running locally, otherwise no limit
report.enabled = true
trace.enabled = true
dag.enabled = true
dag.file = "test_nonSS_dag.svg"
report.file = "test_nonSS_report.html"
params.TRINITY_PARAMS = " --seqType fq"
// Used for both trinity and kallisto jobs!
params.STRAND_SPECIFIC_TRINITY = "" // --SS_lib_type=RF
params.STRAND_SPECIFIC_RNASPADES = "" // "--ss-rf"
params.TRINITY_PARAMS += " --min_glue 2"
params.TRINITY_PARAMS += " --min_kmer_cov 10"
params.TRINITY_PARAMS += " --no_normalize_reads"
}
test_strandSpecific_local {
process.executor = "local"
params.assembly_CPUs = 4 //In cores. Used for Trinity and rnaSPAdes non-parallelized phases
params.assembly_MEM = 8 //In gigabases. Used for Trinity and rnaSPAdes high memory phases
params.storeDB = "./transXpress_db/"
process.maxForks = 2 //if running locally, otherwise no limit
report.enabled = true
trace.enabled = true
dag.enabled = true
dag.file = "test_nonSS_dag.svg"
report.file = "test_nonSS_report.html"
params.TRINITY_PARAMS = " --seqType fq"
// Used for both trinity and kallisto jobs!
params.STRAND_SPECIFIC_TRINITY = "--SS_lib_type=RF"
params.STRAND_SPECIFIC_RNASPADES = "--ss-rf"
params.TRINITY_PARAMS += " --min_glue 2"
params.TRINITY_PARAMS += " --min_kmer_cov 10"
params.TRINITY_PARAMS += " --no_normalize_reads"
}
}