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update template 3.0.2 - versions issues
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@ypriverol
ypriverol committed Oct 19, 2024
1 parent b2875d2 commit 6c7a086
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Showing 10 changed files with 71 additions and 47 deletions.
5 changes: 0 additions & 5 deletions conf/test_dda_id.config
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Expand Up @@ -14,11 +14,6 @@ params {
config_profile_name = 'Real full-size test profile for DDA ID'
config_profile_description = 'Real full-size test dataset to check pipeline function of the DDA identification branch of the pipeline'

// Limit resources so that this can run on GitHub Actions
max_cpus = 2
max_memory = 6.GB
max_time = 48.h

outdir = "./results_lfq_dda_id"

// Input data
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12 changes: 7 additions & 5 deletions conf/test_dia.config
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Expand Up @@ -10,15 +10,17 @@
------------------------------------------------------------------------------------------------
*/

process {
resourceLimits = [
cpus: 4,
memory: '6.GB',
time: '48.h'
]
}
params {
config_profile_name = 'Test profile for DIA'
config_profile_description = 'Minimal test dataset to check pipeline function for the data-independent acquisition pipeline branch.'

// Limit resources so that this can run on GitHub Actions
max_cpus = 2
max_memory = 6.GB
max_time = 48.h

outdir = './results_dia'

// Input data
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13 changes: 8 additions & 5 deletions conf/test_full_dia.config
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Expand Up @@ -10,15 +10,18 @@
------------------------------------------------------------------------------------------------
*/

process {
resourceLimits = [
cpus: 4,
memory: '6.GB',
time: '48.h'
]
}

params {
config_profile_name = 'Real full-size test profile for DIA'
config_profile_description = 'Real full-size test dataset to check pipeline function for the data-independent acquisition pipeline branch.'

// Limit resources so that this can run on GitHub Actions
max_cpus = 2
max_memory = 6.GB
max_time = 48.h

outdir = './results_dia_full'

// Input data
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13 changes: 8 additions & 5 deletions conf/test_full_lfq.config
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Expand Up @@ -10,15 +10,18 @@
------------------------------------------------------------------------------------------------
*/

process {
resourceLimits = [
cpus: 4,
memory: '12.GB',
time: '48.h'
]
}

params {
config_profile_name = 'Real full-size test profile for DDA LFQ'
config_profile_description = 'Real full-size test dataset to check pipeline function of the label-free quantification branch of the pipeline'

// Limit resources so that this can run on GitHub Actions
max_cpus = 2
max_memory = 6.GB
max_time = 48.h

outdir = "./results_lfq_full"

// Input data
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12 changes: 8 additions & 4 deletions conf/test_full_tmt.config
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Expand Up @@ -10,16 +10,20 @@
----------------------------------------------------------------------------------------
*/

process {
resourceLimits = [
cpus: 4,
memory: '12.GB',
time: '48.h'
]
}

params {
config_profile_name = 'Real full test profile DDA ISO'
config_profile_description = 'Real full test dataset in isotopic labelling mode to check pipeline function and sanity of results'

outdir = "./results_iso_full"

max_cpus = 2
max_memory = 6.GB
max_time = 48.h

// Input data for full size test
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/quantms/testdata-aws/tmt_full/PXD005486.sdrf.tsv'

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13 changes: 8 additions & 5 deletions conf/test_latest_dia.config
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Expand Up @@ -10,15 +10,18 @@
------------------------------------------------------------------------------------------------
*/

process {
resourceLimits = [
cpus: 4,
memory: '12.GB',
time: '48.h'
]
}

params {
config_profile_name = 'Test profile for latest DIA'
config_profile_description = 'Minimal test dataset to check pipeline function for the data-independent acquisition pipeline branch for latest DIA-NN.'

// Limit resources so that this can run on GitHub Actions
max_cpus = 2
max_memory = 6.GB
max_time = 48.h

outdir = './results_latest_dia'

// Input data
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13 changes: 8 additions & 5 deletions conf/test_lfq_sage.config
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Expand Up @@ -10,15 +10,18 @@
------------------------------------------------------------------------------------------------
*/

process {
resourceLimits = [
cpus: 4,
memory: '12.GB',
time: '48.h'
]
}

params {
config_profile_name = 'Test profile for DDA LFQ with Sage'
config_profile_description = 'Minimal test dataset to check pipeline function of the label-free quantification branch of the pipeline with the search engine Sage'

// Limit resources so that this can run on GitHub Actions
max_cpus = 2
max_memory = 6.GB
max_time = 48.h

outdir = "./results_lfq"
tracedir = "${params.outdir}/pipeline_info"

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13 changes: 8 additions & 5 deletions conf/test_localize.config
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Expand Up @@ -10,15 +10,18 @@
----------------------------------------------------------------------------------------------------
*/

process {
resourceLimits = [
cpus: 4,
memory: '12.GB',
time: '48.h'
]
}

params {
config_profile_name = 'Test PTM-localization profile'
config_profile_description = 'Minimal test dataset to check pipeline function for PTM-localization, SDRF parsing and ConsensusID.'

// Limit resources so that this can run on Travis
max_cpus = 2
max_memory = 6.GB
max_time = 1.h

outdir = "./results_localize"

// Input data
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12 changes: 8 additions & 4 deletions conf/test_tmt.config
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Expand Up @@ -10,16 +10,20 @@
----------------------------------------------------------------------------------------
*/

process {
resourceLimits = [
cpus: 4,
memory: '12.GB',
time: '48.h'
]
}

params {
config_profile_name = 'Full test profile DDA ISO'
config_profile_description = 'Full test dataset in isotopic labelling mode to check pipeline function and sanity of results'

outdir = "./results_iso"

max_cpus = 2
max_memory = 6.GB
max_time = 48.h

// Input data for full size test
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/quantms/testdata/tmt_ci/PXD000001.sdrf.tsv'

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12 changes: 8 additions & 4 deletions conf/test_tmt_corr.config
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Expand Up @@ -10,16 +10,20 @@
----------------------------------------------------------------------------------------
*/

process {
resourceLimits = [
cpus: 4,
memory: '12.GB',
time: '48.h'
]
}

params {
config_profile_name = 'Full test profile DDA ISO'
config_profile_description = 'Full test dataset in isotopic labelling mode to check pipeline function and sanity of results'

outdir = "./results_iso"

max_cpus = 2
max_memory = 6.GB
max_time = 48.h

// Input data for full size test
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/quantms/testdata/tmt_ci/PXD000001.sdrf.tsv'

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