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Jimmy branch #4

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37f19ab
changed sambamba section and salmon index rule
jimmybgammyknee May 13, 2017
c7dbe63
merged
jimmybgammyknee May 13, 2017
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27 changes: 26 additions & 1 deletion snakefile.py
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Original file line number Diff line number Diff line change
Expand Up @@ -85,8 +85,13 @@
## Specify targets
rule all:
input:
<<<<<<< HEAD
QUANT_feat + QUANT_salmon #QC_trim + QC_raw +

=======
QC_trim + QC_raw + QUANT_feat + QUANT_salmon + KAL + STRING_ass + STRING_geneAbund + STRING_covRefs, STRING_merge, STRING_mergeTranscript
# RG
>>>>>>> 5b6a267cea71fb09bb289c6c3a54ea3b7b8daec7

##--------------------------------------##
## 1. Adapter removal ##
Expand Down Expand Up @@ -179,6 +184,7 @@
unmapped = config["BASE"] + config["BAMS"] + config["unmapped"] + '/{samples}_unmapped.fastq',
B1 = temp(config["BASE"] + config["BAMS"] + '/{samples}_temp.bam'),
B2 = config["BASE"] + config["BAMS"] + '/{samples}.bam'
B3 = config["BASE"] + config["BAMS"] + '/{samples}.nodup.bam'
params:
hisat2 = config["hisat2"],
sambamba = config["sambamba"],
Expand All @@ -193,8 +199,9 @@
shell:
"""
({params.hisat2} -p {threads} -x {params.idx} --un-gz {output.unmapped} -1 {input.R1} -2 {input.R2} | \
samtools view -bhS -q{params.qual} - 1> {output.B1}) 2> {log}
samtools view -bhS -q{params.qual} - 1> {output.B1}) 2> {log}
{params.sambamba} sort -p -t {threads} -o {output.B2} {output.B1}
{params.sambamba} markdup -p -r -t {threads} {output.B2} {output.B3}
"""


Expand All @@ -210,6 +217,22 @@
B1 = temp(config["BASE"] + config["BAMS"] + '/{samples}_temp.bam'),
B2 = config["BASE"] + config["BAMS"] + '/{samples}.bam'
params:
<<<<<<< HEAD
salmon = config["salmon"],
index = config["INDEX_DIR"],
bootstrap = config["bootstrap"],
out = config["BASE"] + config["QUANT_SAL"] + "/{samples}/"
threads: config["SAL_threads"]
message:
"Salmon - Quantification of transcripts"
log:
config["BASE"] + config["LOG"] + config["QUANT_SAL"] + "/{samples}.log"

shell:
"""
{params.salmon} quant -l A -i {params.index} -p {threads} -1 {input.R1} -2 {input.R2} \
--numBootstraps {params.bootstrap} -o {params.out} 2> {log}
=======
sambamba = config["sambamba"],
genomeDir = config["genomeDir"],
compress = config["compress"]
Expand All @@ -228,8 +251,10 @@
--outBAMcompression {params.compress} | \
samtools view -bhS -q{params.qual} - 1> {output.B1}) 2> {log}
{params.sambamba} sort -p -t {threads} -o {output.B2} {output.B1}
>>>>>>> 5b6a267cea71fb09bb289c6c3a54ea3b7b8daec7
"""

#({params.salmon} index -p {threads} -i {params.index_out} -t {input.Tran} --gencode --perfectHash

##--------------------------------------##
## 5. ReadGroup - bam headers ##
Expand Down