adding base seqera

Author: Merritt-Brian

conf/seqera.config

@@ -0,0 +1,53 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run https://github.com/jhuapl-bio/taxtriage -latest -profile test,docker  -r main
+
+----------------------------------------------------------------------------------------
+*/
+aws.client.anonymous = false
+
+params {
+    config_profile_name        = 'MCE profile for the cloud'
+    config_profile_description = 'Default profile for running MCE analysis on a variety of sample types on seqera tower'
+
+    // Limit resources so that this can run on GitHub Actions
+    max_cpus   = 16
+    max_time   = '24.h'
+
+    // Input data
+    // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
+    // TODO nf-core: Give any required params for the test so that command line flags are not needed
+    input  = 'https://raw.githubusercontent.com/jhuapl-bio/taxtriage/main/examples/Samplesheet.csv'
+
+    // Genome references
+    skip_plots = false
+    download_db = true
+    remove_taxids = "9606"
+    ignore_missing = true
+    skip_denovo = true
+    skip_refpull = false
+    demux = true
+    remove_commensal = true
+    classifiers = 'kraken2'
+    outdir = 'test_output'
+    top_hits_count = 20
+    taxtab = 'default'
+    default_download = true
+    annotate = true
+    db = 's3://nftass/databases/k2_standard_20230605/'
+    top_per_taxa = '10239:20:S 2:20:S 4751:20:S'
+    outdir = 'test_output'
+    k2_minimum_hit_groups = 3
+    min_reads_align = 3
+    low_memory = false
+    split_prefix = false
+    min_conf = null
+    compress_species = false
+    remove_reference_file = "s3://nftass/databases/references/HomoSapiens/GrCh38/genome.fa"
+    minmapq = 4
+}

nextflow.config

@@ -369,6 +369,7 @@ profiles {
     local { includeConfig 'conf/local.config' }
     mce { includeConfig 'conf/mce.config' }
     mce_seqera { includeConfig 'conf/mce_seqera.config' }
+    seqera { includeConfig 'conf/seqera.config' }
 }
 apptainer.registry = 'quay.io'
 docker.registry = 'quay.io'