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changes made from origin/samh/amr-dev to run on vwb #18

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34 changes: 0 additions & 34 deletions nextflow/amr-on-wb/modules/Microbiome/kraken2.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -103,37 +103,3 @@ process runbracken {
"""
}

process kronadb {
label "microbiome"
output:
file("krona_db/taxonomy.tab") optional true into krona_db_ch // is this a value ch?

when:
!params.skip_krona

script:
"""
ktUpdateTaxonomy.sh krona_db
"""
}

process kronafromkraken {
publishDir params.outdir, mode: 'copy'
label "microbiome"
input:
file(x) from kraken2krona_ch.collect()
//file(y) from kaiju2krona_ch.collect()
file("krona_db/taxonomy.tab") from krona_db_ch

output:
file("*_taxonomy_krona.html")

when:
!params.skip_krona

script:
"""
mkdir -p krona
ktImportTaxonomy -o kraken2_taxonomy_krona.html -tax krona_db $x
"""
}
16 changes: 8 additions & 8 deletions nextflow/amr-on-wb/nextflow.config
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Expand Up @@ -86,7 +86,7 @@ profiles {

google.region = "${GCS_BUCKET_LOCATION}"
google.project = "$GOOGLE_CLOUD_PROJECT"
google.batch.serviceAccountEmail = "$GOOGLE_SERVICE_ACCOUNT_EMAIL"
google.batch.serviceAccountEmail = "pet-277205028424080dda892@vwb-dev-beaming-sprout-9366.iam.gserviceaccount.com"
google.batch.bootDiskSize = '50 GB'
google.batch.usePrivateAddress = true
google.batch.network = "projects/${GOOGLE_CLOUD_PROJECT}/global/networks/default"
Expand All @@ -102,19 +102,19 @@ profiles {
includeConfig "config/google_batch_resources.config"

process.executor = 'google-batch'
process.container = "us-central1-docker.pkg.dev/${GOOGLE_CLOUD_PROJECT}/${GOOGLE_ARTIFACT_REPO}/amrplusplus-workbench:latest"
process.container = "us-central1-docker.pkg.dev/vwb-dev-beaming-sprout-9366/nf-containers/amrplusplus-workbench:latest"
process.errorStrategy = { task.exitStatus==50001 ? 'retry' : 'terminate' }
process.maxRetries = 5

workDir = "gs://${GCS_BUCKET}/scratch"
workDir = "gs://sam-nextflow-vwb-dev-beaming-sprout-9366/scratch"

google.region = "${GCS_BUCKET_LOCATION}"
google.project = "$GOOGLE_CLOUD_PROJECT"
google.batch.serviceAccountEmail = "$GOOGLE_SERVICE_ACCOUNT_EMAIL"
google.region = "us-central1"
google.project = "vwb-dev-beaming-sprout-9366"
google.batch.serviceAccountEmail = "pet-277205028424080dda892@vwb-dev-beaming-sprout-9366.iam.gserviceaccount.com"
google.batch.bootDiskSize = '50 GB'
google.batch.usePrivateAddress = true
google.batch.network = "projects/${GOOGLE_CLOUD_PROJECT}/global/networks/network"
google.batch.subnetwork = "projects/${GOOGLE_CLOUD_PROJECT}/regions/${GCS_BUCKET_LOCATION}/subnetworks/subnetwork"
google.batch.network = "projects/vwb-dev-beaming-sprout-9366/global/networks/network"
google.batch.subnetwork = "projects/vwb-dev-beaming-sprout-9366/regions/us-central1/subnetworks/subnetwork"
google.httpConnectTimeout = '10m'
google.httpReadTimeout = '10m'
google.batch.maxSpotAttempts = 5
Expand Down
34 changes: 16 additions & 18 deletions nextflow/amr-on-wb/params_google_batch.config
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Original file line number Diff line number Diff line change
@@ -1,20 +1,18 @@
/* * Google Batch Configuration File
* This file sets all parameters for running on Google Cloud Batch.
* It uses the 'GCS_BUCKET' environment variable to define paths.
*/

// Grabs the GCS_BUCKET environment variable. Defaults to 'nf-files' if not set.
def gcs_bucket = System.getenv("GCS_BUCKET") ?: "nf-files"
*/

params {
/* Display help message */
help = false

pipeline = "fast_AMR"

// -----------------------------------------------------------------
// Input Data
// -----------------------------------------------------------------
/* Location of forward and reverse read pairs */
reads = "gs://${gcs_bucket}/data/raw/*_R{1,2}.fastq.gz"
reads = "gs://sam-nextflow-vwb-dev-beaming-sprout-9366/amr-on-wb/data/raw/*_R{1,2}.fastq.gz"

/* Optional input for bam files for use with "--pipeline bam_resistome" */
bam_files = null
Expand All @@ -23,37 +21,37 @@ params {
// Reference Databases
// -----------------------------------------------------------------
/* Location of reference/host genome */
host = "gs://${gcs_bucket}/data/host/chr21.fasta.gz"
host = "gs://sam-nextflow-vwb-dev-beaming-sprout-9366/amr-on-wb/data/host/chr21.fasta.gz"

/* Host index files created with bwa */
host_index = "gs://${gcs_bucket}/data/host/chr21.fasta.gz*"
host_index = "gs://sam-nextflow-vwb-dev-beaming-sprout-9366/amr-on-wb/data/host/chr21.fasta.gz*"

/* Location of amr index files with wildcard - set to null to build automatically */
amr_index = null

/* Location of antimicrobial resistance (MEGARes) database */
amr = "gs://${gcs_bucket}/data/amr/megares_database_v3.00.fasta"
amr = "gs://sam-nextflow-vwb-dev-beaming-sprout-9366/amr-on-wb/data/amr/megares_database_v3.00.fasta"

/* Location of amr annotation file */
annotation = "gs://${gcs_bucket}/data/amr/megares_annotations_v3.00.csv"
annotation = "gs://sam-nextflow-vwb-dev-beaming-sprout-9366/amr-on-wb/data/amr/megares_annotations_v3.00.csv"

/* Kraken database location */
/* Kraken database location */
kraken_db = null

/* Kraken confidence score */
kraken_confidence = 0.0

// -----------------------------------------------------------------
// Output
// -----------------------------------------------------------------
/* Output directory - Saved to Cloud Storage */
output = "gs://${gcs_bucket}/results/test_results"
output = "gs://sam-nextflow-vwb-dev-beaming-sprout-9366/amr-on-wb/results/test_results"

// -----------------------------------------------------------------
// Pipeline Logic & Analysis Toggles
// -----------------------------------------------------------------
/* Add SNP analysis */
snp = "Y"
snp = "N"

/* Add deduplicaation analysis */
deduped = "N"
Expand All @@ -66,7 +64,7 @@ params {
// Trimming Parameters (Trimmomatic)
// -----------------------------------------------------------------
/* Adapters file location */
adapters = "gs://${gcs_bucket}/data/adapters/nextera.fa"
adapters = "gs://sam-nextflow-vwb-dev-beaming-sprout-9366/amr-on-wb/data/adapters/nextera.fa"

leading = 3
trailing = 3
Expand Down Expand Up @@ -95,7 +93,7 @@ params {
// Other Tools
// -----------------------------------------------------------------
/* multiQC config folder */
multiqc = "gs://${gcs_bucket}/data/multiqc"
multiqc = "gs://sam-nextflow-vwb-dev-beaming-sprout-9366/amr-on-wb/data/multiqc"

/* Qiime2 Parameters */
p_trim_left_f = 25
Expand All @@ -104,7 +102,7 @@ params {
p_trunc_len_r = 220

/* qiime2 bayes classifier */
dada2_db = "gs://${gcs_bucket}/data/qiime/gg-13-8-99-515-806-nb-classifier.qza"
dada2_db = "gs://sam-nextflow-vwb-dev-beaming-sprout-9366/amr-on-wb/data/qiime/gg-13-8-99-515-806-nb-classifier.qza"
}

// -----------------------------------------------------------------
Expand All @@ -124,4 +122,4 @@ env {
/* These next tools are optional depending on which analyses you want to run */
KRAKEN2 = "kraken2"
QIIME = "qiime"
}
}
31 changes: 31 additions & 0 deletions nextflow/amr-on-wb/params_google_batch.yaml
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@@ -0,0 +1,31 @@
pipeline: "fast_AMR"
reads: "gs://sam-nextflow-vwb-dev-beaming-sprout-9366/amr-on-wb/data/raw/*_R{1,2}.fastq.gz"
bam_files: null
host: "gs://sam-nextflow-vwb-dev-beaming-sprout-9366/amr-on-wb/data/host/chr21.fasta.gz"
host_index: "gs://sam-nextflow-vwb-dev-beaming-sprout-9366/amr-on-wb/data/host/chr21.fasta.gz*"
amr_index: null
amr: "gs://sam-nextflow-vwb-dev-beaming-sprout-9366/amr-on-wb/data/amr/megares_database_v3.00.fasta"
annotation: "gs://sam-nextflow-vwb-dev-beaming-sprout-9366/amr-on-wb/data/amr/megares_annotations_v3.00.csv"
kraken_db: null
kraken_confidence: 0.0
output: "gs://sam-nextflow-vwb-dev-beaming-sprout-9366/amr-on-wb/results/test_results"
snp: "N"
deduped: "N"
prefix: "AMR"
threads: 4
adapters: "gs://sam-nextflow-vwb-dev-beaming-sprout-9366/amr-on-wb/data/adapters/nextera.fa"
leading: 3
trailing: 3
slidingwindow: "4:15"
minlen: 36
threshold: 80
min: 5
max: 100
skip: 5
samples: 1
multiqc: "gs://sam-nextflow-vwb-dev-beaming-sprout-9366/amr-on-wb/data/multiqc"
p_trim_left_f: 25
p_trim_left_r: 26
p_trunc_len_f: 225
p_trunc_len_r: 220
dada2_db: "gs://sam-nextflow-vwb-dev-beaming-sprout-9366/amr-on-wb/data/qiime/gg-13-8-99-515-806-nb-classifier.qza"
2 changes: 1 addition & 1 deletion nextflow/amr-on-wb/scripts/upload_data.sh
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Expand Up @@ -26,4 +26,4 @@ source "$CONFIG_FILE"
DATA_DIR="${SCRIPT_DIR}/../data"

# Upload data to GCS bucket
gcloud storage cp -r "${DATA_DIR}" gs://${GCS_BUCKET}/
gcloud storage cp -r "${DATA_DIR}" gs://${GCS_BUCKET}/amr-on-wb/