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fix: update actino,streptomyces config
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@chasemc
chasemc committed Jul 24, 2024
1 parent 64f18c4 commit 172e72c
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36 changes: 18 additions & 18 deletions conf/examples/input_examples/by_taxa/actinomycetota.config
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
Defines input files and everything required to run a fast and simple pipeline test.
Use as follows:
outdir='/media/socialgene_nvme/actinomycetota'
outdir='/tmp/socialgene_nvme/actinomycetota'
outdir_download_cache='/tmp/socialgene_data/cache'
nextflow run . \
Expand All @@ -27,19 +27,19 @@
--outdir_download_cache $outdir_download_cache \
--fasta_splits 1000 \
--include_sequences \
--domtblout_path '/media/box3/chase/actinomycetota/htcondor_cache/results/*.domtblout.gz' \
--domtblout_path '/tmp/htcondor_cache/results/*.domtblout.gz' \
-resume
----------------------------------------------------------------------------------------
*/

params {
include_sequences = true
/*
////////////////////////
set which modules to run
////////////////////////
*/
ncbi_datasets_command = 'genome taxon "actinomycetota" --assembly-source refseq --exclude-atypical'
mibig = true
hmmlist = 'antismash,amrfinder,pfam,resfams,tigrfam'
mmseqs_steps = '90,70,50,30'
Expand All @@ -52,49 +52,49 @@ params {
////////////////////////
*/
max_cpus = 96
max_memory = '900.GB'
max_time = 480.h
slurm_queue_size = 40
max_memory = '800.GB'
max_time = 500.h
slurm_queue_size = 48

}

process {
withName:HMMER_HMMSEARCH {
cpus = { check_max (2 * task.attempt, 'cpus' ) }
memory = { check_max (2.GB * task.attempt, 'memory' ) }
time = { check_max (24.h * task.attempt, 'time' ) }
}
withLabel:process_single {
cpus = { check_max( 1 , 'cpus' ) }
memory = { check_max( 5.GB * task.attempt, 'memory' ) }
time = { check_max( 10.h * task.attempt , 'time' ) }
}
withLabel:process_low {
cpus = { check_max( 2 * task.attempt, 'cpus' ) }
cpus = { check_max( 1 * task.attempt, 'cpus' ) }
memory = { check_max( 2.GB * task.attempt, 'memory' ) }
time = { check_max( 40.h * task.attempt, 'time' ) }
}
withLabel:process_medium {
cpus = { check_max( 20 * task.attempt, 'cpus' ) }
cpus = { check_max( 5 * task.attempt, 'cpus' ) }
memory = { check_max( 20.GB * task.attempt, 'memory' ) }
time = { check_max( 80.h * task.attempt, 'time' ) }
}
withLabel:process_high {
cpus = { check_max( 40 * task.attempt, 'cpus' ) }
cpus = { check_max( 24 * task.attempt, 'cpus' ) }
memory = { check_max( 100.GB * task.attempt, 'memory' ) }
time = { check_max( 16.h * task.attempt, 'time' ) }
}
withLabel:process_long {
time = { check_max( 24.h * task.attempt, 'time' ) }
}
withLabel:process_high_memory {
memory = { check_max( 200.GB * task.attempt, 'memory' ) }
}
withName:HMMER_HMMSEARCH {
cpus = { check_max (2 * task.attempt, 'cpus' ) }
memory = { check_max (2.GB * task.attempt, 'memory' ) }
time = { check_max (24.h * task.attempt, 'time' ) }
}
memory = { check_max( 400.GB * task.attempt, 'memory' ) }
}
withName:ANTISMASH {
cpus = 2
memory = { check_max (5.GB * task.attempt, 'memory' ) }
memory = { check_max (3.GB * task.attempt, 'memory' ) }
time = { check_max (24.h * task.attempt, 'time' ) }
ext.args = "--no-abort-on-invalid-records --genefinding-tool none --skip-zip-file --allow-long-headers --skip-sanitisation --minimal --enable-genefunctions --enable-lanthipeptides --enable-lassopeptides --enable-nrps-pks --enable-sactipeptides --enable-t2pks --enable-thiopeptides --enable-tta"
ext.args = "--no-abort-on-invalid-records --genefinding-tool none --skip-zip-file --allow-long-headers --skip-sanitisation"
}
withName:'MMSEQS2_CLUSTER'{
// https://github.com/soedinglab/mmseqs2/wiki#how-to-set-the-right-alignment-coverage-to-cluster
Expand Down
9 changes: 4 additions & 5 deletions conf/examples/input_examples/by_taxa/streptomyces.config
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Original file line number Diff line number Diff line change
Expand Up @@ -48,18 +48,17 @@ params {
// too-few proteins per file (would probably keep <1000 for any size of dataset)
max_cpus = 96
max_memory = '800.GB'
max_time = 48.h
max_time = 500.h
slurm_queue_size = 48
}

process {

withName:HMMER_HMMSEARCH {
cpus = { check_max (2 * task.attempt, 'cpus' ) }
memory = { check_max (5.GB * task.attempt, 'memory' ) }
memory = { check_max (2.GB * task.attempt, 'memory' ) }
time = { check_max (24.h * task.attempt, 'time' ) }
}

withLabel:process_single {
cpus = { check_max( 1 , 'cpus' ) }
memory = { check_max( 5.GB * task.attempt, 'memory' ) }
Expand All @@ -84,7 +83,7 @@ process {
time = { check_max( 24.h * task.attempt, 'time' ) }
}
withLabel:process_high_memory {
memory = { check_max( 2000.GB * task.attempt, 'memory' ) }
memory = { check_max( 400.GB * task.attempt, 'memory' ) }
}
withName:ANTISMASH {
cpus = 2
Expand All @@ -94,6 +93,6 @@ process {
}
withName:'MMSEQS2_CLUSTER'{
// https://github.com/soedinglab/mmseqs2/wiki#how-to-set-the-right-alignment-coverage-to-cluster
ext.args = '-c 0.7 --cov-mode 0 --split 1'
ext.args = '-c 0.7 --cov-mode 0'
}
}

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