From af01fccba1be7ffa4bc1d84d8e31e4f0a3f6c86f Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Tue, 7 Jul 2020 14:31:11 +0200
Subject: [PATCH] Add a HOPS profile for nf-core/eager @ SHH

---
 conf/pipeline/eager/shh.config | 42 ++++++++++++++++++++++++++++++----
 1 file changed, 38 insertions(+), 4 deletions(-)

diff --git a/conf/pipeline/eager/shh.config b/conf/pipeline/eager/shh.config
index 5d8b576..8001823 100644
--- a/conf/pipeline/eager/shh.config
+++ b/conf/pipeline/eager/shh.config
@@ -5,10 +5,6 @@ params {
   config_profile_contact = 'James Fellows Yates (@jfy133)'
   config_profile_description = 'nf-core/eager SHH profile provided by nf-core/configs'
   igenomes_base = "/projects1/public_data/igenomes/"
-  
-  // default BWA
-   bwaalnn = 0.04
-   bwaalnl = 32
 }
 
 // Specific nf-core/eager process configuration
@@ -26,6 +22,44 @@ process {
 }
 
 profiles {
+  hops {
+    pathogen_screening {
+      fasta = '/projects1/Reference_Genomes/Human/HG19/hg19_complete.fasta'
+      bwa_index = '/projects1/Reference_Genomes/Human/HG19/hg19_complete.fasta'
+      fasta_index = '/projects1/Reference_Genomes/Human/HG19/hg19_complete.fasta.fai'
+      seq_dict = '/projects1/Reference_Genomes/Human/HG19/hg19_complete.dict'
+      bwaalnn = 0.04
+      bwaalnl = 32
+      run_bam_filtering = true
+      bam_discard_unmapped = true
+      bam_unmapped_type = 'fastq'
+      run_metagenomic_screening = true
+      metagenomic_tool = 'malt'
+      metagenomic_min_support_reads = 1
+      database = '/projects1/malt/databases/indexed/index040/full-bac-full-vir-etal-nov_2017'
+      percent_identity = 90
+      malt_mode = 'BlastN'
+      malt_alignment_mode = 'SemiGlobal'
+      malt_top_percent = 1
+      malt_min_support_mode = 'percent'
+      malt_min_support_percent = 0.01
+      malt_max_queries = 100
+      malt_memory_mode = 'load'
+      run_maltextract = true
+      maltextract_taxon_list = '/projects1/users/key/anc5h/soi.backup/List_of_pathogens_KB_fmk12_wViruses1.txt'
+      maltextract_ncbifiles = '/projects1/clusterhomes/huebler/RMASifter/RMA_Extractor_Resources/'
+      maltextract_filter = 'def_anc'
+      maltextract_toppercent = 0.01
+      maltextract_destackingoff = false
+      maltextract_downsamplingoff = false
+      maltextract_duplicateremovaloff = false
+      maltextract_matches = false
+      maltextract_megansummary = false
+      maltextract_percentidentity = 90.0
+      maltextract_topalignment =  false
+      maltextract_singlestranded = false
+    }
+  }
   pathogen_loose {
     params {
       config_profile_description = 'Pathogen (loose) MPI-SHH profile, provided by nf-core/configs.'