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

## NOTE: HT-Seq-count expects a GTF with the doctored version being available at the same location. Its only be tested using GENCODE GTFs although other GTFs may work too

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

#********************
# Tasks
#********************
RUNHTSEQCOUNT="1"    # feature counting

#********************
# 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_HTSEQCOUNT=$TASK_TOPHAT

# where to write the output
OUT=$SOURCE

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

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

# specify library type for tophat.
# choose "fr-firststrand" "fr-unstranded" "fr-secondstrand"
RNA_SEQ_LIBRARY_TYPE="fr-firststrand"

# any combination of "union" "intersection-strict" and "intersection-nonempty"
HTSEQCOUNT_MODES=

# e.g. "gene_id" and/or "transcript_id"
HTSEQCOUNT_ATTRIBUTES=

#only use uniquely (NF:i:1) mapping reads for ht-seq-count
HTSEQCOUNT_UNIQUE=1

# ATTENTION: make sure the GTF file matches your genome assembly (chr naming)
# see https://bitbucket.org/allpowerde/gtf_doctor for more informations and
# conversion scripts
# e.g. /share/ClusterShare/biodata/contrib/GENCODE/release_14/gencode.v14.annotation.gtf
# or   /share/ClusterShare/biodata/contrib/GENCODE/release_14/gencode.v14.annotation.b37.gtf
GTF=

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

# additional parameters for HTSEQ-count call
HTSEQCOUNT_ADDPARAMS=

# activate to use doctored GTF file for HTSeq-count (provides additional info)
# assumes the doctored GTF is at the same location as the original one but
# has a different suffix
#DOCTOREDGTFSUFFIX=".doctored.gtf"

# keep intermediate bam files generated for htseqcount (default remove bams)
# e.g. HTSEQCOUNT_KEEPBAMS="yes" to keep files
HTSEQCOUNT_KEEPBAMS=

# whether to skip output with tRNA, rRNA etc masked in gtf
# e.g. HTSEQCOUNT_SKIPMASKED="yes" to skip
HTSEQCOUNT_SKIPMASKED=

#WALLTIME_HTSEQCOUNT=24:00:00
#MEMORY_HTSEQCOUNT=50
#CPU_HTSEQCOUNT=1
#NODES_HTSEQCOUNT="nodes=1:ppn=1"
#MODULE_HTSEQCOUNT=
#PATH_HTSEQCOUNT=








<commit_msg>support custom naming of countstable output folder<commit_after># author: <NAME>
# date: September 2013

## NOTE: HT-Seq-count expects a GTF with the doctored version being available at the same location. Its only be tested using GENCODE GTFs although other GTFs may work too

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

#********************
# Tasks
#********************
RUNHTSEQCOUNT="1"    # feature counting

#********************
# 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_HTSEQCOUNT=$TASK_TOPHAT

# where to write the output
OUT=$SOURCE

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

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

# specify library type for tophat.
# choose "fr-firststrand" "fr-unstranded" "fr-secondstrand"
RNA_SEQ_LIBRARY_TYPE="fr-firststrand"

# any combination of "union" "intersection-strict" and "intersection-nonempty"
HTSEQCOUNT_MODES=

# e.g. "gene_id" and/or "transcript_id"
HTSEQCOUNT_ATTRIBUTES=

#only use uniquely (NF:i:1) mapping reads for ht-seq-count
HTSEQCOUNT_UNIQUE=1

# ATTENTION: make sure the GTF file matches your genome assembly (chr naming)
# see https://bitbucket.org/allpowerde/gtf_doctor for more informations and
# conversion scripts
# e.g. /share/ClusterShare/biodata/contrib/GENCODE/release_14/gencode.v14.annotation.gtf
# or   /share/ClusterShare/biodata/contrib/GENCODE/release_14/gencode.v14.annotation.b37.gtf
GTF=

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

# additional parameters for HTSEQ-count call
HTSEQCOUNT_ADDPARAMS=

# activate to use doctored GTF file for HTSeq-count (provides additional info)
# assumes the doctored GTF is at the same location as the original one but
# has a different suffix
#DOCTOREDGTFSUFFIX=".doctored.gtf"

# keep intermediate bam files generated for htseqcount (default remove bams)
# e.g. HTSEQCOUNT_KEEPBAMS="yes" to keep files
HTSEQCOUNT_KEEPBAMS=

# whether to skip output with tRNA, rRNA etc masked in gtf
# e.g. HTSEQCOUNT_SKIPMASKED="yes" to skip
HTSEQCOUNT_SKIPMASKED=

# name of the folder that will contain the aggregated counts table over all libraries
# if not set, defaults to a concatenation of the library folders
HTSEQCOUNT_TABLE_FOLDERNAME="htseqcount-countstable"

#WALLTIME_HTSEQCOUNT=24:00:00
#MEMORY_HTSEQCOUNT=50
#CPU_HTSEQCOUNT=1
#NODES_HTSEQCOUNT="nodes=1:ppn=1"
#MODULE_HTSEQCOUNT=
#PATH_HTSEQCOUNT=









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