diff --git a/conf/examples/input_examples/by_taxa/actinomycetota.config b/conf/examples/input_examples/by_taxa/actinomycetota.config index 6476318..66dfc0e 100644 --- a/conf/examples/input_examples/by_taxa/actinomycetota.config +++ b/conf/examples/input_examples/by_taxa/actinomycetota.config @@ -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 . \ @@ -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' @@ -52,30 +52,35 @@ 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' ) } } @@ -83,18 +88,13 @@ process { 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 diff --git a/conf/examples/input_examples/by_taxa/streptomyces.config b/conf/examples/input_examples/by_taxa/streptomyces.config index 49f2d54..378ccd7 100644 --- a/conf/examples/input_examples/by_taxa/streptomyces.config +++ b/conf/examples/input_examples/by_taxa/streptomyces.config @@ -48,7 +48,7 @@ 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 } @@ -56,10 +56,9 @@ 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' ) } @@ -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 @@ -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' } }