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nextflow.config
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params {
/* Reference genome
* ----------------
* Shortcut, local path, or URL pointing to the FASTA file (or compressed
* archive contaning one or more FASTA files).
* Shortcuts are of the form: <source>.<version>, where the currently
* recognized sources are "ensembl" and "ucsc", and the version version
* format is specific to the source. For Ensembl human genomes, the version
* can be "ensembl.<release>.GRCh<37|38>"; for all other organisms, the
* format is "ensembl.<release>.<organism>.<build>". For UCSC, it is simply
* "ucsc.<build>".
*/
genome = 'ensembl.75.GRCh37'
/* Annotation
* ----------
* Shortcut, local path, or URL pointing to the annotation file (gff or gtf).
* Shortcuts are of the form: <source>.<version>, where the only currently
* recognized source is "gencode", and the version format is specific to the
* source. For gencode, the format is "gencode.<release>.<content>.<regions>"
* where content is one of "comprehensive" or "lncrna" and regions is "chr"
* or "all".
*/
annotation = 'gencode.19.comprehensive.all'
/* Two-column file mapping transcript ID to gene ID.
* If this file doesn't exist, the program will try
* to create it from information in the sleuth output.
*/
tx2geneFile = 'tx2gene.txt'
/* Directory containing fastq files. */
fastqDir = "fastq"
/* FASTQ filename pattern
* ----------------------
* By default, FASTQ files are named ${UniqueID}.fq.gz (for single-end libraries)
* ${lib['UniqueID']}_${PairIndex}.fq.gz (for paired-end libraries). You can specify a
* different pattern using a similar format; all metadata columns are accessible
* as members of the 'lib' variable, as is the special variables $PairIndex.
*/
fastqPattern = '${lib['UniqueID']}_${PairIndex}.fq.gz'
/* Default condition used for partitioning samples and for differential
* expression testing.
*/
condition = "Condition"
/* Differential expression models to test. Each model is of the form
* [ "<name>", "<formula>", "<var1>[=<value1>][,<var2>=[<value2>],...]"],
* where formula is a valid R formula and the list of variables are the
* response variables to test. The formula may reference any columns in the
* libraries file. If a variable has more than two possible values, "=<value>"
* is used to indicate which value should be used as the basedline for the
* comparison. See the Sleuth and DESeq2 documentation for more details on models.
*/
models [
[ "full", "~Condition", "ConditionCase"]
]
/* File to which the R object containing Sleuth data should be saved. If you
* want to keep this file permanently, this must be an absolute path, otherwise
* it will be deleted when the pipeline completes.
*/
sleuthDataFile = "kallisto_sleuth.RData"
/* File to which the R object(s) containing transcript differential expression
* results to be saved. There will be one file for each model. The variable
* ${model} will be replaced with the model name from the models parameter above.
*/
txDiffExpDataFile = '/path/to/tx_${model}.DRata'
/* File to which the R object(s) containing gene differential expression
* results to be saved. There will be one file for each model. The variable
* ${model} will be replaced with the model name from the models parameter above.
*/
geneDiffExpDataFile = "/path/to/gene_${model}.DRata"
}
process {
/* How to execute jobs. Valid values are:
* sge, lsf, slurm, pbs, drmaa, cirrus, dnanexus.
* See NextFlow documentation for details:
* http://www.nextflow.io/docs/latest/executor.html
*/
executor = "sge"
}