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Merge branch 'master' into master_kraken

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Maxime U. Garcia 2021-07-20 09:26:56 +02:00 committed by GitHub
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43
.github/workflows/main.yml vendored
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@ -16,7 +16,48 @@ jobs:
needs: test_all_profiles needs: test_all_profiles
strategy: strategy:
matrix: matrix:
profile: ['abims', 'awsbatch', 'bi','bigpurple', 'binac', 'biohpc_gen', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'eddie', 'eva', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'ifb_core', 'imperial', 'imperial_mb', 'jax', 'mpcdf', 'munin', 'oist', 'pasteur', 'phoenix', 'prince', 'seg_globe', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh'] profile:
- 'abims'
- 'awsbatch'
- 'aws_tower'
- 'bi'
- 'bigpurple'
- 'binac'
- 'biohpc_gen'
- 'cbe'
- 'ccga_dx'
- 'ccga_med'
- 'cfc'
- 'cfc_dev'
- 'crick'
- 'denbi_qbic'
- 'ebc'
- 'eddie'
- 'eva'
- 'genotoul'
- 'genouest'
- 'gis'
- 'google'
- 'hebbe'
- 'icr_davros'
- 'ifb_core'
- 'imperial'
- 'imperial_mb'
- 'jax'
- 'mpcdf'
- 'munin'
- 'oist'
- 'pasteur'
- 'phoenix'
- 'prince'
- 'sanger'
- 'seg_globe'
- 'shh'
- 'uct_hpc'
- 'uppmax'
- 'utd_ganymede'
- 'utd_sysbio'
- 'uzh'
steps: steps:
- uses: actions/checkout@v1 - uses: actions/checkout@v1
- name: Install Nextflow - name: Install Nextflow

4
README.md
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@ -96,10 +96,12 @@ Currently documentation is available for the following systems:
* [ABIMS](docs/abims.md) * [ABIMS](docs/abims.md)
* [AWSBATCH](docs/awsbatch.md) * [AWSBATCH](docs/awsbatch.md)
* [AWS_TOWER](docs/aws_tower.md)
* [BIGPURPLE](docs/bigpurple.md) * [BIGPURPLE](docs/bigpurple.md)
* [BI](docs/bi.md) * [BI](docs/bi.md)
* [BINAC](docs/binac.md) * [BINAC](docs/binac.md)
* [BIOHPC_GEN](docs/biohpc_gen.md) * [BIOHPC_GEN](docs/biohpc_gen.md)
* [CAMBRIDGE](docs/cambridge.md)
* [CBE](docs/cbe.md) * [CBE](docs/cbe.md)
* [CCGA_DX](docs/ccga_dx.md) * [CCGA_DX](docs/ccga_dx.md)
* [CCGA_MED](docs/ccga_med.md) * [CCGA_MED](docs/ccga_med.md)
@ -122,11 +124,13 @@ Currently documentation is available for the following systems:
* [PASTEUR](docs/pasteur.md) * [PASTEUR](docs/pasteur.md)
* [PHOENIX](docs/phoenix.md) * [PHOENIX](docs/phoenix.md)
* [PRINCE](docs/prince.md) * [PRINCE](docs/prince.md)
* [SANGER](docs/sanger.md)
* [SEG_GLOBE](docs/seg_globe.md) * [SEG_GLOBE](docs/seg_globe.md)
* [SHH](docs/shh.md) * [SHH](docs/shh.md)
* [UCT_HPC](docs/uct_hpc.md) * [UCT_HPC](docs/uct_hpc.md)
* [UPPMAX](docs/uppmax.md) * [UPPMAX](docs/uppmax.md)
* [UTD_GANYMEDE](docs/utd_ganymede.md) * [UTD_GANYMEDE](docs/utd_ganymede.md)
* [UTD_SYSBIO](docs/utd_sysbio.md)
* [UZH](docs/uzh.md) * [UZH](docs/uzh.md)
### Uploading to `nf-core/configs` ### Uploading to `nf-core/configs`

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assets/nf-core-configs_social_preview.png
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Width:  |  Height:  |  Size: 26 KiB

26
bin/cchecker.py
View file

@ -10,6 +10,7 @@ import os
import sys import sys
import argparse import argparse
import re import re
import yaml
############################################ ############################################
############################################ ############################################
@ -51,19 +52,22 @@ def check_config(Config, Github):
### Ignore these profiles ### Ignore these profiles
ignore_me = ['czbiohub_aws'] ignore_me = ['czbiohub_aws']
tests.update(ignore_me) tests.update(ignore_me)
with open(Github, 'r') as ghfile: # parse yaml GitHub actions file
for line in ghfile: try:
if re.search('profile: ', line): with open(Github, 'r') as ghfile:
line = line.replace('\'','').replace('[','').replace(']','').replace('\n','') wf = yaml.safe_load(ghfile)
profiles = line.split(':')[1].split(',') profile_list = wf["jobs"]["profile_test"]["strategy"]["matrix"]["profile"]
for p in profiles: except Exception as e:
tests.add(p.strip()) print("Could not parse yaml file: {}, {}".format(Github, e))
sys.exit(1)
# Add profiles to test
for profile in profile_list:
tests.add(profile.strip())
###Check if sets are equal ###Check if sets are equal
if tests == config_profiles: try:
sys.exit(0) assert tests == config_profiles
else: except (AssertionError):
#Maybe report what is missing here too
print("Tests don't seem to test these profiles properly. Please check whether you added the profile to the Github Actions testing YAML.\n") print("Tests don't seem to test these profiles properly. Please check whether you added the profile to the Github Actions testing YAML.\n")
print(config_profiles.symmetric_difference(tests)) print(config_profiles.symmetric_difference(tests))
sys.exit(1) sys.exit(1)

21
conf/aws_tower.config Normal file
View file

@ -0,0 +1,21 @@
//Nextflow config file for running on AWS batch
params {
config_profile_description = 'AWS Batch with Tower Profile'
config_profile_contact = 'Gisela Gabernet (@ggabernet)'
config_profile_url = 'https://aws.amazon.com/batch/'
}
timeline {
overwrite = true
}
report {
overwrite = true
}
trace {
overwrite = true
}
dag {
overwrite = true
}
process.executor = 'awsbatch'

2
conf/biohpc_gen.config
View file

@ -12,7 +12,7 @@ env {
process { process {
executor = 'slurm' executor = 'slurm'
queue = { task.memory <= 1536.GB ? (task.time > 2.d || task.memory > 384.GB ? 'biohpc_gen_production' : 'biohpc_gen_normal') : 'biohpc_gen_highmem' } queue = { task.memory <= 1536.GB ? (task.time > 2.d || task.memory > 384.GB ? 'biohpc_gen_production' : 'biohpc_gen_normal') : 'biohpc_gen_highmem' }
beforeScript = 'module use /dss/dssfs01/pr53da/pr53da-dss-0000/spack/modules/x86_avx2/linux*' beforeScript = 'module use /dss/dsslegfs02/pn73se/pn73se-dss-0000/spack/modules/x86_avx2/linux*'
module = 'charliecloud/0.22:miniconda3' module = 'charliecloud/0.22:miniconda3'
} }

18
conf/cambridge.config Normal file
View file

@ -0,0 +1,18 @@
params {
config_profile_description = 'Cambridge HPC cluster profile.'
config_profile_contact = 'Andries van Tonder (ajv37@cam.ac.uk)'
config_profile_url = "https://docs.hpc.cam.ac.uk/hpc"
}
singularity {
enabled = true
autoMounts = true
}
process {
executor = 'slurm'
clusterOptions = '-p cclake'
}
params {
max_memory = 192.GB
max_cpus = 56
max_time = 12.h
}

1
conf/cfc.config
View file

@ -11,7 +11,6 @@ singularity {
} }
process { process {
beforeScript = 'module load devel/singularity/3.4.2'
executor = 'slurm' executor = 'slurm'
queue = { task.memory > 60.GB || task.cpus > 20 ? 'qbic' : 'compute' } queue = { task.memory > 60.GB || task.cpus > 20 ? 'qbic' : 'compute' }
scratch = 'true' scratch = 'true'

1
conf/cfc_dev.config
View file

@ -10,7 +10,6 @@ singularity {
} }
process { process {
beforeScript = 'module load devel/singularity/3.4.2'
executor = 'slurm' executor = 'slurm'
queue = { task.memory > 60.GB || task.cpus > 20 ? 'qbic' : 'compute' } queue = { task.memory > 60.GB || task.cpus > 20 ? 'qbic' : 'compute' }
scratch = 'true' scratch = 'true'

2
conf/crick.config
View file

@ -17,7 +17,7 @@ process {
params { params {
max_memory = 224.GB max_memory = 224.GB
max_cpus = 32 max_cpus = 32
max_time = 72.h max_time = '72.h'
igenomes_base = '/camp/svc/reference/Genomics/aws-igenomes' igenomes_base = '/camp/svc/reference/Genomics/aws-igenomes'
} }

2
conf/czbiohub_aws.config
View file

@ -27,7 +27,7 @@ process {
workDir = "s3://czb-nextflow/intermediates/" workDir = "s3://czb-nextflow/intermediates/"
aws.region = 'us-west-2' aws.region = 'us-west-2'
executor.awscli = '/home/ec2-user/miniconda/bin/aws' aws.batch.cliPath = '/home/ec2-user/miniconda/bin/aws'
params.tracedir = './' params.tracedir = './'
params { params {

6
conf/eddie.config
View file

@ -31,7 +31,7 @@ process {
params { params {
saveReference = true saveReference = true
// iGenomes reference base // iGenomes reference base
igenomes_base = '/exports/igmm/eddie/NextGenResources/igenomes' igenomes_base = '/exports/igmm/eddie/BioinformaticsResources/igenomes'
max_memory = 384.GB max_memory = 384.GB
max_cpus = 32 max_cpus = 32
max_time = 240.h max_time = 240.h
@ -42,8 +42,8 @@ env {
} }
singularity { singularity {
envWhitelist = "SINGULARITY_TMPDIR" envWhitelist = "SINGULARITY_TMPDIR,TMPDIR"
runOptions = '-p' runOptions = '-p -B "$TMPDIR"'
enabled = true enabled = true
autoMounts = true autoMounts = true
} }

2
conf/hebbe.config
View file

@ -14,7 +14,7 @@ process {
clusterOptions = { "-A $params.project ${params.clusterOptions ?: ''}" } clusterOptions = { "-A $params.project ${params.clusterOptions ?: ''}" }
/* The Hebbe scheduler fails if you try to request an amount of memory for a job */ /* The Hebbe scheduler fails if you try to request an amount of memory for a job */
withName: '*' { memory = null } withName: '.*' { memory = null }
} }
params { params {

2
conf/imperial.config
View file

@ -27,7 +27,7 @@ executor {
singularity { singularity {
enabled = true enabled = true
autoMounts = true autoMounts = true
runOptions = "-B /rds/,/rdsgpfs/,/rds/general/user/$USER/ephemeral/tmp/:/tmp,/rds/general/user/$USER/ephemeral/tmp/:/var/tmp" runOptions = "-B /rds/,/rds/general/user/$USER/ephemeral/tmp/:/tmp,/rds/general/user/$USER/ephemeral/tmp/:/var/tmp"
} }
process { process {

4
conf/jax.config
View file

@ -19,7 +19,7 @@ singularity{
cacheDir = params.singularity_cache_dir cacheDir = params.singularity_cache_dir
} }
params { params {
max_memory = 768.GB max_memory = 320.GB
max_cpus = 70 max_cpus = 32
max_time = 336.h max_time = 336.h
} }

29
conf/mpcdf.config
View file

@ -1,18 +1,15 @@
params { params {
config_profile_description = 'MPCDF HPC profiles (unoffically) provided by nf-core/configs.' config_profile_description = 'MPCDF HPC profiles (unoffically) provided by nf-core/configs.'
config_profile_contact = 'James Fellows Yates (@jfy133)' config_profile_contact = 'James Fellows Yates (@jfy133)'
config_profile_url = 'https://www.mpcdf.mpg.de/services/computing' config_profile_url = 'https://www.mpcdf.mpg.de/services/supercomputing'
} }
profiles { profiles {
cobra { cobra {
// Does not have singularity! Conda module must be used, but it is
// recommended to set NXF_CONDA_CACHEDIR var in ~/.bash{_profile,rc}
// To create common cache dir
process { process {
beforeScript = 'module load anaconda/3/2020.02' beforeScript = 'module load singularity'
executor = 'slurm' executor = 'slurm'
} }
@ -20,6 +17,13 @@ profiles {
queueSize = 8 queueSize = 8
} }
// Set $NXF_SINGULARITY_CACHEDIR in your ~/.bash_profile
// to stop downloading the same image for every run
singularity {
enabled = true
autoMounts = true
}
params { params {
config_profile_description = 'MPCDF cobra profile (unofficially) provided by nf-core/configs.' config_profile_description = 'MPCDF cobra profile (unofficially) provided by nf-core/configs.'
max_memory = 725.GB max_memory = 725.GB
@ -28,12 +32,9 @@ profiles {
} }
} }
raven { raven {
// Does not have singularity! Conda module must be used, but it is
// recommended to set NXF_CONDA_CACHEDIR var in ~/.bash{_profile,rc}
// to create common cache dir
process { process {
beforeScript = 'module load anaconda/3/2020.02' beforeScript = 'module load singularity'
executor = 'slurm' executor = 'slurm'
} }
@ -41,6 +42,13 @@ profiles {
queueSize = 8 queueSize = 8
} }
// Set $NXF_SINGULARITY_CACHEDIR in your ~/.bash_profile
// to stop downloading the same image for every run
singularity {
enabled = true
autoMounts = true
}
params { params {
config_profile_description = 'MPCDF raven profile (unofficially) provided by nf-core/configs.' config_profile_description = 'MPCDF raven profile (unofficially) provided by nf-core/configs.'
max_memory = 368.GB max_memory = 368.GB
@ -48,4 +56,7 @@ profiles {
max_time = 24.h max_time = 24.h
} }
} }
debug {
cleanup = false
}
} }

16
conf/munin.config
View file

@ -2,8 +2,8 @@
params { params {
// Specific nf-core/configs params // Specific nf-core/configs params
config_profile_contact = 'Szilveszter Juhos (@szilvajuhos)' config_profile_contact = 'Maxime Garcia (@maxulysse)'
config_profile_description = 'MUNIN profile provided by nf-core/configs.' config_profile_description = 'MUNIN profile provided by nf-core/configs'
config_profile_url = 'https://ki.se/forskning/barntumorbanken' config_profile_url = 'https://ki.se/forskning/barntumorbanken'
// Local AWS iGenomes reference file paths on munin // Local AWS iGenomes reference file paths on munin
@ -26,8 +26,12 @@ singularity {
} }
// To use docker, use nextflow run -profile munin,docker // To use docker, use nextflow run -profile munin,docker
docker { profiles {
enabled = false docker {
mountFlags = 'z' docker {
fixOwnership = true enabled = false
mountFlags = 'z'
fixOwnership = true
}
}
} }

10
conf/pipeline/eager/eva.config
View file

@ -61,7 +61,7 @@ process {
// Fixes for SGE and Java incompatibility due to Java using more memory than you tell it to use // Fixes for SGE and Java incompatibility due to Java using more memory than you tell it to use
withName: makeSeqDict { withName: makeSeqDict {
clusterOptions = { "-S /bin/bash -v JAVA_OPTS='-XX:ParallelGCThreads=1' -l h_vmem=${(task.memory.toGiga() + 3)}G,virtual_free=${(task.memory.toGiga() + 3)}G" } clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
} }
withName: fastqc { withName: fastqc {
@ -69,7 +69,7 @@ process {
} }
withName: adapter_removal { withName: adapter_removal {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 4)}G,virtual_free=${(task.memory.toGiga() * 4)}G" }
} }
withName: dedup { withName: dedup {
@ -80,6 +80,10 @@ process {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() + 6)}G,virtual_free=${(task.memory.toGiga() + 6)}G" } clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() + 6)}G,virtual_free=${(task.memory.toGiga() + 6)}G" }
} }
withName: library_merge {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() + 6)}G,virtual_free=${(task.memory.toGiga() + 6)}G" }
}
withName: malt { withName: malt {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
} }
@ -93,7 +97,7 @@ process {
} }
withName: mtnucratio { withName: mtnucratio {
clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" } clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 4)}G,virtual_free=${(task.memory.toGiga() * 4)}G" }
} }
withName: vcf2genome { withName: vcf2genome {

18
conf/pipeline/eager/shh.config
View file

@ -10,7 +10,7 @@ params {
// Specific nf-core/eager process configuration // Specific nf-core/eager process configuration
process { process {
maxRetries = 2 maxRetries = 3
withName: malt { withName: malt {
maxRetries = 1 maxRetries = 1
@ -106,43 +106,43 @@ profiles {
withLabel:'sc_tiny'{ withLabel:'sc_tiny'{
cpus = { check_max( 1, 'cpus' ) } cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 2.GB * task.attempt, 'memory' ) } memory = { check_max( 2.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h } time = { task.attempt == 3 ? 1440.h : 48.h }
} }
withLabel:'sc_small'{ withLabel:'sc_small'{
cpus = { check_max( 1, 'cpus' ) } cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) } memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h } time = { task.attempt == 3 ? 1440.h : 48.h }
} }
withLabel:'sc_medium'{ withLabel:'sc_medium'{
cpus = { check_max( 1, 'cpus' ) } cpus = { check_max( 1, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) } memory = { check_max( 16.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h } time = { task.attempt == 3 ? 1440.h : 48.h }
} }
withLabel:'mc_small'{ withLabel:'mc_small'{
cpus = { check_max( 2, 'cpus' ) } cpus = { check_max( 2, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) } memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h } time = { task.attempt == 3 ? 1440.h : 48.h }
} }
withLabel:'mc_medium' { withLabel:'mc_medium' {
cpus = { check_max( 4, 'cpus' ) } cpus = { check_max( 4, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) } memory = { check_max( 16.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h } time = { task.attempt == 3 ? 1440.h : 48.h }
} }
withLabel:'mc_large'{ withLabel:'mc_large'{
cpus = { check_max( 8, 'cpus' ) } cpus = { check_max( 8, 'cpus' ) }
memory = { check_max( 32.GB * task.attempt, 'memory' ) } memory = { check_max( 32.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h } time = { task.attempt == 3 ? 1440.h : 48.h }
} }
withLabel:'mc_huge'{ withLabel:'mc_huge'{
cpus = { check_max( 32, 'cpus' ) } cpus = { check_max( 32, 'cpus' ) }
memory = { check_max( 512.GB * task.attempt, 'memory' ) } memory = { check_max( 512.GB * task.attempt, 'memory' ) }
time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h } time = { task.attempt == 3 ? 1440.h : 48.h }
} }
} }
} }
@ -164,7 +164,7 @@ profiles {
params { params {
config_profile_description = 'Rough HOPS screening MPI-SHH profile, provided by nf-core/configs.' config_profile_description = 'Rough HOPS screening MPI-SHH profile, provided by nf-core/configs.'
fasta = '/projects1/Reference_Genomes/Human/HG19/hg19_complete.fasta' fasta = '/projects1/Reference_Genomes/Human/HG19/hg19_complete.fasta'
bwa_index = '/projects1/Reference_Genomes/Human/HG19/hg19_complete.fasta' bwa_index = '/projects1/Reference_Genomes/Human/HG19/'
fasta_index = '/projects1/Reference_Genomes/Human/HG19/hg19_complete.fasta.fai' fasta_index = '/projects1/Reference_Genomes/Human/HG19/hg19_complete.fasta.fai'
seq_dict = '/projects1/Reference_Genomes/Human/HG19/hg19_complete.dict' seq_dict = '/projects1/Reference_Genomes/Human/HG19/hg19_complete.dict'
bwaalnn = 0.01 bwaalnn = 0.01

19
conf/pipeline/rnaseq/utd_sysbio.config Normal file
View file

@ -0,0 +1,19 @@
params {
config_profile_description = 'University of Texas at Dallas HPC cluster profile provided by nf-core/configs'
config_profile_contact = 'Edmund Miller(@emiller88)'
config_profile_url = 'http://docs.oithpc.utdallas.edu/'
}
process {
withName : "STAR_ALIGN" {
memory = 36.GB
}
withLabel:process_high {
cpus = { check_max( 16 * task.attempt, 'cpus' ) }
memory = { check_max( 60.GB * task.attempt, 'memory' ) }
time = { check_max( 16.h * task.attempt, 'time' ) }
}
}

25
conf/pipeline/sarek/cfc.config Normal file
View file

@ -0,0 +1,25 @@
// Profile config names for nf-core/configs
params {
// Specific nf-core/configs params
config_profile_contact = 'Friederike Hanssen (@FriederikeHanssen)'
config_profile_description = 'nf-core/sarek CFC profile provided by nf-core/configs'
}
// Specific nf-core/sarek process configuration
process {
withName:'StrelkaSingle|Strelka|StrelkaBP|MantaSingle|Manta' {
memory = 59.GB
cpus = 20
}
withName:'MSIsensor_scan|MSIsensor_msi' {
memory = 55.GB
}
withName:BamQC {
memory = 372.GB
}
withName:MapReads{
cpus = 20
memory = 59.GB
}
}

3
conf/pipeline/sarek/munin.config
View file

@ -2,8 +2,9 @@
params { params {
// Specific nf-core/configs params // Specific nf-core/configs params
config_profile_contact = 'Maxime Garcia (@MaxUlysse)' config_profile_contact = 'Maxime Garcia (@maxulysse)'
config_profile_description = 'nf-core/sarek MUNIN profile provided by nf-core/configs' config_profile_description = 'nf-core/sarek MUNIN profile provided by nf-core/configs'
config_profile_url = 'https://ki.se/forskning/barntumorbanken'
// Specific nf-core/sarek params // Specific nf-core/sarek params
annotation_cache = true annotation_cache = true

24
conf/pipeline/viralrecon/genomes.config
View file

@ -20,21 +20,33 @@ params {
primer_sets { primer_sets {
artic { artic {
'1' { '1' {
fasta = 'https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V1/nCoV-2019.reference.fasta' fasta = 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V1/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' 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/primer-schemes/raw/master/nCoV-2019/V1/nCoV-2019.primer.bed' primer_bed = 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V1/nCoV-2019.primer.bed'
scheme = 'nCoV-2019' scheme = 'nCoV-2019'
} }
'2' { '2' {
fasta = 'https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V2/nCoV-2019.reference.fasta' fasta = 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V2/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' 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/primer-schemes/raw/master/nCoV-2019/V2/nCoV-2019.primer.bed' primer_bed = 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V2/nCoV-2019.primer.bed'
scheme = 'nCoV-2019' scheme = 'nCoV-2019'
} }
'3' { '3' {
fasta = 'https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V3/nCoV-2019.reference.fasta' fasta = 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V3/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' 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/primer-schemes/raw/master/nCoV-2019/V3/nCoV-2019.primer.bed' primer_bed = 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V3/nCoV-2019.primer.bed'
scheme = 'nCoV-2019'
}
'4' {
fasta = 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V4/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/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'
primer_bed = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/primer_schemes/artic/nCoV-2019/V1200/nCoV-2019.bed'
scheme = 'nCoV-2019' scheme = 'nCoV-2019'
} }
} }

32
conf/sanger.config Normal file
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@ -0,0 +1,32 @@
params {
config_profile_description = 'The Wellcome Sanger Institute HPC cluster profile'
config_profile_contact = 'Anthony Underwood (@aunderwo)'
config_profile_url = 'https://www.sanger.ac.uk/group/informatics-support-group/'
}
singularity {
enabled = true
cacheDir = "${baseDir}/singularity"
runOptions = '--bind /lustre --bind /nfs/pathnfs01 --bind /nfs/pathnfs02 --bind /nfs/pathnfs03 --bind /nfs/pathnfs04 --bind /nfs/pathnfs05 --bind /nfs/pathnfs06 --no-home'
}
process{
executor = 'lsf'
queue = 'normal'
errorStrategy = { task.attempt <= 5 ? "retry" : "finish" }
process.maxRetries = 5
}
executor{
name = 'lsf'
perJobMemLimit = true
poolSize = 4
submitRateLimit = '5 sec'
killBatchSize = 50
}
params {
max_memory = 128.GB
max_cpus = 64
max_time = 12.h
}

35
conf/utd_sysbio.config Normal file
View file

@ -0,0 +1,35 @@
//Profile config names for nf-core/configs
params {
config_profile_description = 'University of Texas at Dallas HPC cluster profile provided by nf-core/configs'
config_profile_contact = 'Edmund Miller(@emiller88)'
config_profile_url = 'http://docs.oithpc.utdallas.edu/'
singularity_cache_dir = '/scratch/applied-genomics/singularity'
}
env {
TMPDIR = '/home/$USER/scratch/tmp'
}
singularity {
enabled = true
envWhitelist='SINGULARITY_BINDPATH'
autoMounts = true
cacheDir = params.singularity_cache_dir
}
process {
beforeScript = 'module load singularity/3.4.1'
executor = 'slurm'
queue = { task.memory >= 30.GB && task.cpu <= 16 ? 'normal': 'smallmem' }
}
// Preform work directory cleanup after a successful run
cleanup = true
params {
// TODO Need to initialize this
// igenomes_base = '/scratch/applied-genomics/references/iGenomes/references/'
max_memory = 90.GB
max_cpus = 16
max_time = 96.h
}

5
docs/aws_tower.md Normal file
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@ -0,0 +1,5 @@
# nf-core/configs: AWS Batch with Tower Configuration
To be used when submitting jobs to AWS Batch by using Tower Forge. If you are not using Tower Forge, consider using the profile `awsbatch` where you can directly specify the Batch queue, AWS region and AWS cli path.
This profile defines `awsbatch` as executor, and allows `overwrite` of `trace`, `timeline`, `report` and `dag` to allow resuming pipelines.

18
docs/cambridge.md Normal file
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@ -0,0 +1,18 @@
# nf-core/configs: Cambridge HPC Configuration
All nf-core pipelines have been successfully configured for use on the Cambridge HPC cluster at the [The University of Cambridge](https://www.cam.ac.uk/).
To use, run the pipeline with `-profile cambridge`. This will download and launch the [`cambridge.config`](../conf/cambridge.config) whichhas been pre-configured
with a setup suitable for the Cambridge HPC cluster. Using this profile, either a docker image containing all of the required software will be downloaded,
and converted to a Singularity image or a Singularity image downloaded directly before execution of the pipeline.
The latest version of Nextflow is not installed by default on the Cambridge HPC cluster. You will need to install it into a directory you have write access to.
Follow these instructions from the Nextflow documentation.
- Install Nextflow : [here](https://www.nextflow.io/docs/latest/getstarted.html#)
All of the intermediate files required to run the pipeline will be stored in the `work/` directory. It is recommended to delete this directory after the pipeline
has finished successfully because it can get quite large, and all of the main output files will be saved in the `results/` directory anyway.
> NB: You will need an account to use the Cambridge HPC cluster in order to run the pipeline. If in doubt contact IT.
> NB: Nextflow will need to submit the jobs via SLURM to the Cambridge HPC cluster and as such the commands above will have to be executed on one of the login
nodes. If in doubt contact IT.

14
docs/mpcdf.md
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@ -4,18 +4,16 @@ All nf-core pipelines have been successfully configured for use on the HPCs at [
> :warning: these profiles are not officially supported by the MPCDF. > :warning: these profiles are not officially supported by the MPCDF.
To run Nextflow, the `jdk` module must be loaded. To use the nf-core profile(s), run the pipeline with `-profile <cluster>,mpcdf`. To run Nextflow, the `jdk` module must be loaded. To use the nf-core profile(s), run the pipeline with `-profile mpcdf,<cluster>`.
Currently the following clusters are supported: cobra, raven Currently profiles for the following clusters are supported: `cobra`, `raven`
All profiles use `singularity` as the corresponding containerEngine. To prevent repeatedly downloading the same singularity image for every pipeline run, for all profiles we recommend specifying a cache location in your `~/.bash_profile` with the `$NXF_SINGULARITY_CACHEDIR` bash variable.
>NB: Nextflow will need to submit the jobs via SLURM to the clusters and as such the commands above will have to be executed on one of the head nodes. Check the [MPCDF documentation](https://www.mpcdf.mpg.de/services/computing). >NB: Nextflow will need to submit the jobs via SLURM to the clusters and as such the commands above will have to be executed on one of the head nodes. Check the [MPCDF documentation](https://www.mpcdf.mpg.de/services/computing).
## cobra ## cobra
Cobra does not currently support singularity, therefore the anaconda/module is loaded for each process.
Due to this, we also recommend setting the `$NXF_CONDA_CACHEDIR` to a location of your choice to store all environments (so to prevent nextflow building the environment on every run).
To use: `-profile cobra,mpcdf` To use: `-profile cobra,mpcdf`
Sets the following parameters: Sets the following parameters:
@ -31,10 +29,6 @@ Sets the following parameters:
## raven ## raven
Raven does not currently support singularity, therefore `module load anaconda/3/2020.02` is loaded for each process.
Due to this, we also recommend setting the `$NXF_CONDA_CACHEDIR` to a location of your choice to store all environments (so to prevent nextflow building the environment on every run).
To use: `-profile raven,mpcdf` To use: `-profile raven,mpcdf`
Sets the following parameters: Sets the following parameters:

23
docs/pipeline/rnaseq/utd_sysbio.md Normal file
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@ -0,0 +1,23 @@
# nf-core/configs: UTD sysbio rnaseq specific configuration
Extra specific configuration for rnaseq pipeline
## Usage
To use, run the pipeline with `-profile sysbio`.
This will download and launch the eager specific [`utd_sysbio.config`](../../../conf/pipeline/rnaseq/utd_sysbio.config) which has been pre-configured with a setup suitable for the shh cluster.
Example: `nextflow run nf-core/rnaseq -profile sysbio`
## rnaseq specific configurations for UTD sysbio
Specific configurations for UTD Sysbio has been made for rnaseq.
### General profiles
<!-- TODO -->
### Contextual profiles
<!-- TODO -->

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@ -0,0 +1,54 @@
# nf-core/configs: Wellcome Sanger Institute Configuration
To use, run the pipeline with `-profile sanger`. This will download and launch the [`sanger.config`](../conf/sanger.config) which has been
pre-configured with a setup suitable for the Wellcome Sanger Institute LSF cluster.
Using this profile, either a docker image containing all of the required software will be downloaded, and converted to a Singularity image or
a Singularity image downloaded directly before execution of the pipeline.
## Running the workflow on the Wellcome Sanger Institute cluster
The latest version of Nextflow is not installed by default on the cluster. You will need to install it into a directory you have write access to
- Install Nextflow : [here](https://www.nextflow.io/docs/latest/getstarted.html#)
A recommended place to move the `nextflow` executable to is `~/bin` so that it's in the `PATH`.
Nextflow manages each process as a separate job that is submitted to the cluster by using the `bsub` command.
Since the Nextflow pipeline will submit individual jobs for each process to the cluster and dependencies will be provided bu Singularity images you shoudl make sure that your account has access to the Singularity binary by adding these lines to your `.bashrc` file
```bash
[[ -f /software/pathogen/farm5 ]] && module load ISG/singularity
```
Nextflow shouldn't run directly on the submission node but on a compute node.
To do so make a shell script with a similar structure to the following code and submit with `bsub < $PWD/my_script.sh`
```bash
#!/bin/bash
#BSUB -o /path/to/a/log/dir/%J.o
#BSUB -e /path/to/a/log/dir//%J.e
#BSUB -M 8000
#BSUB -q long
#BSUB -n 4
export HTTP_PROXY='http://wwwcache.sanger.ac.uk:3128'
export HTTPS_PROXY='http://wwwcache.sanger.ac.uk:3128'
export NXF_ANSI_LOG=false
export NXF_OPTS="-Xms8G -Xmx8G -Dnxf.pool.maxThreads=2000"
export NXF_VER=21.04.0-edge
nextflow run \
/path/to/nf-core/pipeline/main.nf \
-w /path/to/some/dir/work \
-profile sanger \
-c my_specific.config \
-qs 1000 \
-resume
## clean up on exit 0 - delete this if you want to keep the work dir
status=$?
if [[ $status -eq 0 ]]; then
rm -r /path/to/some/dir/work
fi
```

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@ -8,42 +8,47 @@ We have a Slack channel dedicated to UPPMAX users on the nf-core Slack: [https:/
## Using the UPPMAX config profile ## Using the UPPMAX config profile
Before running the pipeline you will need to either install `Nextflow` or load it using the environment module system (this can be done with e.g. `module load bioinfo-tools Nextflow/<VERSION>` where `VERSION` is e.g. `20.10`).
To use, run the pipeline with `-profile uppmax` (one hyphen). To use, run the pipeline with `-profile uppmax` (one hyphen).
This will download and launch the [`uppmax.config`](../conf/uppmax.config) which has been pre-configured with a setup suitable for the UPPMAX servers. This will download and launch the [`uppmax.config`](../conf/uppmax.config) which has been pre-configured with a setup suitable for the UPPMAX servers.
Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline. It will enable `Nextflow` to manage the pipeline jobs via the `Slurm` job scheduler.
Using this profile, `Docker` image(s) containing required software(s) will be downloaded, and converted to `Singularity` image(s) if needed before execution of the pipeline.
Recent version of `Nextflow` also support the environment variable `NXF_SINGULARITY_CACHEDIR` which can be used to supply images.
Images for some `nf-core` pipelines are available under `/sw/data/ToolBox/nf-core/` and those can be used by `NXF_SINGULARITY_CACHEDIR=/sw/data/ToolBox/nf-core/; export NXF_SINGULARITY_CACHEDIR`.
In addition to this config profile, you will also need to specify an UPPMAX project id. In addition to this config profile, you will also need to specify an UPPMAX project id.
You can do this with the `--project` flag (two hyphens) when launching nextflow. For example: You can do this with the `--project` flag (two hyphens) when launching `Nextflow`.
For example:
```bash ```bash
nextflow run nf-core/PIPELINE -profile uppmax --project snic2018-1-234 # ..rest of pipeline flags # Launch a nf-core pipeline with the uppmax profile for the project id snic2018-1-234
$ nextflow run nf-core/<PIPELINE> -profile uppmax --project snic2018-1-234 [...]
``` ```
> NB: If you're not sure what your UPPMAX project ID is, try running `groups` or checking SUPR. > NB: If you're not sure what your UPPMAX project ID is, try running `groups` or checking SUPR.
Before running the pipeline you will need to either install Nextflow or load it using the environment module system. Just run `Nextflow` on a login node and it will handle everything else.
This config enables Nextflow to manage the pipeline jobs via the Slurm job scheduler and using Singularity for software management. Remember to use `-bg` to launch `Nextflow` in the background, so that the pipeline doesn't exit if you leave your terminal session.
Alternatively, you can also launch `Nextflow` in a `screen` or a `tmux` session.
Just run Nextflow on a login node and it will handle everything else. ## Using AWS iGenomes references
Remember to use `-bg` to launch Nextflow in the background, so that the pipeline doesn't exit if you leave your terminal session. A local copy of the `AWS iGenomes` resource has been made available on all UPPMAX clusters so you should be able to run the pipeline against any reference available in the `conf/igenomes.config`.
## Using iGenomes references
A local copy of the iGenomes resource has been made available on all UPPMAX clusters so you should be able to run the pipeline against any reference available in the `igenomes.config`.
You can do this by simply using the `--genome <GENOME_ID>` parameter. You can do this by simply using the `--genome <GENOME_ID>` parameter.
## Getting more memory ## Getting more memory
If your nf-core pipeline run is running out of memory, you can run on a fat node with more memory using the following nextflow flags: If your `nf-core` pipeline run is running out of memory, you can run on a fat node with more memory using the following `Nextflow` flags:
```bash ```bash
--clusterOptions "-C mem256GB" --max_memory "256GB" --clusterOptions "-C mem256GB -p node" --max_memory "256GB"
``` ```
This raises the ceiling of available memory from the default of `128.GB` to `256.GB`. This raises the ceiling of available memory from the default of `128.GB` to `256.GB`.
Rackham has nodes with 128GB, 256GB and 1TB memory available. `rackham` has nodes with 128GB, 256GB and 1TB memory available.
Note that each job will still start with the same request as normal, but restarted attempts with larger requests will be able to request greater amounts of memory. Note that each job will still start with the same request as normal, but restarted attempts with larger requests will be able to request greater amounts of memory.
@ -53,15 +58,15 @@ All jobs will be submitted to fat nodes using this method, so it's only for use
The UPPMAX nf-core configuration profile uses the `hostname` of the active environment to automatically apply the following resource limits: The UPPMAX nf-core configuration profile uses the `hostname` of the active environment to automatically apply the following resource limits:
* `rackham`
* cpus available: 20 cpus
* memory available: 125 GB
* `bianca` * `bianca`
* cpus available: 16 cpus * cpus available: 16 cpus
* memory available: 109 GB * memory available: 109 GB
* `irma` * `irma`
* cpus available: 16 cpus * cpus available: 16 cpus
* memory available: 250 GB * memory available: 250 GB
* `rackham`
* cpus available: 20 cpus
* memory available: 125 GB
## Development config ## Development config
@ -74,14 +79,197 @@ It is not suitable for use with real data.
To use it, submit with `-profile uppmax,devel`. To use it, submit with `-profile uppmax,devel`.
## Running on Bianca ## Running on bianca
For security reasons, there is no internet access on Bianca so you can't download from or upload files to the cluster directly. Before running a nf-core pipeline on Bianca you will first have to download the pipeline and singularity images needed elsewhere and transfer them via the wharf area to your Bianca project. > :warning: For more information, please follow the following guides:
>
> * [UPPMAX `bianca` user guide](http://uppmax.uu.se/support/user-guides/bianca-user-guide/).
> * [nf-core guide for running offline](https://nf-co.re/usage/offline)
> * [nf-core `tools` guide for downloading pipelines for offline use](https://nf-co.re/tools#downloading-pipelines-for-offline-use).
> * [UPPMAX `Singularity` guide](https://www.uppmax.uu.se/support-sv/user-guides/singularity-user-guide/).
You can follow the guide for downloading pipelines [for offline use](https://nf-co.re/tools#downloading-pipelines-for-offline-use). Note that you will have to download the singularity images as well. For security reasons, there is no internet access on `bianca` so you can't download from or upload files to the cluster directly.
Before running a nf-core pipeline on `bianca` you will first have to download the pipeline and singularity images needed elsewhere and transfer them via the `wharf` area to your own `bianca` project.
Next transfer the pipeline and the singularity images to your project. Before running the pipeline you will have to indicate to nextflow where the singularity images are located by setting `NXF_SINGULARITY_CACHEDIR` : In this guide, we use `rackham` to download and transfer files to the `wharf` area, but it can also be done on your own computer.
If you use `rackham` to download the pipeline and the singularity containers, we recommend using an interactive session (cf [interactive guide](https://www.uppmax.uu.se/support/faq/running-jobs-faq/how-can-i-run-interactively-on-a-compute-node/)), which is what we do in the following guide.
`export NXF_SINGULARITY_CACHEDIR=Your_Location_For_The_Singularity_directory/.` ### Download and install Nextflow
You should now be able to run your nf-core pipeline on bianca. You can use the `Nextflow` UPPMAX provided `module`, but if necessary, you can also download a more recent version.
```bash
# Connect to bianca
$ ssh -A <USER>-<BIANCA_PROJECT>@bianca.uppmax.uu.se
# See the available versions for the module
module spider Nextflow
# Load a specific version of the Nextflow module
module load bioinfo-tools Nextflow/<VERSION>`
```
```bash
# Connect to rackham
$ ssh -X <USER>@rackham.uppmax.uu.se
# Or stay in your terminal
# Download the nextflow-all bundle
$ wget https://github.com/nextflow-io/nextflow/releases/download/v<NEXTFLOW_VERSION>/nextflow-<NEXTFLOW_VERSION>-all
# Connect to the wharf area using sftp
$ sftp <USER>-<BIANCA_PROJECT>@bianca-sftp.uppmax.uu.se:<USER>-<BIANCA_PROJECT>
# Transfer nextflow to the wharf area
sftp> put nextflow-<NEXTFLOW_VERSION>-all .
# Exit sftp
$ exit
# Connect to bianca
$ ssh -A <USER>-<BIANCA_PROJECT>@bianca.uppmax.uu.se
# Go to your project
$ cd /castor/project/proj_nobackup
# Make folder for Nextflow
$ mkdir tools
$ mkdir tools/nextflow
# Move Nextflow from the wharf area to its directory
$ mv /castor/project/proj_nobackup/wharf/<USER>/<USER>-<BIANCA_PROJECT>/nextflow-<NEXTFLOW_VERSION>-all /castor/project/proj_nobackup/tools/nextflow
# Establish permission
$ chmod a+x /castor/project/proj_nobackup/tools/nextflow/nextflow-<NEXTFLOW_VERSION>-all
# If you want other people to use it
# Be sure that your group has rights to the directory as well
$ chown -R .<BIANCA_PROJECT> /castor/project/proj_nobackup/tools/nextflow/nextflow-<NEXTFLOW_VERSION>-all
# Make a link to it
$ ln -s /castor/project/proj_nobackup/tools/nextflow/nextflow-<NEXTFLOW_VERSION>-all /castor/project/proj_nobackup/tools/nextflow/nextflow
# And every time you're launching Nextflow, don't forget to export the following ENV variables
# Or add them to your .bashrc file
$ export NXF_HOME=/castor/project/proj/nobackup/tools/nextflow/
$ export PATH=${NXF_HOME}:${PATH}
$ export NXF_TEMP=$SNIC_TMP
$ export NXF_LAUNCHER=$SNIC_TMP
$ export NXF_SINGULARITY_CACHEDIR=/castor/project/proj_nobackup/singularity-images
```
### Install nf-core tools
You can use the `nf-core` UPPMAX provided `module`, but if necessary, you can also download a more recent version.
```bash
# Connect to rackham
$ ssh -X <USER>@rackham.uppmax.uu.se
# See the available versions for the module
module spider nf-core
# Load a specific version of the nf-core module
module load bioinfo-tools nf-core/<VERSION>`
```
```bash
# Connect to rackham
$ ssh -X <USER>@rackham.uppmax.uu.se
# Or stay in your terminal
# Install the latest pip version
$ pip3 install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev --user
```
### Download and transfer a nf-core pipeline
```bash
# Connect to rackham
$ ssh -X <USER>@rackham.uppmax.uu.se
# Or stay in your terminal
# Open an interactive session (if you are on rackham)
$ interactive <rackham_project>
# Download a pipeline with the singularity images
$ nf-core download <PIPELINE> -r <PIPELINE_VERSION> -s --compress none
# If necessary, extra singularity images can be download separately
# For example, if you downloaded nf-core/sarek, you will need extra images for annotation
# Here we download the nf-core/sarek GRCh38 specific images
$ singularity pull --name nfcore-sareksnpeff-2.7.GRCh38.img docker://nfcore/sareksnpeff:2.7.GRCh38
$ singularity pull --name nfcore-sarekvep-2.7.GRCh38.img docker://nfcore/sarekvep:2.7.GRCh38
# Which can then be moved into the nf-core/sarek download folder
$ mv *.img nf-core-sarek-2.7/singularity-images/.
# Connect to the wharf area using sftp
$ sftp <USER>-<BIANCA_PROJECT>@bianca-sftp.uppmax.uu.se:<USER>-<BIANCA_PROJECT>
# Transfer <PIPELINE> folder from rackham to the wharf area
sftp> put -r nf-core-<PIPELINE>-<PIPELINE_VERSION> .
# The archives will be in the wharf folder in your user home on your bianca project
# Connect to bianca
$ ssh -A <USER>-<BIANCA_PROJECT>@bianca.uppmax.uu.se
# Go to your project
$ cd /castor/project/proj_nobackup
# Make and go into a nf-core directory (where you will store all nf-core pipelines')
$ mkdir nf-core
$ cd nf-core
# Move the folder from the wharf area to the project
$ cp /castor/project/proj_nobackup/wharf/<USER>/<USER>-<BIANCA_PROJECT>/nf-core-<PIPELINE>-<PIPELINE_VERSION> .
# If you want other people to use it,
# Be sure that your group has rights to the directory as well
$ chown -R .<BIANCA_PROJECT> nf-core-<PIPELINE>-<PIPELINE_VERSION>
# Make a symbolic link to the extracted repository
$ ln -s nf-core-<PIPELINE>-<PIPELINE_VERSION> nf-core-<PIPELINE>-default
```
The principle is to have every member of your project to be able to use the same `nf-core/<PIPELINE>` version at the same time.
So every member of the project who wants to use `nf-core/<PIPELINE>` will need to do:
```bash
# Connect to bianca
$ ssh -A <USER>-<BIANCA_PROJECT>@bianca.uppmax.uu.se
# Go to your user directory
$ cd /home/<USER>
# Make a symbolic link to the default nf-core/<PIPELINE>
$ ln -s /castor/project/proj_nobackup/nf-core/nf-core-<PIPELINE>-default nf-core-<PIPELINE>
```
And then `nf-core/<PIPELINE>` can be used with:
```bash
# run <PIPELINE> on bianca
$ nextflow run ~/<PIPELINE> -profile uppmax --project <BIANCA_PROJECT> --genome <GENOME_ASSEMBLY> ...
```
## Update a pipeline
To update, repeat the same steps as for installing and update the link.
```bash
# Connect to bianca (Connect to rackham first if needed)
$ ssh -A <USER>-<BIANCA_PROJECT>@bianca.uppmax.uu.se
# Go to the nf-core directory in your project
$ cd /castor/project/proj_nobackup/nf-core
# Remove link
$ unlink nf-core-<PIPELINE>-default
# Link to new nf-core/<PIPELINE> version
$ ln -s nf-core-<PIPELINE>-<PIPELINE_VERSION> nf-core-<PIPELINE>-default
```
You can for example keep a `nf-core-<PIPELINE>-default` version that you are sure is working, an make a link for a `nf-core-<PIPELINE>-testing` or `nf-core-<PIPELINE>-development`.

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@ -0,0 +1,16 @@
# nf-core/configs: UTD Sysbio Configuration
All nf-core pipelines have been successfully configured for use on the Sysbio HPC cluster at the [The Univeristy of Texas at Dallas](https://www.utdallas.edu/).
To use, run the pipeline with `-profile utd_sysbio`. This will download and launch the [`utd_sysbio.config`](../conf/utd_sysbio.config) which has been pre-configured with a setup suitable for the Sysbio HPC cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.
Before running the pipeline you will need to load Singularity using the environment module system on Sysbio. You can do this by issuing the commands below:
```bash
## Singularity environment modules
module purge
module load singularity
```
>NB: You will need an account to use the HPC cluster on Sysbio in order to run the pipeline. If in doubt contact OIT.
>NB: Nextflow will need to submit the jobs via SLURM to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact OIT.

6
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@ -12,6 +12,7 @@
profiles { profiles {
abims { includeConfig "${params.custom_config_base}/conf/abims.config" } abims { includeConfig "${params.custom_config_base}/conf/abims.config" }
awsbatch { includeConfig "${params.custom_config_base}/conf/awsbatch.config" } awsbatch { includeConfig "${params.custom_config_base}/conf/awsbatch.config" }
aws_tower { includeConfig "${params.custom_config_base}/conf/aws_tower.config" }
bi { includeConfig "${params.custom_config_base}/conf/bi.config" } bi { includeConfig "${params.custom_config_base}/conf/bi.config" }
bigpurple { includeConfig "${params.custom_config_base}/conf/bigpurple.config" } bigpurple { includeConfig "${params.custom_config_base}/conf/bigpurple.config" }
binac { includeConfig "${params.custom_config_base}/conf/binac.config" } binac { includeConfig "${params.custom_config_base}/conf/binac.config" }
@ -42,11 +43,13 @@ profiles {
pasteur { includeConfig "${params.custom_config_base}/conf/pasteur.config" } pasteur { includeConfig "${params.custom_config_base}/conf/pasteur.config" }
phoenix { includeConfig "${params.custom_config_base}/conf/phoenix.config" } phoenix { includeConfig "${params.custom_config_base}/conf/phoenix.config" }
prince { includeConfig "${params.custom_config_base}/conf/prince.config" } prince { includeConfig "${params.custom_config_base}/conf/prince.config" }
sanger { includeConfig "${params.custom_config_base}/conf/sanger.config"}
seg_globe { includeConfig "${params.custom_config_base}/conf/seg_globe.config"} seg_globe { includeConfig "${params.custom_config_base}/conf/seg_globe.config"}
shh { includeConfig "${params.custom_config_base}/conf/shh.config" } shh { includeConfig "${params.custom_config_base}/conf/shh.config" }
uct_hpc { includeConfig "${params.custom_config_base}/conf/uct_hpc.config" } uct_hpc { includeConfig "${params.custom_config_base}/conf/uct_hpc.config" }
uppmax { includeConfig "${params.custom_config_base}/conf/uppmax.config" } uppmax { includeConfig "${params.custom_config_base}/conf/uppmax.config" }
utd_ganymede { includeConfig "${params.custom_config_base}/conf/utd_ganymede.config" } utd_ganymede { includeConfig "${params.custom_config_base}/conf/utd_ganymede.config" }
utd_sysbio { includeConfig "${params.custom_config_base}/conf/utd_sysbio.config" }
uzh { includeConfig "${params.custom_config_base}/conf/uzh.config" } uzh { includeConfig "${params.custom_config_base}/conf/uzh.config" }
jax { includeConfig "${params.custom_config_base}/conf/jax.config" } jax { includeConfig "${params.custom_config_base}/conf/jax.config" }
} }
@ -67,6 +70,7 @@ params {
genotoul: ['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'], genotoul: ['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'],
genouest: ['.genouest.org'], genouest: ['.genouest.org'],
uppmax: ['.uppmax.uu.se'], uppmax: ['.uppmax.uu.se'],
utd_ganymede: ['ganymede.utdallas.edu'] utd_ganymede: ['ganymede.utdallas.edu'],
utd_sysbio: ['sysbio.utdallas.edu']
] ]
} }

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@ -10,4 +10,5 @@
profiles { profiles {
eddie { includeConfig "${params.custom_config_base}/conf/pipeline/rnaseq/eddie.config" } eddie { includeConfig "${params.custom_config_base}/conf/pipeline/rnaseq/eddie.config" }
utd_sysbio { includeConfig "${params.custom_config_base}/conf/pipeline/rnaseq/utd_sysbio.config" }
} }

2
pipeline/sarek.config
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@ -12,5 +12,7 @@ profiles {
munin { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/munin.config" } munin { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/munin.config" }
uppmax { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/uppmax.config" } uppmax { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/uppmax.config" }
icr_davros { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/icr_davros.config" } icr_davros { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/icr_davros.config" }
cfc { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/cfc.config" }
cfc_dev { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/cfc.config" }
eddie { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/eddie.config" } eddie { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/eddie.config" }
} }