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Merge pull request #199 from nf-core/fix-emillers-comments
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Shameless self merge as this is only reviewers comments :-)
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@apeltzer
apeltzer authored Oct 24, 2022
2 parents 6363ae3 + bf3ef92 commit 5f84f21
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Showing 2 changed files with 105 additions and 105 deletions.
2 changes: 1 addition & 1 deletion docs/usage.md
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Expand Up @@ -32,7 +32,7 @@ Different parameters can be set for the two supported databases. By default `miR

If MirGeneDB should be used instead it needs to be specified using `--mirgenedb` and use the parameters below .

- `mirgenedb_gff`: The data can not be downloaded automatically, thus the user needs to supply the gff file for either his species, or all species downloaded from `https://mirgenedb.org/download`. The total set will automatically be subsetted to the species specified with `--mirgenedb_species`.
- `mirgenedb_gff`: The data can not be downloaded automatically (URLs are created with short term tokens in it), thus the user needs to supply the gff file for either his species, or all species downloaded from `https://mirgenedb.org/download`. The total set will automatically be subsetted to the species specified with `--mirgenedb_species`.
- `mirgenedb_mature`: points to the FASTA file of mature miRNA sequences. Download from `https://mirgenedb.org/download`.
- `mirgenedb_hairpin`: points to the FASTA file of precursor miRNA sequences. Download from `https://mirgenedb.org/download`. Note that MirGeneDB does not have a dedicated `hairpin` file, but the `Precursor sequences` are to be used.

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208 changes: 104 additions & 104 deletions nextflow.config
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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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