start_nf.sh

#!/bin/bash
# Start the nf_wochenende pipeline

# get most current version
git pull -q

# ignore system JAVA_HOME, use that supplied by wochenende conda env for nextflow
unset JAVA_HOME

# get test
cp test/data/*.fastq . && bwa index test/data/ref.fa

# run pipeline, no bash variables allowed as empty strings evaluate to true in groovy
#nextflow run nf_wochenende.nf  -with-timeline -with-report -with-dag flowchart.dot --metagenome Ath --aligner minimap2long --remove_mismatching 250 --mq30 --readType SE --longread --no_dup_removal --no_abra --fastq test_sm.fastq
# run test
nextflow run nf_wochenende.nf  -with-timeline -with-report --metagenome testdb --aligner bwamem --remove_mismatching 2 --mq30 --readType PE  --no_dup_removal --no_abra --fastq *R1.fastq


# python3 /run_Wochenende.py --ref  --threads 16 --aligner minimap2-long   250 SE  --debug --force_restart test_sm.fastq





# All options
# --threads 12
#--longread (implies aligner is not bwa-mem, no prinseq, no duplicate removal)
#--aligner bwamem
#--aligner minimap2short   (for Illumina reads)
#--aligner minimap2long    (for nanopore reads)
#--aligner ngmlr
#--nextera  - remove Nextera adapters with Trimmomatic, not default Ultra II / Truseq adapters
#--no_abra  - no read realignment
#--mq20     - remove reads with a mapping quality of less than 20. Less stringent than MQ30, required for raspir https://github.com/mmpust/raspir
#--mq30     - remove reads with a mapping quality of less than 30
#--readType SE - single ended reads
#--readType PE - paired end reads
#--debug
#--force_restart
#--remove_mismatching 3 (remove those reads with 3 or more mismatches) # questionable for very long reads
#--remove_mismatching 250 (remove those reads with 250 or more mismatches) # for long reads set to ~10% of median read length.
#--no_duplicate_removal  - do not remove duplicate reads
#--no_prinseq   - do not filter out low complexity initial reads using prinseq (default in this file after 2020_11)
#--no_fastqc
#--testWochenende - runs the test scripts with test reads vs a testDB and checks if all seems well.
#--fastp - fastp is recommended as an alternative trimmer to Trimmomatic if you are having adapter problems
#--trim_galore - trim_galore is the best adapter trimmer for nextera reads