mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 07:42:05 +00:00
801240a971
* create files with nf-core command * update meta.yml files * starting to work on index main.nf * prelim test for index * index test working; not finding all output files * index passing tests * index and align passing tests * prototyping biscuitblaster and pileup * update containers * updates to pileup * pileup passing tests * template creation for more biscuit tools * tests passing on blaster,bsconv,pupsom * epiread passing tests, but need to update SNP bed file path * vcf2bed working; change test file * all biscuit commands passing tests * biscuitblaster rename * try to fix permissions * more permission fixes * trying a couple more permission changes * hopefully last permission fixes * really last permission changes * few more permissions * add when blocks * Remove read group meta Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * remove read group meta Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * changes for first round of review * update meta.yml with more specific links * Update modules/biscuit/biscuitblaster/main.nf Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Apply new version reporting Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Update modules/biscuit/pileup/main.nf Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Update main.nf * Update modules/biscuit/pileupsomatic/main.nf Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * update test file path * Update modules/biscuit/align/main.nf Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Update modules/biscuit/align/main.nf Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * tests passing again * Update modules/biscuit/align/main.nf * Update modules/biscuit/bsconv/main.nf * Update modules/biscuit/epiread/main.nf * Update modules/biscuit/index/main.nf * Update test.yml * Update modules/biscuit/pileupsomatic/main.nf * remove module-specific extension/prefix * remove module-specific extension/prefix * add missing args * switch pileup strategy * update test.yml * remove debug * whitespace cleanup * add in newline escapes * requested changes * Update modules/biscuit/pileup/meta.yml Co-authored-by: Spix <nathan.spix@submit.cm.cluster> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: Spix <nathan.spix@node107.cm.cluster> Co-authored-by: njspix <nathan.spix@vai.org>
32 lines
660 B
Text
32 lines
660 B
Text
params {
|
|
outdir = "output/"
|
|
publish_dir_mode = "copy"
|
|
enable_conda = false
|
|
singularity_pull_docker_container = false
|
|
}
|
|
|
|
process {
|
|
cpus = 2
|
|
memory = 3.GB
|
|
time = 2.h
|
|
}
|
|
|
|
if ("$PROFILE" == "singularity") {
|
|
singularity.enabled = true
|
|
singularity.autoMounts = true
|
|
} else if ("$PROFILE" == "conda") {
|
|
params.enable_conda = true
|
|
} else {
|
|
docker.enabled = true
|
|
docker.userEmulation = true
|
|
}
|
|
|
|
// Increase time available to build Conda environment
|
|
conda { createTimeout = "120 min" }
|
|
|
|
// Load test_data.config containing paths to test data
|
|
includeConfig 'test_data.config'
|
|
|
|
manifest {
|
|
nextflowVersion = '!>=21.10.0'
|
|
}
|