mirror of
https://github.com/MillironX/nf-configs.git
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commit
0da2c57784
12 changed files with 105 additions and 58 deletions
43
.github/workflows/main.yml
vendored
43
.github/workflows/main.yml
vendored
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@ -16,7 +16,48 @@ jobs:
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needs: test_all_profiles
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strategy:
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matrix:
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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', 'kraken', 'mpcdf', 'munin', 'oist', 'pasteur', 'phoenix', 'prince', 'sanger', 'seg_globe', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'utd_sysbio', 'uzh']
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profile:
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- 'abims'
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- 'awsbatch'
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- 'aws_tower'
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- 'bi'
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- 'bigpurple'
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- 'binac'
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- 'biohpc_gen'
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- 'cbe'
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- 'ccga_dx'
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- 'ccga_med'
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- 'cfc'
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- 'cfc_dev'
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- 'crick'
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- 'denbi_qbic'
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- 'ebc'
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- 'eddie'
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- 'eva'
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- 'genotoul'
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- 'genouest'
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- 'gis'
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- 'google'
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- 'hebbe'
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- 'icr_davros'
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- 'ifb_core'
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- 'imperial'
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- 'imperial_mb'
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- 'jax'
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- 'mpcdf'
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- 'munin'
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- 'oist'
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- 'pasteur'
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- 'phoenix'
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- 'prince'
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- 'sanger'
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- 'seg_globe'
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- 'shh'
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- 'uct_hpc'
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- 'uppmax'
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- 'utd_ganymede'
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- 'utd_sysbio'
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- 'uzh'
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steps:
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- uses: actions/checkout@v1
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- name: Install Nextflow
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@ -96,6 +96,7 @@ Currently documentation is available for the following systems:
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* [ABIMS](docs/abims.md)
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* [AWSBATCH](docs/awsbatch.md)
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* [AWS_TOWER](docs/aws_tower.md)
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* [BIGPURPLE](docs/bigpurple.md)
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* [BI](docs/bi.md)
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* [BINAC](docs/binac.md)
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@ -117,7 +118,6 @@ Currently documentation is available for the following systems:
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* [HEBBE](docs/hebbe.md)
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* [ICR_DAVROS](docs/icr_davros.md)
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* [JAX](docs/jax.md)
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* [KRAKEN](docs/kraken.md)
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* [MPCDF](docs/mpcdf.md)
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* [MUNIN](docs/munin.md)
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* [OIST](docs/oist.md)
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@ -10,6 +10,7 @@ import os
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import sys
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import argparse
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import re
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import yaml
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############################################
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############################################
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@ -51,19 +52,22 @@ def check_config(Config, Github):
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### Ignore these profiles
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ignore_me = ['czbiohub_aws']
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tests.update(ignore_me)
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with open(Github, 'r') as ghfile:
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for line in ghfile:
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if re.search('profile: ', line):
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line = line.replace('\'','').replace('[','').replace(']','').replace('\n','')
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profiles = line.split(':')[1].split(',')
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for p in profiles:
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tests.add(p.strip())
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# parse yaml GitHub actions file
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try:
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with open(Github, 'r') as ghfile:
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wf = yaml.safe_load(ghfile)
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profile_list = wf["jobs"]["profile_test"]["strategy"]["matrix"]["profile"]
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except Exception as e:
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print("Could not parse yaml file: {}, {}".format(Github, e))
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sys.exit(1)
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# Add profiles to test
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for profile in profile_list:
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tests.add(profile.strip())
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###Check if sets are equal
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if tests == config_profiles:
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sys.exit(0)
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else:
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#Maybe report what is missing here too
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try:
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assert tests == config_profiles
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except (AssertionError):
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print("Tests don't seem to test these profiles properly. Please check whether you added the profile to the Github Actions testing YAML.\n")
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print(config_profiles.symmetric_difference(tests))
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sys.exit(1)
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21
conf/aws_tower.config
Normal file
21
conf/aws_tower.config
Normal file
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@ -0,0 +1,21 @@
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//Nextflow config file for running on AWS batch
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params {
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config_profile_description = 'AWS Batch with Tower Profile'
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config_profile_contact = 'Gisela Gabernet (@ggabernet)'
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config_profile_url = 'https://aws.amazon.com/batch/'
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}
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timeline {
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overwrite = true
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}
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report {
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overwrite = true
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}
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trace {
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overwrite = true
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}
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dag {
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overwrite = true
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}
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process.executor = 'awsbatch'
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@ -12,7 +12,6 @@ singularity {
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process {
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executor = 'slurm'
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beforeScript = 'module load devel/singularity/3.4.2'
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queue = { task.memory > 60.GB || task.cpus > 20 ? 'qbic' : 'compute' }
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scratch = 'true'
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}
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@ -10,7 +10,6 @@ singularity {
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}
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process {
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beforeScript = 'module load devel/singularity/3.4.2'
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executor = 'slurm'
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queue = { task.memory > 60.GB || task.cpus > 20 ? 'qbic' : 'compute' }
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scratch = 'true'
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@ -1,24 +0,0 @@
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//Profile config names for nf-core/configs
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params {
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config_profile_name = 'KRAKEN'
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config_profile_description = 'Jenkins cluster provided by nf-core/configs.'
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config_profile_contact = 'Maxime Garcia or Johannes Alneberg'
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config_profile_url = 'kraken.dyn.scilifelab.se'
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}
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process {
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executor = 'local'
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}
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docker {
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enabled = true
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mountFlags = 'z'
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fixOwnership = true
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}
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params {
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max_memory = 60.GB
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max_cpus = 16
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max_time = 72.h
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igenomes_base = '/share/igenomes/'
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}
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@ -69,7 +69,7 @@ process {
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}
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withName: adapter_removal {
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 4)}G,virtual_free=${(task.memory.toGiga() * 4)}G" }
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}
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withName: dedup {
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@ -97,7 +97,7 @@ process {
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}
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withName: mtnucratio {
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
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clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 4)}G,virtual_free=${(task.memory.toGiga() * 4)}G" }
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}
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withName: vcf2genome {
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@ -20,21 +20,33 @@ params {
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primer_sets {
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artic {
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'1' {
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fasta = 'https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V1/nCoV-2019.reference.fasta'
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fasta = 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V1/nCoV-2019.reference.fasta'
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gff = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz'
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primer_bed = 'https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V1/nCoV-2019.primer.bed'
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primer_bed = 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V1/nCoV-2019.primer.bed'
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scheme = 'nCoV-2019'
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}
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'2' {
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fasta = 'https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V2/nCoV-2019.reference.fasta'
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fasta = 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V2/nCoV-2019.reference.fasta'
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gff = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz'
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primer_bed = 'https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V2/nCoV-2019.primer.bed'
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primer_bed = 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V2/nCoV-2019.primer.bed'
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scheme = 'nCoV-2019'
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}
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'3' {
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fasta = 'https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V3/nCoV-2019.reference.fasta'
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fasta = 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V3/nCoV-2019.reference.fasta'
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gff = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz'
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primer_bed = 'https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V3/nCoV-2019.primer.bed'
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primer_bed = 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V3/nCoV-2019.primer.bed'
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scheme = 'nCoV-2019'
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}
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'4' {
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fasta = 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V4/SARS-CoV-2.reference.fasta'
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gff = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz'
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primer_bed = 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V4/SARS-CoV-2.scheme.bed'
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scheme = 'SARS-CoV-2'
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}
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'1200' {
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fasta = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/primer_schemes/artic/nCoV-2019/V1200/nCoV-2019.reference.fasta'
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gff = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz'
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primer_bed = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/primer_schemes/artic/nCoV-2019/V1200/nCoV-2019.bed'
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scheme = 'nCoV-2019'
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}
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}
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5
docs/aws_tower.md
Normal file
5
docs/aws_tower.md
Normal file
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@ -0,0 +1,5 @@
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# nf-core/configs: AWS Batch with Tower Configuration
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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.
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This profile defines `awsbatch` as executor, and allows `overwrite` of `trace`, `timeline`, `report` and `dag` to allow resuming pipelines.
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@ -1,10 +0,0 @@
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# nf-core/configs: KRAKEN Configuration
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This profile can be **only** combined with `jenkins.config`. It is used for
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testing pipeline with real data on **in-house** cluster located at SciLifeLab.
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To use, run the pipeline with `-profile kraken`. This will download and launch
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the [`kraken.config`](../conf/kraken.config) which has been pre-configured to
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test the pipeline using `docker` by default.
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Example: `nextflow run -profile kraken,jenkins`
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@ -12,6 +12,7 @@
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profiles {
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abims { includeConfig "${params.custom_config_base}/conf/abims.config" }
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awsbatch { includeConfig "${params.custom_config_base}/conf/awsbatch.config" }
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aws_tower { includeConfig "${params.custom_config_base}/conf/aws_tower.config" }
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bi { includeConfig "${params.custom_config_base}/conf/bi.config" }
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bigpurple { includeConfig "${params.custom_config_base}/conf/bigpurple.config" }
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binac { includeConfig "${params.custom_config_base}/conf/binac.config" }
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@ -36,7 +37,6 @@ profiles {
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genouest { includeConfig "${params.custom_config_base}/conf/genouest.config" }
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gis { includeConfig "${params.custom_config_base}/conf/gis.config" }
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hebbe { includeConfig "${params.custom_config_base}/conf/hebbe.config" }
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kraken { includeConfig "${params.custom_config_base}/conf/kraken.config" }
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mpcdf { includeConfig "${params.custom_config_base}/conf/mpcdf.config" }
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munin { includeConfig "${params.custom_config_base}/conf/munin.config" }
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oist { includeConfig "${params.custom_config_base}/conf/oist.config" }
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