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Remove check_max and max_ parameters
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@jfy133
jfy133 committed Oct 23, 2024
1 parent 0f893df commit c762ac9
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Showing 10 changed files with 50 additions and 95 deletions.
100 changes: 50 additions & 50 deletions conf/base.config
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Original file line number Diff line number Diff line change
Expand Up @@ -64,168 +64,168 @@ process {
*/

withName: GUNZIP {
memory = { check_max(2.GB * task.attempt, 'memory') }
memory = { 2.GB * task.attempt }
cpus = 1
}

withName: UNTAR {
memory = { check_max(2.GB * task.attempt, 'memory') }
memory = { 2.GB * task.attempt }
cpus = 1
}

withName: PROKKA {
memory = { check_max(8.GB * task.attempt, 'memory') }
cpus = { check_max(4 * task.attempt, 'cpus') }
time = { check_max(8.h * task.attempt, 'time') }
memory = { 8.GB * task.attempt }
cpus = { 4 * task.attempt }
time = { 8.h * task.attempt }
}

withName: PRODIGAL_GBK {
memory = { check_max(2.GB * task.attempt, 'memory') }
memory = { 2.GB * task.attempt }
cpus = 1
}

withName: BAKTA_BAKTA {
memory = { check_max(64.GB * task.attempt, 'memory') }
cpus = { check_max(8 * task.attempt, 'cpus') }
time = { check_max(8.h * task.attempt, 'time') }
memory = { 64.GB * task.attempt }
cpus = { 8 * task.attempt }
time = { 8.h * task.attempt }
}

withName: ABRICATE_RUN {
memory = { check_max(2.GB * task.attempt, 'memory') }
cpus = { check_max(4 * task.attempt, 'cpus') }
memory = { 2.GB * task.attempt }
cpus = { 4 * task.attempt }
}

withName: AMRFINDERPLUS_RUN {
memory = { check_max(2.GB * task.attempt, 'memory') }
memory = { 2.GB * task.attempt }
cpus = 1
}

withName: DEEPARG_DOWNLOADDATA {
memory = { check_max(2.GB * task.attempt, 'memory') }
memory = { 2.GB * task.attempt }
cpus = 1
time = { check_max(2.h * task.attempt, 'time') }
time = { 2.h * task.attempt }
}

withName: DEEPARG_PREDICT {
memory = { check_max(2.GB * task.attempt, 'memory') }
memory = { 2.GB * task.attempt }
cpus = 1
}

withName: FARGENE {
memory = { check_max(2.GB * task.attempt, 'memory') }
cpus = { check_max(4 * task.attempt, 'cpus') }
memory = { 2.GB * task.attempt }
cpus = { 4 * task.attempt }
}

withName: RGI_MAIN {
memory = { check_max(28.GB * task.attempt, 'memory') }
cpus = { check_max(4 * task.attempt, 'cpus') }
memory = { 28.GB * task.attempt }
cpus = { 4 * task.attempt }
}

withName: AMPIR {
memory = { check_max(8.GB * task.attempt, 'memory') }
memory = { 8.GB * task.attempt }
cpus = 1
}

withName: AMPLIFY_PREDICT {
memory = { check_max(16.GB * task.attempt, 'memory') }
memory = { 16.GB * task.attempt }
cpus = 1
time = { check_max(24.h * task.attempt, 'time') }
time = { 24.h * task.attempt }
}

withName: AMP_HMMER_HMMSEARCH {
memory = { check_max(2.GB * task.attempt, 'memory') }
cpus = { check_max(4 * task.attempt, 'cpus') }
memory = { 2.GB * task.attempt }
cpus = { 4 * task.attempt }
}

withName: MACREL_CONTIGS {
memory = { check_max(4.GB * task.attempt, 'memory') }
cpus = { check_max(4 * task.attempt, 'cpus') }
memory = { 4.GB * task.attempt }
cpus = { 4 * task.attempt }
}

withName: BGC_HMMER_HMMSEARCH {
memory = { check_max(2.GB * task.attempt, 'memory') }
cpus = { check_max(4 * task.attempt, 'cpus') }
memory = { 2.GB * task.attempt }
cpus = { 4 * task.attempt }
}

withName: ANTISMASH_ANTISMASHLITE {
memory = { check_max(64.GB * task.attempt, 'memory') }
cpus = { check_max(8 * task.attempt, 'cpus') }
time = { check_max(12.h * task.attempt, 'time') }
memory = { 64.GB * task.attempt }
cpus = { 8 * task.attempt }
time = { 12.h * task.attempt }
}

withName: ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES {
memory = { check_max(4.GB * task.attempt, 'memory') }
memory = { 4.GB * task.attempt }
cpus = 1
}

withName: DEEPBGC_DOWNLOAD {
memory = { check_max(2.GB * task.attempt, 'memory') }
memory = { 2.GB * task.attempt }
cpus = 1
}

withName: DEEPBGC_PIPELINE {
memory = { check_max(2.GB * task.attempt, 'memory') }
memory = { 2.GB * task.attempt }
cpus = 1
time = { check_max(24.h * task.attempt, 'time') }
time = { 24.h * task.attempt }
}

withName: GECCO_RUN {
memory = { check_max(16.GB * task.attempt, 'memory') }
cpus = { check_max(4 * task.attempt, 'cpus') }
memory = { 16.GB * task.attempt }
cpus = { 4 * task.attempt }
}

withName: HAMRONIZATION_ABRICATE {
memory = { check_max(4.GB * task.attempt, 'memory') }
memory = { 4.GB * task.attempt }
cpus = 1
}

withName: HAMRONIZATION_AMRFINDERPLUS {
memory = { check_max(4.GB * task.attempt, 'memory') }
memory = { 4.GB * task.attempt }
cpus = 1
}

withName: HAMRONIZATION_DEEPARG {
memory = { check_max(8.GB * task.attempt, 'memory') }
memory = { 8.GB * task.attempt }
cpus = 1
}

withName: HAMRONIZATION_RGI {
memory = { check_max(4.GB * task.attempt, 'memory') }
memory = { 4.GB * task.attempt }
cpus = 1
}

withName: HAMRONIZATION_FARGENE {
memory = { check_max(4.GB * task.attempt, 'memory') }
memory = { 4.GB * task.attempt }
cpus = 1
}

withName: HAMRONIZATION_SUMMARIZE {
memory = { check_max(4.GB * task.attempt, 'memory') }
memory = { 4.GB * task.attempt }
cpus = 1
}

withName: ARGNORM_DEEPARG {
memory = { check_max(4.GB * task.attempt, 'memory') }
memory = { 4.GB * task.attempt }
cpus = 1
}

withName: ARGNORM_ABRICATE {
memory = { check_max(4.GB * task.attempt, 'memory') }
memory = { 4.GB * task.attempt }
cpus = 1
}

withName: ARGNORM_AMRFINDERPLUS {
memory = { check_max(4.GB * task.attempt, 'memory') }
memory = { 4.GB * task.attempt }
cpus = 1
}

withName: AMPCOMBI2_PARSETABLES {
memory = { check_max(8.GB * task.attempt, 'memory') }
time = { check_max(2.h * task.attempt, 'time') }
memory = { 8.GB * task.attempt }
time = { 2.h * task.attempt }
}

withName: AMPCOMBI2_CLUSTER {
memory = { check_max(6.GB * task.attempt, 'memory') }
time = { check_max(2.h * task.attempt, 'time') }
memory = { 6.GB * task.attempt }
time = { 2.h * task.attempt }
}
}
5 changes: 0 additions & 5 deletions conf/test_bgc_prokka.config
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Original file line number Diff line number Diff line change
Expand Up @@ -22,11 +22,6 @@ params {
config_profile_name = 'BGC Prokka test profile'
config_profile_description = 'Minimal test dataset to check BGC workflow function'

// Limit resources so that this can run on GitHub Actions
max_cpus = 2
max_memory = '8.GB'
max_time = '6.h'

// Input data
input = params.pipelines_testdata_base_path + 'funcscan/samplesheet_reduced.csv'

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5 changes: 0 additions & 5 deletions conf/test_bgc_pyrodigal.config
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Original file line number Diff line number Diff line change
Expand Up @@ -22,11 +22,6 @@ params {
config_profile_name = 'BGC Pyrodigal test profile'
config_profile_description = 'Minimal test dataset to check BGC workflow function'

// Limit resources so that this can run on GitHub Actions
max_cpus = 2
max_memory = '8.GB'
max_time = '6.h'

// Input data
input = params.pipelines_testdata_base_path + 'funcscan/samplesheet_reduced.csv'

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5 changes: 0 additions & 5 deletions conf/test_nothing.config
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Original file line number Diff line number Diff line change
Expand Up @@ -24,11 +24,6 @@ params {
config_profile_name = 'Test nothing profile'
config_profile_description = 'Minimal test dataset to check pipeline function'

// Limit resources so that this can run on GitHub Actions
max_cpus = 2
max_memory = '8.GB'
max_time = '6.h'

// Input data
input = params.pipelines_testdata_base_path + 'funcscan/samplesheet_reduced.csv'
amp_hmmsearch_models = params.pipelines_testdata_base_path + 'funcscan/hmms/mybacteriocin.hmm'
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5 changes: 0 additions & 5 deletions conf/test_preannotated.config
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Original file line number Diff line number Diff line change
Expand Up @@ -22,11 +22,6 @@ params {
config_profile_name = 'ARG/AMP test profile - preannotated input'
config_profile_description = 'Minimal test dataset to check pipeline function'

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

// Input data
input = params.pipelines_testdata_base_path + 'funcscan/samplesheet_preannotated.csv'

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5 changes: 0 additions & 5 deletions conf/test_preannotated_bgc.config
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Original file line number Diff line number Diff line change
Expand Up @@ -22,11 +22,6 @@ params {
config_profile_name = 'BGC test profile - preannotated input'
config_profile_description = 'Minimal test dataset to check BGC workflow function'

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

// Input data
input = params.pipelines_testdata_base_path + 'funcscan/samplesheet_preannotated.csv'

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5 changes: 0 additions & 5 deletions conf/test_prokka.config
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Original file line number Diff line number Diff line change
Expand Up @@ -22,11 +22,6 @@ params {
config_profile_name = 'AMP/ARG Prokka test profile'
config_profile_description = 'Minimal test dataset to check pipeline function'

// Limit resources so that this can run on GitHub Actions
max_cpus = 2
max_memory = '8.GB'
max_time = '6.h'

// Input data
input = params.pipelines_testdata_base_path + 'funcscan/samplesheet_reduced.csv'

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5 changes: 0 additions & 5 deletions conf/test_taxonomy_bakta.config
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Original file line number Diff line number Diff line change
Expand Up @@ -25,11 +25,6 @@ params {
config_profile_name = 'Taxonomic classification test profile'
config_profile_description = 'Minimal test dataset to check taxonomic classification workflow function'

// Limit resources so that this can run on GitHub Actions
max_cpus = 2
max_memory = '14.GB'
max_time = '6.h'

// Input data
input = params.pipelines_testdata_base_path + 'funcscan/samplesheet_reduced.csv'
amp_hmmsearch_models = params.pipelines_testdata_base_path + 'funcscan/hmms/mybacteriocin.hmm'
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5 changes: 0 additions & 5 deletions conf/test_taxonomy_prokka.config
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Original file line number Diff line number Diff line change
Expand Up @@ -25,11 +25,6 @@ params {
config_profile_name = 'Taxonomic classification test profile'
config_profile_description = 'Minimal test dataset to check taxonomic classification workflow function'

// Limit resources so that this can run on GitHub Actions
max_cpus = 2
max_memory = '14.GB'
max_time = '6.h'

// Input data
input = params.pipelines_testdata_base_path + 'funcscan/samplesheet_reduced.csv'
bgc_hmmsearch_models = 'https://raw.githubusercontent.com/antismash/antismash/fd61de057e082fbf071732ac64b8b2e8883de32f/antismash/detection/hmm_detection/data/ToyB.hmm'
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5 changes: 0 additions & 5 deletions conf/test_taxonomy_pyrodigal.config
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Original file line number Diff line number Diff line change
Expand Up @@ -25,11 +25,6 @@ params {
config_profile_name = 'Taxonomic classification test profile'
config_profile_description = 'Minimal test dataset to check taxonomic classification workflow function'

// Limit resources so that this can run on GitHub Actions
max_cpus = 2
max_memory = '14.GB'
max_time = '6.h'

// Input data
input = params.pipelines_testdata_base_path + 'funcscan/samplesheet_reduced.csv'
bgc_hmmsearch_models = 'https://raw.githubusercontent.com/antismash/antismash/fd61de057e082fbf071732ac64b8b2e8883de32f/antismash/detection/hmm_detection/data/ToyB.hmm'
Expand Down

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