8000 Remove netmhcii specs and deactivate corresponding tests by christopher-mohr · Pull Request #123 · nf-core/epitopeprediction · GitHub
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Remove netmhcii specs and deactivate corresponding tests #123

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Merged
merged 1 commit into from
Dec 16, 2021
Merged

Remove netmhcii specs and deactivate corresponding tests #123

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6 changes: 0 additions & 6 deletions .github/workflows/ci.yml
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Expand Up @@ -125,12 +125,6 @@ jobs:
- name: Run pipeline with NetMHC
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test_netmhc,docker
- name: Run pipeline with NetMHCII
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test_netmhcii,docker
- name: Run pipeline with NetMHCpan
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test_netmhcpan,docker
- name: Run pipeline with NetMHCIIpan
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test_netmhciipan,docker
2 changes: 0 additions & 2 deletions nextflow.config
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Expand Up @@ -140,9 +140,7 @@ profiles {
test_mhcnuggets { includeConfig 'conf/test_mhcnuggets.config' }
test_mhcflurry { includeConfig 'conf/test_mhcflurry.config' }
test_netmhc { includeConfig 'conf/test_netmhc.config' }
test_netmhcii { includeConfig 'conf/test_netmhcii.config' }
test_netmhcpan { includeConfig 'conf/test_netmhcpan.config' }
test_netmhciipan { includeConfig 'conf/test_netmhciipan.config' }
test_full { includeConfig 'conf/test_full.config' }
}

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16 changes: 1 addition & 15 deletions workflows/epitopeprediction.nf
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Expand Up @@ -128,20 +128,6 @@ workflow EPITOPEPREDICTION {
data_url : "https://services.healthtech.dtu.dk/services/NetMHCpan-4.0/data.Linux.tar.gz",
data_md5 : "26cbbd99a38f6692249442aeca48608f",
binary_name : "netMHCpan"
],
netmhcii: [
version : "2.2",
software_md5 : "918b7108a37599887b0725623d0974e6",
data_url : "https://services.healthtech.dtu.dk/services/NetMHCII-2.2/data.tar.gz",
data_md5 : "11579b61d3bfe13311f7b42fc93b4dd8",
binary_name : "netMHCII"
],
netmhciipan: [
version : "3.1",
software_md5 : "0962ce799f7a4c9631f8566a55237073",
data_url : "https://services.healthtech.dtu.dk/services/NetMHCIIpan-3.1/data.tar.gz",
data_md5 : "f833df245378e60ca6e55748344a36f6",
binary_name : "netMHCIIpan"
]
]

Expand Down Expand Up @@ -224,7 +210,7 @@ workflow EPITOPEPREDICTION {
}

// Retrieve meta data for external tools
["netmhc", "netmhcpan", "netmhcii", "netmhciipan"].each {
["netmhc", "netmhcpan"].each {
// Check if the _path parameter was set for this tool
if (params["${it}_path"] as Boolean && ! tools.contains(it))
{
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