diff --git a/conf/modules.config b/conf/modules.config index aaff4a1..477d268 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -18,7 +18,7 @@ process { saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] withName: TAR2REFS { - container = 'docker.io/jdj0303/vaper-base:1.0' + container = 'public.ecr.aws/o8h2f0o1/vaper-base:1.0' publishDir = [ path: { "${params.outdir}/" }, pattern: "none" @@ -73,7 +73,7 @@ process { ] } withName: 'FASTP2TBL' { - container = 'docker.io/jdj0303/vaper-base:1.0' + container = 'public.ecr.aws/o8h2f0o1/vaper-base:1.0' ext.args = "" ext.when = { } publishDir = [ @@ -147,7 +147,7 @@ process { ] } withName: 'SUMMARIZE_TAXA' { - container = 'docker.io/jdj0303/vaper-base:1.0' + container = 'public.ecr.aws/o8h2f0o1/vaper-base:1.0' ext.args = "" ext.when = { } publishDir = [ @@ -163,6 +163,29 @@ process { ] ] } + withName: 'SM2REFS' { + container = 'public.ecr.aws/o8h2f0o1/vaper-base:1.0' + ext.args = "" + ext.when = { } + publishDir = [ + [ + path: { "${params.outdir}/${meta.id}/taxonomy/" }, + pattern: "*.csv", + mode: 'copy' + ], + ] + } + withName: 'NCBI_DATASETS' { + ext.args = "" + ext.when = { } + publishDir = [ + [ + path: { "${params.outdir}/${meta.id}/taxonomy/" }, + pattern: "*.csv", + mode: 'copy' + ], + ] + } withName: 'BWA_MEM' { ext.args = "" ext.when = { } @@ -236,7 +259,7 @@ process { ] } withName: 'NEXTCLADE_CONFIG' { - container = 'docker.io/jdj0303/vaper-base:1.0' + container = 'public.ecr.aws/o8h2f0o1/vaper-base:1.0' ext.args = "" ext.when = { } publishDir = [ @@ -247,7 +270,7 @@ process { ] } withName: 'SUMMARYLINE' { - container = 'docker.io/jdj0303/vaper-base:1.0' + container = 'public.ecr.aws/o8h2f0o1/vaper-base:1.0' ext.args = "" ext.when = { } publishDir = [ @@ -257,7 +280,7 @@ process { ] } withName: 'COMBINE_SUMMARYLINES' { - container = 'docker.io/jdj0303/vaper-base:1.0' + container = 'public.ecr.aws/o8h2f0o1/vaper-base:1.0' ext.args = "" ext.when = { } publishDir = [ @@ -304,7 +327,7 @@ process { ] } withName: 'REPORT' { - container = 'docker.io/jdj0303/vaper-base:1.0' + container = 'public.ecr.aws/o8h2f0o1/vaper-base:1.0' ext.args = "" ext.when = { } publishDir = [ diff --git a/modules/local/irma.nf b/modules/local/irma.nf index 8a49dea..7e50d27 100644 --- a/modules/local/irma.nf +++ b/modules/local/irma.nf @@ -3,7 +3,7 @@ process IRMA { label 'process_high' stageInMode 'copy' - container "docker.io/staphb/irma:1.1.4" + container "public.ecr.aws/o8h2f0o1/irma:1.1.4" input: tuple val(meta), path(refs), path(reads) diff --git a/modules/local/ivar_consensus.nf b/modules/local/ivar_consensus.nf index 2590a6d..9cbead2 100644 --- a/modules/local/ivar_consensus.nf +++ b/modules/local/ivar_consensus.nf @@ -3,7 +3,7 @@ process IVAR_CONSENSUS { label 'process_high' conda "bioconda::ivar" - container "staphb/ivar:1.4.2" + container "public.ecr.aws/o8h2f0o1/ivar:1.4.2" input: tuple val(meta), val(ref_id), path(bam) diff --git a/modules/local/kraken2.nf b/modules/local/kraken2.nf deleted file mode 100644 index d3b9d80..0000000 --- a/modules/local/kraken2.nf +++ /dev/null @@ -1,48 +0,0 @@ -process KRAKEN2 { - tag "$meta.id" - label 'process_high' - - conda "bioconda::kraken2" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0' : - 'biocontainers/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0' }" - - input: - tuple val(meta), path(contigs) - path db_tar - - output: - tuple val(meta), path('*report.txt'), emit: report - tuple val(meta), path('*output.txt'), path('*cov.csv'), emit: output - path "versions.yml", emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - - """ - # extract Kraken2 database - mkdir k2_db - tar -xzvhf ${db_tar} -C k2_db - # run Kraken2 - kraken2 \\ - --db k2_db \\ - --threads $task.cpus \\ - --report ${prefix}.k2.report.txt \\ - --output ${prefix}.k2.output.txt \\ - --use-names \\ - $args \\ - $contigs - - # create summary of contig stats from Shovill output - cat $contigs | grep ">" | tr -d '>' | cut -f 1,3 -d ' ' | sed 's/ ...=/,/g' > ${prefix}.cov.csv - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - kraken2: \$(echo \$(kraken2 --version 2>&1) | sed 's/^.*Kraken version //; s/ .*\$//') - END_VERSIONS - """ -} \ No newline at end of file diff --git a/modules/local/ncbi-datasets.nf b/modules/local/ncbi-datasets.nf index 2b45cae..298d92c 100644 --- a/modules/local/ncbi-datasets.nf +++ b/modules/local/ncbi-datasets.nf @@ -1,6 +1,7 @@ process NCBI_DATASETS { tag "${ref_id}" label 'process_low' + container 'public.ecr.aws/o8h2f0o1/ncbi-datasets:16.15.0' input: tuple val(ref_id), val(accession) diff --git a/modules/local/samtoolstats2tbl.nf b/modules/local/samtoolstats2tbl.nf deleted file mode 100644 index d6ea3ab..0000000 --- a/modules/local/samtoolstats2tbl.nf +++ /dev/null @@ -1,22 +0,0 @@ -process SAMTOOLSTATS2TBL { - tag "${meta.id}" - label 'process_low' - - container "docker.io/jdj0303/waphl-viral-base:1.0.0" - - input: - tuple val(meta), val(ref_id), path(stats) - - output: - tuple val(meta), val(ref_id), path("*.csv"), emit: tbl - - when: - task.ext.when == null || task.ext.when - - prefix = task.ext.prefix ?: "${meta.id}" - script: // This script is bundled with the pipeline, in nf-core/waphlviral/bin/ - """ - # convert Fastp read summary to table - samtoolstats2tbl.sh ${stats} > ${prefix}.${ref_id}.samtoolstats2tbl.csv - """ -} diff --git a/modules/local/sm2refs.nf b/modules/local/sm2refs.nf index 48dcbed..c8c66a2 100644 --- a/modules/local/sm2refs.nf +++ b/modules/local/sm2refs.nf @@ -1,8 +1,6 @@ process SM2REFS { label 'process_low' - container 'docker.io/jdj0303/vaper-base:beta' - input: tuple val(meta), path(sm_species)