Commit 056a884b authored by Jean Mainguy's avatar Jean Mainguy
Browse files

clean and simplify config file #172

parent 03bcdd54
Pipeline #47494 skipped with stage
...@@ -10,13 +10,12 @@ process { ...@@ -10,13 +10,12 @@ process {
// Process-specific resource requirements // Process-specific resource requirements
cpus = { 1 * task.attempt } cpus = { 1 * task.attempt }
memory = { 2.GB * task.attempt } memory = { 20.GB * task.attempt }
errorStrategy = 'finish' errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
//{ task.exitStatus in [1,143,137,104,134,139] ? 'retry' : 'finish' }
maxRetries = 1 maxRetries = 1
maxErrors = '-1' maxErrors = '-1'
container = 'file://metagwgs/env/metagwgs.sif'
withName: CUTADAPT { withName: CUTADAPT {
cpus = 8 cpus = 8
memory = { 8.GB * task.attempt } memory = { 8.GB * task.attempt }
...@@ -48,14 +47,14 @@ process { ...@@ -48,14 +47,14 @@ process {
memory = { 440.GB * task.attempt } memory = { 440.GB * task.attempt }
cpus = 20 cpus = 20
} }
withName: QUAST { withLabel: QUAST {
cpus = 4 cpus = 4
memory = { 32.GB * task.attempt } memory = { 32.GB * task.attempt }
} }
withName: READS_DEDUPLICATION { withName: READS_DEDUPLICATION {
memory = { 32.GB * task.attempt } memory = { 32.GB * task.attempt }
} }
withName: ASSEMBLY_FILTER { withLabel: ASSEMBLY_FILTER {
memory = { 8.GB * task.attempt } memory = { 8.GB * task.attempt }
cpus = 4 cpus = 4
} }
...@@ -70,11 +69,8 @@ process { ...@@ -70,11 +69,8 @@ process {
memory = { 50.GB * task.attempt } memory = { 50.GB * task.attempt }
cpus = 16 cpus = 16
} }
withName: QUANTIFICATION {
memory = { 50.GB * task.attempt }
}
withName: QUANTIFICATION_TABLE { withName: QUANTIFICATION_TABLE {
memory = { 100.GB * task.attempt } memory = { 2.GB * task.attempt }
} }
withName: DIAMOND { withName: DIAMOND {
cpus = 8 cpus = 8
...@@ -83,13 +79,6 @@ process { ...@@ -83,13 +79,6 @@ process {
withName: GET_SOFTWARE_VERSIONS { withName: GET_SOFTWARE_VERSIONS {
memory = { 1.GB * task.attempt } memory = { 1.GB * task.attempt }
} }
withLabel: BINNING {
memory = { 50.GB * task.attempt }
}
withName: CAT {
cpus = 8
memory = { 16.GB * task.attempt }
}
withName: EGGNOG_MAPPER_DB { withName: EGGNOG_MAPPER_DB {
cpus = 2 cpus = 2
memory = { 2.GB * task.attempt } memory = { 2.GB * task.attempt }
...@@ -106,7 +95,12 @@ process { ...@@ -106,7 +95,12 @@ process {
cpus = 1 cpus = 1
memory = { 50.GB * task.attempt } memory = { 50.GB * task.attempt }
} }
withLabel: EGGNOG { withName: ASSIGN_TAXONOMY {
container = 'file://metagwgs/env/eggnog_mapper.sif' memory = { 5.GB * task.attempt }
cpus = 1
}
withLabel: MINIMAP2 {
memory = { 30.GB * task.attempt }
cpus = 10
} }
} }
process.executor = 'slurm'
includeConfig 'singularity.config'
singularity.runOptions = "-B /work/bank/ -B /bank -B /work2 -B /work -B /save -B /home -B /work/project"
process.queue = 'workq'
process {
// Process-specific resource requirements
cpus = { 1 * task.attempt }
memory = { 2.GB * task.attempt }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139] ? 'retry' : 'finish' }
maxRetries = 4
maxErrors = '-1'
withName: cutadapt {
cpus = 8
memory = { 4.GB * task.attempt }
}
withName: sickle {
memory = { 2.GB * task.attempt }
}
withLabel: fastqc {
cpus = 8
memory = { 2.GB * task.attempt }
}
withName: multiqc {
memory = { 8.GB * task.attempt }
}
withName: host_filter {
memory = { 6.GB * task.attempt }
time = '48h'
cpus = 6
}
withName: index_db_kaiju {
memory = { 200.GB * task.attempt }
cpus = 6
}
withName: kaiju {
memory = { 60.GB * task.attempt }
cpus = 20
}
withName: kaiju_merge {
memory = { 2.GB * task.attempt }
cpus = 20
}
withName: assembly {
memory = { 60.GB * task.attempt }
cpus = 14
}
withName: quast {
cpus = 3
memory = { 8.GB * task.attempt }
}
withName: reads_deduplication {
memory = { 4.GB * task.attempt }
}
withName: assembly_filter {
memory = { 4.GB * task.attempt }
cpus = 2
}
withName: prokka {
memory = { 45.GB * task.attempt }
cpus = 8
}
withName: rename_contigs_genes{
memory = { 2.GB * task.attempt }
}
withLabel: cd_hit {
memory = { 50.GB * task.attempt }
cpus = 16
}
withName: quantification {
memory = { 50.GB * task.attempt }
}
withName: quantification_table {
memory = { 100.GB * task.attempt }
}
withName: diamond {
cpus = 8
memory = { 22.GB * task.attempt }
}
withName: get_software_versions {
memory = { 1.GB * task.attempt }
}
withLabel: binning {
memory = { 5.GB * task.attempt }
}
withName: cat {
cpus = 8
memory = { 16.GB * task.attempt }
}
withName: eggnog_mapper_db {
cpus = 2
memory = { 2.GB * task.attempt }
}
withName: eggnog_mapper {
cpus = 4
memory = { 20.GB * task.attempt }
}
withName: merge_quantif_and_functional_annot {
cpus = 1
memory = { 50.GB * task.attempt }
}
withName: make_functional_annotation_tables {
cpus = 1
memory = { 50.GB * task.attempt }
}
}
process.conda = "file://metagwgs/env/metagWGS.yml"
process { process {
withLabel: eggnog { conda = "${baseDir}/env/metagWGS.yml"
conda = 'file://metagwgs/env/eggnog_mapper.yml' withLabel: EGGNOG {
} conda = "${baseDir}/env/eggnog_mapper.yml"
} }
}
process.executor = 'slurm'
includeConfig 'singularity.config' includeConfig 'singularity.config'
process.executor = 'slurm'
singularity.runOptions = "-B /work/bank/ -B /bank -B /work2 -B /work -B /save -B /home -B /work/project -B /usr/local/bioinfo" singularity.runOptions = "-B /work/bank/ -B /bank -B /work2 -B /work -B /save -B /home -B /work/project -B /usr/local/bioinfo"
process.queue = 'workq' process.queue = 'workq'
...@@ -2,8 +2,9 @@ singularity.enabled = true ...@@ -2,8 +2,9 @@ singularity.enabled = true
singularity.autoMounts = true singularity.autoMounts = true
process { process {
container = '<PATH>/metagwgs.sif' container = "file://${baseDir}/env/metagwgs.sif"
withLabel: eggnog { withLabel: EGGNOG {
container = '<PATH>/eggnog_mapper.sif' container = "file://${baseDir}/env/eggnog_mapper.sif"
} }
} }
\ No newline at end of file
process.executor = 'slurm'
includeConfig 'singularity.config'
singularity.runOptions = "-B /work/bank/ -B /bank -B /work -B /work2 -B /save -B /home -B /work/project -B /usr/local/bioinfo"
process.queue = 'workq'
process { process {
// Process-specific resource requirements // Process-specific resource requirements
cpus = { 1 * task.attempt } cpus = { 1 * task.attempt }
memory = { 20.GB * task.attempt } memory = { 2.GB * task.attempt }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139] ? 'finish' : 'finish' }
maxRetries = 3
maxErrors = '-1'
withName: CUTADAPT { withName: CUTADAPT {
cpus = 3 cpus = 3
...@@ -60,16 +52,13 @@ process { ...@@ -60,16 +52,13 @@ process {
memory = { 1.GB * task.attempt } memory = { 1.GB * task.attempt }
cpus = 1 cpus = 1
} }
withName: RENAME_CONTIGS_AND_GENES{ withName: RENAME_CONTIGS_AND_GENES {
memory = { 1.GB * task.attempt } memory = { 1.GB * task.attempt }
} }
withLabel: CD_HIT { withLabel: CD_HIT {
memory = { 16.GB * task.attempt } memory = { 16.GB * task.attempt }
cpus = 2 cpus = 2
} }
withName: QUANTIFICATION {
memory = { 1.GB * task.attempt }
}
withName: DIAMOND { withName: DIAMOND {
cpus = 8 cpus = 8
memory = { 10.GB * task.attempt } memory = { 10.GB * task.attempt }
...@@ -77,4 +66,29 @@ process { ...@@ -77,4 +66,29 @@ process {
withName: GET_SOFTWARE_VERSIONS { withName: GET_SOFTWARE_VERSIONS {
memory = { 1.GB * task.attempt } memory = { 1.GB * task.attempt }
} }
withName: EGGNOG_MAPPER_DB {
cpus = 2
memory = { 2.GB * task.attempt }
}
withName: EGGNOG_MAPPER {
cpus = 4
memory = { 20.GB * task.attempt }
}
withName: MERGE_QUANT_ANNOT_BEST {
cpus = 1
memory = { 50.GB * task.attempt }
}
withName: FUNCTIONAL_ANNOT_TABLE {
cpus = 1
memory = { 50.GB * task.attempt }
}
withName: ASSIGN_TAXONOMY {
memory = { 5.GB * task.attempt }
cpus = 1
}
withLabel: MINIMAP2 {
memory = { 10.GB * task.attempt }
cpus = 5
}
} }
process.executor = 'slurm'
includeConfig 'singularity.config'
singularity.runOptions = "-B /work/bank/ -B /bank -B /work2 -B /work -B /save -B /home -B /work/project -B /usr/local/bioinfo"
process.queue = 'testq'
process {
// Process-specific resource requirements
cpus = { 1 * task.attempt }
memory = { 2.GB * task.attempt }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139] ? 'retry' : 'finish' }
maxRetries = 3
maxErrors = '-1'
withName: cutadapt {
cpus = 3
memory = { 1.GB * task.attempt }
}
withName: sickle {
memory = { 1.GB * task.attempt }
}
withLabel: fastqc {
cpus = 6
memory = { 1.GB * task.attempt }
}
withName: multiqc {
memory = { 2.GB * task.attempt }
}
withName: host_filter {
memory = { 20.GB * task.attempt }
time = '48h'
cpus = 6
}
withName: index_db_kaiju {
memory = { 50.GB * task.attempt }
cpus = 6
}
withName: kaiju {
memory = { 36.GB * task.attempt }
cpus = 4
}
withName: assembly {
memory = { 10.GB * task.attempt }
cpus = 8
}
withName: quast {
cpus = 2
memory = { 2.GB * task.attempt }
}
withName: reads_deduplication {
memory = { 1.GB * task.attempt }
}
withName: assembly_filter {
memory = { 1.GB * task.attempt }
cpus = 2
}
withName: prokka {
memory = { 1.GB * task.attempt }
cpus = 1
}
withName: rename_contigs_genes{
memory = { 1.GB * task.attempt }
}
withLabel: cd_hit {
memory = { 16.GB * task.attempt }
cpus = 2
}
withName: quantification {
memory = { 1.GB * task.attempt }
}
withName: diamond {
cpus = 2
memory = { 4.GB * task.attempt }
}
withName: get_software_versions {
memory = { 1.GB * task.attempt }
}
withLabel: binning {
memory = { 1.GB * task.attempt }
}
withName: cat {
cpus = 1
memory = { 4.GB * task.attempt }
}
}
includeConfig 'singularity.config'
singularity.runOptions = "-B /work/bank/ -B /bank -B /work2 -B /work -B /save -B /home -B /work/project -B /usr/local/bioinfo"
process {
// Process-specific resource requirements
errorStrategy = { task.exitStatus in [1,143,137,104,134,139] ? 'retry' : 'finish' }
maxRetries = 3
maxErrors = '-1'
withName: CUTADAPT {
cpus = 1
memory = { 1.GB * task.attempt }
}
withName: SICKLE {
memory = { 1.GB * task.attempt }
}
withLabel: FASTQC {
cpus = 2
memory = { 1.GB * task.attempt }
}
withName: MULTIQC {
memory = { 2.GB * task.attempt }
}
withName: HOST_FILTER {
memory = { 1.GB * task.attempt }
time = '48h'
cpus = 2
}
withName: INDEX_KAIJU {
memory = { 10.GB * task.attempt }
cpus = 2
}
withName: KAIJU {
memory = { 10.GB * task.attempt }
cpus = 2
}
withName: ASSEMBLY {
memory = { 2.GB * task.attempt }
cpus = 3
}
withName: QUAST {
cpus = 2
memory = { 2.GB * task.attempt }
}
withName: READS_DEDUPLICATION {
memory = { 1.GB * task.attempt }
}
withName: ASSEMBLY_FILTER {
memory = { 1.GB * task.attempt }
cpus = 2
}
withName: PROKKA {
memory = { 1.GB * task.attempt }
cpus = 1
}
withName: RENAME_CONTIGS_AND_GENES{
memory = { 1.GB * task.attempt }
}
withLabel: CD_HIT {
memory = { 2.GB * task.attempt }
cpus = 2
}
withName: QUANTIFICATION {
memory = { 1.GB * task.attempt }
}
withName: DIAMOND {
cpus = 2
memory = { 2.GB * task.attempt }
}
withName: GET_SOFTWARE_VERSIONS {
memory = { 1.GB * task.attempt }
}
withLabel: BINNING {
memory = { 1.GB * task.attempt }
}
withName: CAT {
cpus = 1
memory = { 4.GB * task.attempt }
}
}
...@@ -74,22 +74,13 @@ includeConfig 'conf/base.config' ...@@ -74,22 +74,13 @@ includeConfig 'conf/base.config'
profiles { profiles {
debug { includeConfig 'conf/debug.config' } debug { includeConfig 'conf/debug.config' }
genotoul { includeConfig 'conf/genotoul.config' } genotoul { includeConfig 'conf/genotoul.config' }
test_genotoul_testq { includeConfig 'conf/test_genotoul_testq.config' } test { includeConfig 'conf/test.config' }
test_genotoul_workq { includeConfig 'conf/test_genotoul_workq.config' } local { process.executor = 'local'}
big_test_genotoul { includeConfig 'conf/big_test_genotoul.config' }
test_local { includeConfig 'conf/test_local.config' }
conda { includeConfig 'conf/conda.config' } conda { includeConfig 'conf/conda.config' }
singularity { includeConfig 'conf/singularity.config' } singularity { includeConfig 'conf/singularity.config' }
} }
// Location of each singularity image (modify with proper path)
process {
container = '$SING_IMG_FOLDER/metagwgs.sif'
withLabel: EGGNOG {
container = '$SING_IMG_FOLDER/eggnog_mapper.sif'
}
}
// Manifest. // Manifest.
manifest { manifest {
......
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