millironx/nf-configs
1
0
Fork 0
mirror of https://github.com/MillironX/nf-configs.git synced 2024-12-22 10:38:16 +00:00
Code Issues Releases Packages Activity

Merge pull request #330 from nf-core/master

Browse source 
Pulling master to branch
This commit is contained in:
Combiz Khozoie 2022-02-11 14:18:01 +00:00 committed by GitHub
commit a77f718ae2
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
7 changed files with 70 additions and 34 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

4
.github/workflows/linting.yml vendored
View file

@ -7,9 +7,7 @@ jobs:
runs-on: ubuntu-18.04
steps:
- uses: actions/checkout@v1
- uses: actions/setup-node@v1
with:
node-version: '10'
- uses: actions/setup-node@v2
- name: Install markdownlint
run: |
npm install -g markdownlint-cli

8
conf/cbe.config
View file

@ -7,11 +7,9 @@ params {
process {
executor = 'slurm'
queue = { task.memory <= 170.GB ? 'c' : 'm' }
module = 'anaconda3/2019.10'
// --signal option will be handled by nextflow after 21.10.0 release (see https://github.com/nextflow-io/nextflow/issues/2163)
clusterOptions = { '--signal B:USR2 ' << ( (queue == 'c' & task.time <= 1.h) ? '--qos rapid' : ( task.time <= 8.h ? '--qos short': ( task.time <= 48.h ? '--qos medium' : '--qos long' ) ) ) }
queue = { task.memory <= 120.GB ? 'c' : 'm' }
module = ['build-env/.f2021', 'build-env/f2021', 'anaconda3/2021.11']
clusterOptions = { ( task.queue == 'g' ? '--gres gpu:1 ' : '' ) << ( (task.queue == 'c' & task.time <= 1.h) ? '--qos rapid' : ( task.time <= 8.h ? '--qos short': ( task.time <= 48.h ? '--qos medium' : '--qos long' ) ) ) }
}
singularity {

2
conf/eva.config
View file

@ -30,7 +30,7 @@ profiles {
config_profile_description = 'MPI-EVA archgen profile, provided by nf-core/configs.'
max_memory = 256.GB
max_cpus = 32
max_time = 720.h
max_time = 365.d
//Illumina iGenomes reference file path
}

80
conf/pipeline/eager/eva.config
View file

@ -19,57 +19,60 @@ process {
withLabel:'sc_tiny'{
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 1.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
time = '365.d'
}
withLabel:'sc_small'{
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
time = '365.d'
}
withLabel:'sc_medium'{
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
time = '365.d'
}
withLabel:'mc_small'{
cpus = { check_max( 2, 'cpus' ) }
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
time = '365.d'
}
withLabel:'mc_medium' {
cpus = { check_max( 4, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
time = '365.d'
}
withLabel:'mc_large'{
cpus = { check_max( 8, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
time = '365.d'
}
withLabel:'mc_huge'{
cpus = { check_max( 32, 'cpus' ) }
memory = { check_max( 256.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
time = '365.d'
}
// Fixes for SGE and Java incompatibility due to Java using more memory than you tell it to use
withName: makeSeqDict {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: fastqc {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: adapter_removal {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: samtools_flagstat {
@ -82,10 +85,13 @@ process {
withName: dedup {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: markduplicates {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
memory = { check_max( 20.GB * task.attempt, 'memory' ) }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: library_merge {
@ -113,34 +119,43 @@ process {
withName: maltextract {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: multivcfanalyzer {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: mtnucratio {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: vcf2genome {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: qualimap {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : task.exitStatus in [255] ? 'ignore' : 'finish' }
}
withName: damageprofiler {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: circularmapper {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: circulargenerator {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: preseq {
@ -150,6 +165,7 @@ process {
withName: genotyping_ug {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
}
@ -180,57 +196,53 @@ profiles {
withLabel:'sc_tiny'{
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 1.5.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
}
withLabel:'sc_small'{
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 6.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
}
withLabel:'sc_medium'{
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 12.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
}
withLabel:'mc_small'{
cpus = { check_max( 2, 'cpus' ) }
memory = { check_max( 6.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
}
withLabel:'mc_medium' {
cpus = { check_max( 4, 'cpus' ) }
memory = { check_max( 12.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
}
withLabel:'mc_large'{
cpus = { check_max( 8, 'cpus' ) }
memory = { check_max( 24.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
}
withLabel:'mc_huge'{
cpus = { check_max( 32, 'cpus' ) }
memory = { check_max( 256.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
}
// Fixes for SGE and Java incompatibility due to (and also some samtools?!) using more memory than you tell it to use
withName: makeSeqDict {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: fastqc {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: adapter_removal {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: samtools_flagstat {
@ -243,10 +255,13 @@ profiles {
withName: dedup {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: markduplicates {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
memory = { check_max( 32.GB * task.attempt, 'memory' ) }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: library_merge {
@ -270,47 +285,57 @@ profiles {
clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G,virtual_free=1000G" }
cpus = { check_max( 32, 'cpus' ) }
memory = { check_max( 955.GB * task.attempt, 'memory' ) }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName:hostremoval_input_fastq {
memory = { check_max( 32.GB * task.attempt, 'memory' ) }
time = 1440.h
}
withName: maltextract {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: multivcfanalyzer {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: mtnucratio {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: vcf2genome {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: qualimap {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : task.exitStatus in [255] ? 'ignore' : 'finish' }
}
withName: damageprofiler {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: circularmapper {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: circulargenerator {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: genotyping_ug {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: preseq {
@ -345,57 +370,53 @@ profiles {
withLabel:'sc_tiny'{
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 2.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
}
withLabel:'sc_small'{
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
}
withLabel:'sc_medium'{
cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
}
withLabel:'mc_small'{
cpus = { check_max( 2, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
}
withLabel:'mc_medium' {
cpus = { check_max( 4, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
}
withLabel:'mc_large'{
cpus = { check_max( 8, 'cpus' ) }
memory = { check_max( 32.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
}
withLabel:'mc_huge'{
cpus = { check_max( 32, 'cpus' ) }
memory = { check_max( 512.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
}
// Fixes for SGE and Java incompatibility due to Java using more memory than you tell it to use
withName: makeSeqDict {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: fastqc {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: adapter_removal {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: samtools_flagstat {
@ -408,10 +429,13 @@ profiles {
withName: dedup {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: markduplicates {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
memory = { check_max( 48.GB * task.attempt, 'memory' ) }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: library_merge {
@ -430,7 +454,6 @@ profiles {
withName:hostremoval_input_fastq {
memory = { check_max( 32.GB * task.attempt, 'memory' ) }
time = 1440.h
}
withName: metagenomic_complexity_filter {
@ -441,42 +464,53 @@ profiles {
clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G,virtual_free=1000G" }
cpus = { check_max( 32, 'cpus' ) }
memory = { check_max( 955.GB * task.attempt, 'memory' ) }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: maltextract {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: multivcfanalyzer {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: mtnucratio {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: vcf2genome {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: qualimap {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : task.exitStatus in [255] ? 'ignore' : 'finish' }
}
withName: damageprofiler {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
memory = { check_max( 32.GB * task.attempt, 'memory' ) }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: circularmapper {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: circulargenerator {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: genotyping_ug {
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
}
withName: preseq {

6
conf/pipeline/viralrecon/genomes.config
View file

@ -51,6 +51,12 @@ params {
primer_bed = 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V4/SARS-CoV-2.scheme.bed'
scheme = 'SARS-CoV-2'
}
'4.1' {
fasta = 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V4.1/SARS-CoV-2.reference.fasta'
gff = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz'
primer_bed = 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V4.1/SARS-CoV-2.scheme.bed'
scheme = 'SARS-CoV-2'
}
'1200' {
fasta = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/primer_schemes/artic/nCoV-2019/V1200/nCoV-2019.reference.fasta'
gff = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz'

2
docs/cbe.md
View file

@ -9,7 +9,7 @@ Before running the pipeline you will need to load Nextflow using the environment
```bash
## Load Nextflow environment module
module purge
module load nextflow/19.04.0
module load nextflow/21.10.6
```
A local copy of the [AWS-iGenomes](https://registry.opendata.aws/aws-igenomes/) resource has been made available on CBE so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline. You can do this by simply using the `--genome <GENOME_ID>` parameter.

2
docs/czbiohub.md
View file

@ -125,7 +125,7 @@ For Human and Mouse, we use [GENCODE](https://www.gencodegenes.org/) gene annota
## High Priority Queue
If you would like to run with the _High Priority_ queue, specify the `highpriority` config profile after `czbiohub_aws`. When applied after the main `czbiohub_aws` config, it overwrites the process `queue` identifier.
If you would like to run with the *High Priority* queue, specify the `highpriority` config profile after `czbiohub_aws`. When applied after the main `czbiohub_aws` config, it overwrites the process `queue` identifier.
To use it, submit your run with with `-profile czbiohub_aws,highpriority`.