<commit_before># author: <NAME>
# date: May 2013

#####################################
# Resources
#####################################

#********************
# Tasks
#********************

RUNMAPPINGBWA="1"     # mapping with bwa

#********************
# Paths
#********************

SOURCE=$(pwd)

# which folder to run on (i.e. folders within fastq directory)
declare -a DIR; DIR=( sample1 sample2 )

# folder/task containing the data this task operates on
INPUT_BWA="fastq"

# where to write the output
OUT=$SOURCE

# where to write the log files
QOUT=$OUT/qout

#********************
# PARAMETER (mandatory)
#********************

# fastq file suffix
FASTQ="fastq.gz"

# read indicator immediately preceding the fastq file suffix
READONE="_R1"
READTWO="_R2"

# reference genome
# e.g. /share/ClusterShare/biodata/contrib/genomeIndices_garvan/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/genome.fa
# or ${NGSANE_REFERENCE}/b37/human_g1k_v37.fasta
FASTA=

# library tags
EXPID="Celltype"
LIBRARY="RNAseq"
PLATFORM="Illumina"

#********************
# PARAMETER (optional overwriting defaults)
#********************

# FASTQ encoding (Phred score), leave empty to detect automatically
# e.g. "Phred33" (Sanger, Illumina 1.8+), "Phred64" (Solexa, Illumina 1.5)
FASTQ_ENCODING=

# Activate iterative mapping by providing 3 arguments. 
# 1) maximum read length, 2) negative step size 3) minimum read length
# e.g. “90 -10 20” for all reads from 100bp to 20bp with step size 10bp
BWA_ITERATIVE=

## additional bwa parameters
BWAALNADDPARAM=
BWASAMPLEADDPARAM=

#WALLTIME_BWA=50:00:00
#MEMORY_BWA=50
#CPU_BWA=32
#NODES_BWA="nodes=4:ppn=8"
#MODULE_BWA=
#PATH_BWA=<commit_msg>quote characters replaced<commit_after># author: <NAME>
# date: May 2013

#####################################
# Resources
#####################################

#********************
# Tasks
#********************

RUNMAPPINGBWA="1"     # mapping with bwa

#********************
# Paths
#********************

SOURCE=$(pwd)

# which folder to run on (i.e. folders within fastq directory)
declare -a DIR; DIR=( sample1 sample2 )

# folder/task containing the data this task operates on
INPUT_BWA="fastq"

# where to write the output
OUT=$SOURCE

# where to write the log files
QOUT=$OUT/qout

#********************
# PARAMETER (mandatory)
#********************

# fastq file suffix
FASTQ="fastq.gz"

# read indicator immediately preceding the fastq file suffix
READONE="_R1"
READTWO="_R2"

# reference genome
# e.g. /share/ClusterShare/biodata/contrib/genomeIndices_garvan/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/genome.fa
# or ${NGSANE_REFERENCE}/b37/human_g1k_v37.fasta
FASTA=

# library tags
EXPID="Celltype"
LIBRARY="RNAseq"
PLATFORM="Illumina"

#********************
# PARAMETER (optional overwriting defaults)
#********************

# FASTQ encoding (Phred score), leave empty to detect automatically
# e.g. "Phred33" (Sanger, Illumina 1.8+), "Phred64" (Solexa, Illumina 1.5)
FASTQ_ENCODING=

# Activate iterative mapping by providing 3 arguments. 
# 1) maximum read length, 2) negative step size 3) minimum read length
# e.g. "90 -10 20" for all reads from 100bp to 20bp with step size 10bp
BWA_ITERATIVE=

## additional bwa parameters
BWAALNADDPARAM=
BWASAMPLEADDPARAM=

#WALLTIME_BWA=50:00:00
#MEMORY_BWA=50
#CPU_BWA=32
#NODES_BWA="nodes=4:ppn=8"
#MODULE_BWA=
#PATH_BWA=
{'fraction_non_alphanumeric': 0.23529411764705882, 'fraction_numerical': 0.0314913844325609, 'mean_word_length': 6.029227557411273, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 5, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '1656731', 'n_tokens_mistral': 1251, 'n_tokens_neox': 1156, 'n_words': 299}