diff --git a/configs/docker.config b/configs/docker.config index 86b195b..1a6759e 100755 --- a/configs/docker.config +++ b/configs/docker.config @@ -19,7 +19,7 @@ process { withLabel: filtlong { container = 'nanozoo/filtlong:v0.2.0--afa175e' } withLabel: flye { container = 'nanozoo/flye:2.8.3--2769e9b' } withLabel: ggplot2 { container = 'nanozoo/ggplot2:3.3.1--303f617' } - withLabel: gtdbtk { container = 'nanozoo/gtdb:1.6.0--5383545' } + withLabel: gtdbtk { container = 'nanozoo/gtdbtk:2.3.2--641ec99' } withLabel: kraken2 { container = 'nanozoo/kraken2:2.1.1--d5ded30'} withLabel: krakentools { container = 'nanozoo/krakentools:1.2--13d5ba5'} withLabel: krona { container = 'nanozoo/krona:2.7.1--e7615f7'} diff --git a/modules/fargene.nf b/modules/fargene.nf index 7b23332..d939bd9 100755 --- a/modules/fargene.nf +++ b/modules/fargene.nf @@ -1,9 +1,7 @@ process fargene { label 'fargene' - errorStrategy 'ignore' - validExitStatus 0,1 input: - tuple val(name), val(splitname), val(type), path(fasta) + tuple val(name), val(splitname), val(type), path(fasta) optional true each method output: path("${method}_${type}_${name}_*.fargene") @@ -19,7 +17,6 @@ process fargene { process fargene_plasmid_screen { label 'fargene' - validExitStatus 0,1 //publishDir "${params.output}/fargene/", mode: 'copy' input: tuple val(name), path(fasta) diff --git a/modules/gtdbtk.nf b/modules/gtdbtk.nf index 24dc1c1..8330792 100755 --- a/modules/gtdbtk.nf +++ b/modules/gtdbtk.nf @@ -21,6 +21,6 @@ process gtdbtk { # file suffix get SUFFIXNAME=\$(ls ${dir} | head -1 | rev | cut -f1 -d "." | rev) - gtdbtk classify_wf --genome_dir ${dir} --cpus 1 --out_dir ${name}-results -x \${SUFFIXNAME} --scratch_dir scratch_dir + gtdbtk classify_wf --genome_dir ${dir} --skip_ani_screen --pplacer_cpus 1 --out_dir ${name}-results -x \${SUFFIXNAME} --scratch_dir scratch_dir """ } \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index 98edbae..b834544 100755 --- a/nextflow.config +++ b/nextflow.config @@ -116,9 +116,9 @@ profiles { google { project = 'case-dev-302214' zone = 'europe-west1-b' - lifeSciences.preemptible = false - lifeSciences.bootDiskSize = 50.GB - } + lifeSciences { preemptible = false + bootDiskSize = 100.GB + } } includeConfig 'configs/docker.config' includeConfig 'configs/gcloud.config'