Add viral reference, only use after removing human and bacterial read…

…s eg with unmapped.fastq
MHH-RCUG · Mar 9, 2020 · c062aab · c062aab
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diff --git a/run_Wochenende.py b/run_Wochenende.py
@@ -4,16 +4,11 @@
 A whole genome/metagenome analysis pipeline in Python3
 Author: Tobias Scheithauer
 Author: Dr. Colin Davenport
-Author: Fabian Friedrich
 
 TODOs:
-- Also trial with far more comprehensive bbmap adapters
-- Add test slurmscripts to check errors
 - handle TruSeq and NEB Next adapters
   and test this vs alternatives to Trimmomatic, eg
-
 Changelog
-1.5 restructure wochenende_reporting, requires Python3.6+
 1.4 add wochenende_plot.py file plotting
 1.3 add samtools flagstat to get per cent reads aligned
 1.3 add --testWochenende tests to test pipeline functionality and report success on a small reference
@@ -30,13 +25,13 @@
 import argparse
 import time
 
-version = "1.5 - Mar 2020"
+version = "1.4 - Feb 2020"
 
 ##############################
 # CONFIGURATION
 ##############################
 
-## Paths to commands - please edit as appropriate. If it is in your PATH just type the command. We recommend conda.
+## Paths to commands. If it is in your PATH just type the command. We recommend conda.
 path_fastqc      = 'fastqc'
 path_afterqc     = '/mnt/ngsnfs/tools/afterQC/AfterQC-0.9.6/after.py'
 path_fastp       = '/mnt/ngsnfs/tools/fastp/fastp'
@@ -53,7 +48,7 @@
 path_java        = 'java'
 path_abra_jar    = '/mnt/ngsnfs/tools/abra2/abra2_latest.jar'
 path_minimap2    = 'minimap2'
-## Paths to reference seqs. Edit as appropriate!
+## Paths to reference seqs
 path_refseq_dict = {
     "2016_06_1p_genus" : "/working2/tuem/metagen/refs/2016/bwa/2016_06_PPKC_metagenome_test_1p_genus.fa",
     "2016_06_1p_spec_corrected" : "/lager2/rcug/seqres/metagenref/bwa/2016_06_PPKC_metagenome_test_1p_spec_change_cln.fa",
@@ -75,9 +70,9 @@
     "zf10": "/lager2/rcug/seqres/DR/bwa/GRCz10.fa",
     "ss11": "/lager2/rcug/seqres/SS/bwa/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa",
     "PA14": "/lager2/rcug/seqres/PA/bwa/NC_008463.fna",
+    "nci_viruses": "/lager2/rcug/seqres/metagenref/bwa/nci_viruses.fa",
     "testdb": "testdb/ref.fa",
 }
-# Adapters - edit as appropriate
 ea_adapter_fasta = '/mnt/ngsnfs/tools/miniconda2/pkgs/bbmap-37.17-0/opt/bbmap-37.17/resources/adapters.fa'
 adapter_fasta = '/mnt/ngsnfs/tools/miniconda3/envs/wochenende/share/trimmomatic-0.38-0/adapters/TruSeq3-PE.fa'
 ## Other
@@ -262,7 +257,6 @@ def runFastpPE(stage_infile_1, stage_infile_2, noThreads):
     fastpcmd = [path_fastp, '--in1='+ stage_infile_1, '--out1='+ stage_outfile,
                 '--in2='+ stage_infile_2, '--out2='+ deriveRead2Name(stage_outfile),
                 '--disable_quality_filtering', '--disable_length_filtering',
-                '--length_required=35',
                 '--cut_by_quality5', '--cut_window_size=5',
                 '--cut_mean_quality=15', '--html='+ prefix + '.html',
                 '--json='+ prefix + '.json', '--thread='+ noThreads]

diff --git a/run_Wochenende_SLURM.sh b/run_Wochenende_SLURM.sh
@@ -1,6 +1,5 @@
 #!/bin/bash
-## A SLURM sbatch script which is part of the Wochenende Pipeline
-## Supply the FASTA input as arg1, bash run_Wochenende_slurm.sh in_R1.fastq
+## Supply the FASTA input as arg1, bash run_Wochenende_slurm.sh in.fastq
 
 # set partition
 #SBATCH -p normal
@@ -61,7 +60,7 @@ cpus=12
 # Run script - Paired end reads R2 will be calculated by replacing R1 with R2
 
 # Test wochenende pipeline. Run tests with sbatch run_Wochenende_SLURM.sh testdb/reads_R1.fastq
-python3 run_Wochenende.py --metagenome testdb --threads $cpus --testWochenende --aligner bwamem --mq30 --remove_mismatching --readType SE --debug --force_restart $fastq
+#python3 run_Wochenende.py --metagenome testdb --threads $cpus --testWochenende --aligner bwamem --mq30 --remove_mismatching --readType SE --debug --force_restart $fastq
 
 # Test wochenemde with fastp - the auto tests here will fail here since fastp not trm is in the filename
 #python3 run_Wochenende.py --metagenome testdb --fastp --threads $cpus --testWochenende --aligner bwamem --mq30 --remove_mismatching --readType SE --debug --force_restart $fastq
@@ -79,6 +78,11 @@ python3 run_Wochenende.py --metagenome testdb --threads $cpus --testWochenende -
 #python3 run_Wochenende.py --metagenome 2019_01_meta_mouse_ASF --threads $cpus --aligner bwamem --no_abra --mq30 --remove_mismatching --readType SE --debug --force_restart $fastq
 #python3 run_Wochenende.py --metagenome 2019_01_meta_mouse_OMM --threads $cpus --aligner bwamem --no_abra --mq30 --remove_mismatching --readType SE --debug --force_restart $fastq
 
+## 2020 03 NCI viruses only - with mq30
+#python3 run_Wochenende.py --metagenome nci_viruses --threads $cpus --aligner bwamem --no_abra --mq30 --remove_mismatching --readType SE --debug --force_restart $fastq
+## 2020 03 NCI viruses only - no mq30
+python3 run_Wochenende.py --metagenome nci_viruses --threads $cpus --aligner bwamem --no_abra --remove_mismatching --readType SE --debug --force_restart $fastq
+
 #2016 2016_06_PPKC_metagenome_test_1p_spec_change
 #python3 run_Wochenende.py --metagenome 2016_06_1p_spec_corrected --threads $cpus  --readType SE --debug --force_restart $fastq
 #python3 run_Wochenende.py --metagenome 2016_06_1p_spec_corrected --threads $cpus --aligner bwamem --no_abra --mq30 --readType SE --debug --force_restart $fastq