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Adjust = to be same everywhere
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@apeltzer
apeltzer committed Oct 24, 2022
1 parent 9fe7a4f commit 2ff08d9
Showing 1 changed file with 104 additions and 104 deletions.
208 changes: 104 additions & 104 deletions nextflow.config
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Original file line number Diff line number Diff line change
Expand Up @@ -10,84 +10,84 @@
params {

// Input options
input = null
input = null

// Workflow flags
protocol = 'illumina'
protocol = 'illumina'

// References
genome = null
igenomes_base = 's3://ngi-igenomes/igenomes'
igenomes_ignore = false
mirna_gtf = null
mature = "https://mirbase.org/ftp/CURRENT/mature.fa.gz"
hairpin = "https://mirbase.org/ftp/CURRENT/hairpin.fa.gz"
mirgenedb = false
mirgenedb_mature = null
mirgenedb_hairpin = null
mirgenedb_gff = null
mirgenedb_species = null
genome = null
igenomes_base = 's3://ngi-igenomes/igenomes'
igenomes_ignore = false
mirna_gtf = null
mature = "https://mirbase.org/ftp/CURRENT/mature.fa.gz"
hairpin = "https://mirbase.org/ftp/CURRENT/hairpin.fa.gz"
mirgenedb = false
mirgenedb_mature = null
mirgenedb_hairpin = null
mirgenedb_gff = null
mirgenedb_species = null

// Trimming options
clip_r1 = null
three_prime_clip_r1 = null
three_prime_adapter = null
trim_fastq = true
fastp_min_length = 17
fastp_known_mirna_adapters = "$projectDir/assets/known_adapters.fa"
save_trimmed_fail = false
skip_qc = false
skip_fastqc = false
skip_multiqc = false
skip_mirdeep = false
skip_fastp = false
save_reference = false
fastp_max_length = 40
clip_r1 = null
three_prime_clip_r1 = null
three_prime_adapter = null
trim_fastq = true
fastp_min_length = 17
fastp_known_mirna_adapters = "$projectDir/assets/known_adapters.fa"
save_trimmed_fail = false
skip_qc = false
skip_fastqc = false
skip_multiqc = false
skip_mirdeep = false
skip_fastp = false
save_reference = false
fastp_max_length = 40

// Contamination filtering
filter_contamination = false
rrna = null
trna = null
cdna = null
ncrna = null
pirna = null
other_contamination = null
filter_contamination = false
rrna = null
trna = null
cdna = null
ncrna = null
pirna = null
other_contamination = null

// MultiQC options
multiqc_config = null
multiqc_title = null
multiqc_logo = null
max_multiqc_email_size = '25.MB'
multiqc_config = null
multiqc_title = null
multiqc_logo = null
max_multiqc_email_size = '25.MB'
multiqc_methods_description = null

// Boilerplate options
outdir = null
tracedir = "${params.outdir}/pipeline_info"
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
hook_url = null
help = false
validate_params = true
show_hidden_params = false
schema_ignore_params = 'genomes'
enable_conda = false
outdir = null
tracedir = "${params.outdir}/pipeline_info"
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
hook_url = null
help = false
validate_params = true
show_hidden_params = false
schema_ignore_params = 'genomes'
enable_conda = false

// Config options
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
config_profile_description = null
config_profile_contact = null
config_profile_url = null
config_profile_name = null
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
config_profile_description = null
config_profile_contact = null
config_profile_url = null
config_profile_name = null

// Max resource options
// Defaults only, expecting to be overwritten
max_memory = '128.GB'
max_cpus = 16
max_time = '240.h'
max_memory = '128.GB'
max_cpus = 16
max_time = '240.h'

}

Expand All @@ -112,64 +112,64 @@ try {
profiles {
debug { process.beforeScript = 'echo $HOSTNAME' }
conda {
params.enable_conda = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
params.enable_conda = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
mamba {
params.enable_conda = true
conda.useMamba = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
params.enable_conda = true
conda.useMamba = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
docker {
docker.enabled = true
docker.userEmulation = true
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
docker.runOptions = '-u $(id -u):$(id -g)'
docker.enabled = true
docker.userEmulation = true
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
docker.runOptions = '-u $(id -u):$(id -g)'
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
singularity.enabled = true
singularity.autoMounts = true
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
podman {
podman.enabled = true
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
podman.enabled = true
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
shifter {
shifter.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
shifter.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
}
charliecloud {
charliecloud.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
}
gitpod {
executor.name = 'local'
executor.cpus = 16
executor.memory = 60.GB
executor.name = 'local'
executor.cpus = 16
executor.memory = 60.GB
}
test { includeConfig 'conf/test.config' }
test_no_genome { includeConfig 'conf/test_no_genome.config' }
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