<commit_before>################################################################
#
#
# Pipeline pipeline_scrnaseq.py configuration file for sphinxreport
#
# This pipeline.ini file lists some configuration options that you might
# want a user to set automatically.
#
# Add pipeline specific options into separate sections
#
################################################################
# general options
[general]

# Project name
projectname=SingleCellRNASeq001

# Copyright statement
copyright=Sansom Group, Kennedy Institute of Rheumatology (2014-2015)

# The short X.Y version.
version=0.1

# The full version, including alpha/beta/rc tags.
release=0.1

# Sample name specification
# Only hypens or underscores should be used for sql
# compatibility
name_field_separator=-
name_field_titles=source,condition,plate,row,column



########################################################
# the genome to use (UCSC convention)
genome=mm10_ercc92

# if not set it is assummed that the accompanying python module
# is in the same location as the executed pipeline
# when executing P.submit() functions.
code_dir=

rsource=PipelineScRnaseq.R

# specify the input file type
# can be either "fastq" or "bam"
# mixed input files types are not supported
input=fastq


[fastq]
# Directory with Fastq files
# Fastq files names are expected to follow the syntax:
# source-condition-plate-row-column.fastq[.1|2].gz
dir=data.dir

# input is paired fastq files - if single end data set to 0
paired=1



[bam]
# Directory with BAM files + indexes
# - Bam files must be sorted by position
# - Bam file names are expected to follow the format eg :
# source-condition-plate-row-column.mapper.bam
dir=data.dir

# input is paired bam files - if single end data set to 0
paired=1



################################################################
#
# Location of annotation database
#
################################################################
[annotations]
genome_dir=/gfs/mirror/genomes/plain/
database=/gfs/mirror/annotations/mm10_ensembl83/csvdb

# directory with annotation information
dir=/gfs/mirror/annotations/mm10_ensembl83
ensembl_geneset=ensembl.dir/geneset_all.gtf.gz
ercc92_geneset=/gfs/projects/proj006/annotations/ercc92/ERCC92.gtf.gz
ercc92_info=/gfs/projects/proj006/annotations/ercc92/ercc.txt

[hisat]
executable=hisat2

# In order to map against known splice sites
# an index built with the transcriptome should be used
# or the option --known-splice-infile specified
# Note that the authors advise use of a transcriptome
# index to be superior
index=/gfs/mirror/genomes/hisat2/mm10_ercc92.ensembl83.genome_trans.dir/mm10_ercc92
threads=4
options="-k 20 --score-min L,0.0,-0.2"

[cufflinks]
cuffquant_threads=4
cuffnorm_threads=16

[picard]
geneset_flat=/gfs/mirror/ucsc/mm10/database/refFlat.txt.gz
strand_specificity=NONE
validation_stringency=SILENT
threads=3
memory=2G

#use to pass additional options to picard
alignmentsummarymetrics_options=
collectrnaseqmetrics_options=
estimatelibrarycomplexity_options=
insertsizemetric_options=

[qcthresholds]



################################################################
#
# sphinxreport build options
#
################################################################
[report]

# prefix to use for publishing the report from this pipeline<commit_msg>Removed -k option from hisat2 settings, added --dta option to hisat2 settings.<commit_after>################################################################
#
#
# Pipeline pipeline_scrnaseq.py configuration file for sphinxreport
#
# This pipeline.ini file lists some configuration options that you might
# want a user to set automatically.
#
# Add pipeline specific options into separate sections
#
################################################################
# general options
[general]

# Project name
projectname=SingleCellRNASeq001

# Copyright statement
copyright=Sansom Group, Kennedy Institute of Rheumatology (2014-2015)

# The short X.Y version.
version=0.1

# The full version, including alpha/beta/rc tags.
release=0.1

# Sample name specification
# Only hypens or underscores should be used for sql
# compatibility
name_field_separator=-
name_field_titles=source,condition,plate,row,column



########################################################
# the genome to use (UCSC convention)
genome=mm10_ercc92

# if not set it is assummed that the accompanying python module
# is in the same location as the executed pipeline
# when executing P.submit() functions.
code_dir=

rsource=PipelineScRnaseq.R

# specify the input file type
# can be either "fastq" or "bam"
# mixed input files types are not supported
input=fastq


[fastq]
# Directory with Fastq files
# Fastq files names are expected to follow the syntax:
# source-condition-plate-row-column.fastq[.1|2].gz
dir=data.dir

# input is paired fastq files - if single end data set to 0
paired=1



[bam]
# Directory with BAM files + indexes
# - Bam files must be sorted by position
# - Bam file names are expected to follow the format eg :
# source-condition-plate-row-column.mapper.bam
dir=data.dir

# input is paired bam files - if single end data set to 0
paired=1



################################################################
#
# Location of annotation database
#
################################################################
[annotations]
genome_dir=/gfs/mirror/genomes/plain/
database=/gfs/mirror/annotations/mm10_ensembl83/csvdb

# directory with annotation information
dir=/gfs/mirror/annotations/mm10_ensembl83
ensembl_geneset=ensembl.dir/geneset_all.gtf.gz
ercc92_geneset=/gfs/projects/proj006/annotations/ercc92/ERCC92.gtf.gz
ercc92_info=/gfs/projects/proj006/annotations/ercc92/ercc.txt

[hisat]
executable=hisat2

# In order to map against known splice sites
# an index built with the transcriptome should be used
# or the option --known-splice-infile specified
# Note that the authors advise use of a transcriptome
# index to be superior
index=/gfs/mirror/genomes/hisat2/mm10_ercc92.ensembl83.genome_trans.dir/mm10_ercc92
threads=4
options="--dta --score-min L,0.0,-0.2"

[cufflinks]
cuffquant_threads=4
cuffnorm_threads=16

[picard]
geneset_flat=/gfs/mirror/ucsc/mm10/database/refFlat.txt.gz
strand_specificity=NONE
validation_stringency=SILENT
threads=3
memory=2G

#use to pass additional options to picard
alignmentsummarymetrics_options=
collectrnaseqmetrics_options=
estimatelibrarycomplexity_options=
insertsizemetric_options=

[qcthresholds]



################################################################
#
# sphinxreport build options
#
################################################################
[report]

# prefix to use for publishing the report from this pipeline
{'fraction_non_alphanumeric': 0.19943190312453282, 'fraction_numerical': 0.022424876663178352, 'mean_word_length': 6.027310924369748, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, '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': '7544907', 'n_tokens_mistral': 2098, 'n_tokens_neox': 1897, 'n_words': 577}