From 3918e0aa9dc64183da65d38d672b8103aac583be Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Tue, 13 Apr 2021 15:14:14 +0200 Subject: [PATCH 01/13] feat: remove kraken profile --- .github/workflows/main.yml | 2 +- README.md | 1 - conf/kraken.config | 24 ------------------------ docs/kraken.md | 10 ---------- nfcore_custom.config | 1 - 5 files changed, 1 insertion(+), 37 deletions(-) delete mode 100644 conf/kraken.config delete mode 100644 docs/kraken.md diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index cd2170c..a2bcf8e 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -16,7 +16,7 @@ jobs: needs: test_all_profiles strategy: 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', 'kraken', 'mpcdf', 'munin', 'oist', 'pasteur', 'phoenix', 'prince', 'seg_globe', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh'] + 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'] steps: - uses: actions/checkout@v1 - name: Install Nextflow diff --git a/README.md b/README.md index 7637725..3e51bb5 100644 --- a/README.md +++ b/README.md @@ -116,7 +116,6 @@ Currently documentation is available for the following systems: * [HEBBE](docs/hebbe.md) * [ICR_DAVROS](docs/icr_davros.md) * [JAX](docs/jax.md) -* [KRAKEN](docs/kraken.md) * [MPCDF](docs/mpcdf.md) * [MUNIN](docs/munin.md) * [OIST](docs/oist.md) diff --git a/conf/kraken.config b/conf/kraken.config deleted file mode 100644 index 59417e9..0000000 --- a/conf/kraken.config +++ /dev/null @@ -1,24 +0,0 @@ -//Profile config names for nf-core/configs -params { - config_profile_name = 'KRAKEN' - config_profile_description = 'Jenkins cluster provided by nf-core/configs.' - config_profile_contact = 'Maxime Garcia or Johannes Alneberg' - config_profile_url = 'kraken.dyn.scilifelab.se' -} - -process { - executor = 'local' -} - -docker { - enabled = true - mountFlags = 'z' - fixOwnership = true -} - -params { - max_memory = 60.GB - max_cpus = 16 - max_time = 72.h - igenomes_base = '/share/igenomes/' -} diff --git a/docs/kraken.md b/docs/kraken.md deleted file mode 100644 index 9426087..0000000 --- a/docs/kraken.md +++ /dev/null @@ -1,10 +0,0 @@ -# nf-core/configs: KRAKEN Configuration - -This profile can be **only** combined with `jenkins.config`. It is used for -testing pipeline with real data on **in-house** cluster located at SciLifeLab. - -To use, run the pipeline with `-profile kraken`. This will download and launch -the [`kraken.config`](../conf/kraken.config) which has been pre-configured to -test the pipeline using `docker` by default. - -Example: `nextflow run -profile kraken,jenkins` diff --git a/nfcore_custom.config b/nfcore_custom.config index 88d7a62..f208d1b 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -36,7 +36,6 @@ profiles { genouest { includeConfig "${params.custom_config_base}/conf/genouest.config" } gis { includeConfig "${params.custom_config_base}/conf/gis.config" } hebbe { includeConfig "${params.custom_config_base}/conf/hebbe.config" } - kraken { includeConfig "${params.custom_config_base}/conf/kraken.config" } mpcdf { includeConfig "${params.custom_config_base}/conf/mpcdf.config" } munin { includeConfig "${params.custom_config_base}/conf/munin.config" } oist { includeConfig "${params.custom_config_base}/conf/oist.config" } From 93cfc48afd7bf36c9df939847f5275ff31fcec0d Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Mon, 21 Jun 2021 21:04:16 +0100 Subject: [PATCH 02/13] Add ARTIC v4 primers to genomes config --- conf/pipeline/viralrecon/genomes.config | 18 ++++++++++++------ 1 file changed, 12 insertions(+), 6 deletions(-) diff --git a/conf/pipeline/viralrecon/genomes.config b/conf/pipeline/viralrecon/genomes.config index 27f7162..e7b1c2f 100644 --- a/conf/pipeline/viralrecon/genomes.config +++ b/conf/pipeline/viralrecon/genomes.config @@ -20,23 +20,29 @@ params { primer_sets { artic { '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' - 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' } '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' - 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' } '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' - 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' + } } } } From 5f4b915ae8a99f419edf2e4a16dbb5a3f7b52008 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 29 Jun 2021 11:31:00 +0200 Subject: [PATCH 03/13] Update eva.config --- conf/pipeline/eager/eva.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config index 0b7bbae..87d679e 100644 --- a/conf/pipeline/eager/eva.config +++ b/conf/pipeline/eager/eva.config @@ -69,7 +69,7 @@ process { } 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=${(task.memory.toGiga() * 4)}G" } } withName: dedup { @@ -97,7 +97,7 @@ process { } withName: mtnucratio { - clusterOptions = { "-S /bin/bash -l h_vmem=${(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 { From d59d099fe815eb4826b8da9d5aadae4c63fc5a7c Mon Sep 17 00:00:00 2001 From: ggabernet Date: Thu, 1 Jul 2021 10:52:54 +0200 Subject: [PATCH 04/13] remove load module in cfc configs --- conf/cfc.config | 1 - conf/cfc_dev.config | 1 - 2 files changed, 2 deletions(-) diff --git a/conf/cfc.config b/conf/cfc.config index 15d4a47..1948e14 100644 --- a/conf/cfc.config +++ b/conf/cfc.config @@ -12,7 +12,6 @@ singularity { process { executor = 'slurm' - beforeScript = 'module load devel/singularity/3.4.2' queue = { task.memory > 60.GB || task.cpus > 20 ? 'qbic' : 'compute' } scratch = 'true' } diff --git a/conf/cfc_dev.config b/conf/cfc_dev.config index 6190314..1d61baf 100644 --- a/conf/cfc_dev.config +++ b/conf/cfc_dev.config @@ -10,7 +10,6 @@ singularity { } process { - beforeScript = 'module load devel/singularity/3.4.2' executor = 'slurm' queue = { task.memory > 60.GB || task.cpus > 20 ? 'qbic' : 'compute' } scratch = 'true' From ee2e8392ab4c9b13ac2a6d4ee1dd9164527c07a5 Mon Sep 17 00:00:00 2001 From: ggabernet Date: Sat, 3 Jul 2021 12:17:21 +0200 Subject: [PATCH 05/13] add aws_tower profile --- README.md | 1 + conf/aws_tower.config | 21 +++++++++++++++++++++ docs/aws_tower.md | 5 +++++ nfcore_custom.config | 1 + 4 files changed, 28 insertions(+) create mode 100644 conf/aws_tower.config create mode 100644 docs/aws_tower.md diff --git a/README.md b/README.md index 6daff2a..dbe220e 100644 --- a/README.md +++ b/README.md @@ -96,6 +96,7 @@ Currently documentation is available for the following systems: * [ABIMS](docs/abims.md) * [AWSBATCH](docs/awsbatch.md) +* [AWS_TOWER](docs/aws_tower.md) * [BIGPURPLE](docs/bigpurple.md) * [BI](docs/bi.md) * [BINAC](docs/binac.md) diff --git a/conf/aws_tower.config b/conf/aws_tower.config new file mode 100644 index 0000000..ab7786d --- /dev/null +++ b/conf/aws_tower.config @@ -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' diff --git a/docs/aws_tower.md b/docs/aws_tower.md new file mode 100644 index 0000000..6274bf3 --- /dev/null +++ b/docs/aws_tower.md @@ -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. diff --git a/nfcore_custom.config b/nfcore_custom.config index 9b4fbda..237bc30 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -12,6 +12,7 @@ profiles { abims { includeConfig "${params.custom_config_base}/conf/abims.config" } awsbatch { includeConfig "${params.custom_config_base}/conf/awsbatch.config" } + aws_tower { includeConfig "${params.custom_config_base}/conf/aws_tower.config" } bi { includeConfig "${params.custom_config_base}/conf/bi.config" } bigpurple { includeConfig "${params.custom_config_base}/conf/bigpurple.config" } binac { includeConfig "${params.custom_config_base}/conf/binac.config" } From f8690d49e84c92d504843e031b2f0e419cf82431 Mon Sep 17 00:00:00 2001 From: ggabernet Date: Sat, 3 Jul 2021 12:21:03 +0200 Subject: [PATCH 06/13] add to tests --- .github/workflows/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 65cabe5..a6468fa 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -16,7 +16,7 @@ jobs: needs: test_all_profiles strategy: 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', 'kraken', 'mpcdf', 'munin', 'oist', 'pasteur', 'phoenix', 'prince', 'sanger', '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', 'kraken', 'mpcdf', 'munin', 'oist', 'pasteur', 'phoenix', 'prince', 'sanger', 'seg_globe', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh'] steps: - uses: actions/checkout@v1 - name: Install Nextflow From f3274c49b56011622cbeacb7fdb59565e7a52017 Mon Sep 17 00:00:00 2001 From: ggabernet Date: Sat, 3 Jul 2021 14:36:56 +0200 Subject: [PATCH 07/13] test profile multiline --- .github/workflows/main.yml | 43 +++++++++++++++++++++++++++++++++++++- 1 file changed, 42 insertions(+), 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index a6468fa..7dcdd29 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -16,7 +16,48 @@ jobs: needs: test_all_profiles strategy: matrix: - 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', 'kraken', 'mpcdf', 'munin', 'oist', 'pasteur', 'phoenix', 'prince', 'sanger', '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' + - 'kraken' + - 'mpcdf' + - 'munin' + - 'oist' + - 'pasteur' + - 'phoenix' + - 'prince' + - 'sanger' + - 'seg_globe' + - 'shh' + - 'uct_hpc' + - 'uppmax' + - 'utd_ganymede' + - 'uzh' steps: - uses: actions/checkout@v1 - name: Install Nextflow From 926f3ba24f8b8b13a313748247283ef6cea4c534 Mon Sep 17 00:00:00 2001 From: ggabernet Date: Sat, 3 Jul 2021 14:52:44 +0200 Subject: [PATCH 08/13] update checker script --- bin/cchecker.py | 18 +++++++++++------- 1 file changed, 11 insertions(+), 7 deletions(-) diff --git a/bin/cchecker.py b/bin/cchecker.py index 9629cf8..71dd2c9 100644 --- a/bin/cchecker.py +++ b/bin/cchecker.py @@ -10,6 +10,7 @@ import os import sys import argparse import re +import yaml ############################################ ############################################ @@ -51,13 +52,16 @@ def check_config(Config, Github): ### Ignore these profiles ignore_me = ['czbiohub_aws'] tests.update(ignore_me) - with open(Github, 'r') as ghfile: - for line in ghfile: - if re.search('profile: ', line): - line = line.replace('\'','').replace('[','').replace(']','').replace('\n','') - profiles = line.split(':')[1].split(',') - for p in profiles: - tests.add(p.strip()) + # parse yaml GitHub actions file + try: + with open(Github, 'r') as ghfile: + wf = yaml.safe_load(ghfile) + profile_list = wf["profile_test"]["strategy"]["matrix"]["profile"] + except Exception as e: + return {"failed": ["Could not parse yaml file: {}, {}".format(Github, e)]} + # Add profiles to test + for profile in profile_list: + tests.add(profile.strip()) ###Check if sets are equal if tests == config_profiles: From 6475671c384c8ea48bab33319eac56e6b2fa8eda Mon Sep 17 00:00:00 2001 From: ggabernet Date: Sat, 3 Jul 2021 14:57:58 +0200 Subject: [PATCH 09/13] test that it fails --- .github/workflows/main.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index f66db3d..6daa819 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -19,7 +19,6 @@ jobs: profile: - 'abims' - 'awsbatch' - - 'aws_tower' - 'bi' - 'bigpurple' - 'binac' From 2a69b90be62106eec003b789fccc5478cb1dd000 Mon Sep 17 00:00:00 2001 From: ggabernet Date: Sat, 3 Jul 2021 15:09:43 +0200 Subject: [PATCH 10/13] fix cchecker --- bin/cchecker.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/bin/cchecker.py b/bin/cchecker.py index 71dd2c9..8caf920 100644 --- a/bin/cchecker.py +++ b/bin/cchecker.py @@ -58,16 +58,16 @@ def check_config(Config, Github): wf = yaml.safe_load(ghfile) profile_list = wf["profile_test"]["strategy"]["matrix"]["profile"] except Exception as e: - return {"failed": ["Could not parse yaml file: {}, {}".format(Github, e)]} + 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 - if tests == config_profiles: - sys.exit(0) - else: - #Maybe report what is missing here too + try: + assert tests == config_profiles + except (AssertionError): 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)) sys.exit(1) From 68e12f85ec437a0a6464294363336a3cad4d1bec Mon Sep 17 00:00:00 2001 From: ggabernet Date: Sat, 3 Jul 2021 15:11:51 +0200 Subject: [PATCH 11/13] fix cchecker --- bin/cchecker.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/cchecker.py b/bin/cchecker.py index 8caf920..cac7e4a 100644 --- a/bin/cchecker.py +++ b/bin/cchecker.py @@ -56,7 +56,7 @@ def check_config(Config, Github): try: with open(Github, 'r') as ghfile: wf = yaml.safe_load(ghfile) - profile_list = wf["profile_test"]["strategy"]["matrix"]["profile"] + profile_list = wf["jobs"]["profile_test"]["strategy"]["matrix"]["profile"] except Exception as e: print("Could not parse yaml file: {}, {}".format(Github, e)) sys.exit(1) From e6f1bfaa1a7bebe1796a79f14bc4d0ef69173c88 Mon Sep 17 00:00:00 2001 From: ggabernet Date: Sat, 3 Jul 2021 15:13:10 +0200 Subject: [PATCH 12/13] finally add profile --- .github/workflows/main.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 6daa819..f66db3d 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -19,6 +19,7 @@ jobs: profile: - 'abims' - 'awsbatch' + - 'aws_tower' - 'bi' - 'bigpurple' - 'binac' From 962dca7a4661665c883037a8f43286b383ab984a Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Mon, 12 Jul 2021 12:24:49 +0100 Subject: [PATCH 13/13] Add ARTIC v1200 primers to genomes config for viralrecon --- conf/pipeline/viralrecon/genomes.config | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/conf/pipeline/viralrecon/genomes.config b/conf/pipeline/viralrecon/genomes.config index e7b1c2f..3e3e299 100644 --- a/conf/pipeline/viralrecon/genomes.config +++ b/conf/pipeline/viralrecon/genomes.config @@ -43,6 +43,12 @@ 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' } + '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' + } } } }