diff --git a/docker/Dockerfile b/docker/Dockerfile
index ccdb6d4b053430dd68cdfecf1f920ab06fade9fb..c80203158859a30424a20b203691c5c72e7b7d68 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -24,6 +24,7 @@ RUN apt-get update \
&& apt-get install -yq bioperl=1.6.923-1 tabix=0.2.6-2 zlib1g zlib1g-dev samtools gnuplot python3 \
&& apt-get install -yq r-base r-base-dev \
&& apt-get install -yq libncurses5 libncurses5-dev sudo libatlas-base-dev python2.7 gfortran python-dev \
+ && apt-get install -yq python-matplotlib \
&& update-alternatives --set java /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/java
diff --git a/lib/imp.html b/lib/imp.html
index a0f4041dabdccf4d1ea6755a94e51e4e365658b5..c47f137d2eefa15422e70b13d4dd5eced40a6379 100644
--- a/lib/imp.html
+++ b/lib/imp.html
@@ -68,7 +68,7 @@
<div class="tab-content">
-
+ <!-- RAW STATISTICS -->
<div role="tabpanel" class="tab-pane fade" id="raw">
<section id="raw-section" class="row">
<h2><small>Raw data statistics</small></h2>
@@ -89,12 +89,11 @@
<div class="row">
<iframe id="ifr-raw-stat" src="Analysis/stats/MG/MG.R1.fq_fastqc.html" style="position: absolute; width: 100%;height: 100%; border: none"></iframe>
</div>
-
</section>
</div>
- <!-- STATISTICS -->
+ <!-- PREPROCESS STATISTICS -->
<div role="tabpanel" class="tab-pane fade active" id="preprocess">
<section id="preprocess-section" class="row">
<h2><small>Preprocessed data statistics</small></h2>
@@ -121,8 +120,9 @@
<div class="row">
<iframe id="ifr-preprocess-stat" src="Analysis/stats/MG/MG.R1_preprocessed_fastqc.html" style="position: absolute; width: 100%;height: 100%; border: none"></iframe>
</div>
-
</section>
+
+
<!-- FILTERING -->
<section id="filtering-section" class="row">
<div class="row">
@@ -132,8 +132,26 @@
</section>
</div>
<!-- ASSEMBLY -->
+
<div role="tabpanel" class="tab-pane fade" id="assembly">
<section id="assembly-section" class="row">
+ <div id="but-assembly" class="row btn-group" data-toggle="buttons" name="assembly-data">
+ <label class="btn btn-primary active">
+ <input id="but-assembly1" type="radio" value="Analysis/stats/MT/MT.SE_preprocessed_fastqc.html" class="btn btn-default" name="assembly-data" checked>Quast
+ </label>
+ <label class="btn btn-primary">
+ <input id="but-assembly2" type="radio" value="Analysis/results/IMP-vizbin_length.png" class="btn btn-default" name="assembly-data">Vizbin length
+ </label>
+ <label class="btn btn-primary">
+ <input id="but-assembly3" type="radio" value="Analysis/results/IMP-vizbin_length_GC.png" class="btn btn-default" name="assembly-data">Vizbin GC
+ </label>
+ </div>
+ <div class="row">
+ <div class="row" id="assembly-wrapper"></div>
+ </div>
+
+
+ <!-- <div role="tabpanel" class="tab-pane fade" id="assembly">
<h2><small>Assembly </small></h2>
<div class="row">
<div class="col-sm-3 col-md-3"></div>
@@ -143,7 +161,7 @@
<div class="row">
<div id="carousel-assembly-wrapper"></div>
- </div>
+ </div> -->
</section>
</div>
@@ -219,12 +237,6 @@
<section class="row">
<section id="impstatistics-section">
<h2><small>Statistics </small></h2>
- <div id="imp-stats-alert" class="row" style="display: none;">
- <div class="alert alert-warning alert-dismissible" role="alert">
- <button type="button" class="close" data-dismiss="alert"><span aria-hidden="true">×</span><span class="sr-only">Close</span></button>
- <strong>Warning!</strong> You don't have any statistics about the run. Next time don't forget to use Snakemake with the <kbd>--stats stats.json</kbd> option.
- </div>
- </div>
<div id="imp-stats" class="row">
<div id="basic-info"></div>
<div id="time-charts-mean"></div>
diff --git a/lib/imp.js b/lib/imp.js
index df1017c1b9564ae4bb40ea3dbac2eb40e5c2581d..a87dd2a0473ad4c8f7fbae24c6c933b3c0b44af7 100644
--- a/lib/imp.js
+++ b/lib/imp.js
@@ -269,10 +269,19 @@ $('#but-annot').on('change', function(){
});
-renderSimpleCarousel('carousel-assembly', 'Analysis/results', [
- 'IMP-vizbin_length.png',
- 'IMP-vizbin_length_GC.png'
-]);
+$('#but-assembly').on('change', function(){
+ var val = $('input[name="assembly-data"]:checked').val();
+ if(val.endsWith('png')){
+ $("#assembly-wrapper").replaceWith("<div id='assembly-wrapper' class='row'><img class='img-responsive' src='" + val + "'/></div>");
+ } else {
+ $("#assembly-wrapper").replaceWith("<div id='assembly-wrapper' class='row'><iframe style='position: absolute; width: 100%;height: 100%; border: none' src='" + val + "'></iframe></div>");
+ }
+});
+
+// renderSimpleCarousel('carousel-assembly', 'Analysis/results', [
+// 'IMP-vizbin_length.png',
+// 'IMP-vizbin_length_GC.png'
+// ]);
renderSimpleCarousel('carousel-mapping', 'Analysis/results', [
'IMP-reads_density.png',
diff --git a/rules/Preprocessing/MG.rules b/rules/Preprocessing/MG.rules
index d74f2b3defb462a5391bfb1781e54c9eb4164415..d46af75528ecc83c3ee08416320fba5a66feb166 100644
--- a/rules/Preprocessing/MG.rules
+++ b/rules/Preprocessing/MG.rules
@@ -11,32 +11,18 @@ rule PREPROCESSING_MG_GET_FILES:
prepare_input_files(input, 'MG')
-rule PREPROCESSING_MG_DEDUPLICATE:
- log:
- P_LOG
- input:
- expand('{dir}/{raw}', raw=['MG.R1.fq', 'MG.R2.fq'], dir=P_OUT)
- output:
- expand('{dir}/{uniq}', uniq=['MG.R1.uniq.fq', 'MG.R2.uniq.fq'], dir=P_OUT)
- benchmark:
- "%s/benchmarks/PREPROCESSING_MG_DEDUPLICATE.json" % P_OUT
- shell:
- """
- fastuniq -i <(echo -e "{input[0]}\\n{input[1]}") -o {output[0]} -p {output[1]} >> {log} 2>&1
- """
-
rule PREPROCESSING_MG_TRIM:
log:
P_LOG
input:
- expand('{dir}/{uniq}', uniq=['MG.R1.uniq.fq', 'MG.R2.uniq.fq'], dir=P_OUT),
+ expand('{dir}/{uniq}', uniq=['MG.R1.fq', 'MG.R2.fq'], dir=P_OUT),
DBPATH + "/adapters/adapters.done"
output:
expand('{dir}/{trim}', trim=[
- 'MG.R1.uniq.trimmed.fq',
- 'MG.SE1.uniq.trimmed.fq',
- 'MG.R2.uniq.trimmed.fq',
- 'MG.SE2.uniq.trimmed.fq'], dir=P_OUT)
+ 'MG.R1.trimmed.fq',
+ 'MG.SE1.trimmed.fq',
+ 'MG.R2.trimmed.fq',
+ 'MG.SE2.trimmed.fq'], dir=P_OUT)
shell:
"""
java -jar {config[trimmomatic][jarfile]} PE -threads {THREADS} {input[0]} {input[1]} {output} \
@@ -56,10 +42,10 @@ rule PREPROCESSING_MG_CAT_TRIMMED_SE:
P_LOG
input:
expand('{dir}/{trim}', trim=[
- 'MG.SE1.uniq.trimmed.fq',
- 'MG.SE2.uniq.trimmed.fq'], dir=P_OUT)
+ 'MG.SE1.trimmed.fq',
+ 'MG.SE2.trimmed.fq'], dir=P_OUT)
output:
- expand('{dir}/{cat}', cat='MG.SE.uniq.trimmed.fq', dir=P_OUT)
+ expand('{dir}/{cat}', cat='MG.SE.trimmed.fq', dir=P_OUT)
shell:
"cat {input[0]} {input[1]} > {output}"
benchmark:
@@ -70,18 +56,18 @@ rule PREPROCESSING_MG_FILTER_HG:
P_LOG
input:
expand('{dir}/{trim}', trim=[
- 'MG.R1.uniq.trimmed.fq',
- 'MG.R2.uniq.trimmed.fq',
- 'MG.SE.uniq.trimmed.fq'], dir=P_OUT),
+ 'MG.R1.trimmed.fq',
+ 'MG.R2.trimmed.fq',
+ 'MG.SE.trimmed.fq'], dir=P_OUT),
'{dir}/{ref}.fa'.format(dir=DBPATH + "/human", ref=config['human_filtering']['filter']),
expand(
"{p}/human/{filter}.{ext}", filter=config["human_filtering"]["filter"],
ext=['fa', 'fa.amb', 'fa.ann', 'fa.bwt', 'fa.pac', 'fa.sa'], p=DBPATH)
output:
expand('{dir}/{filter}', filter=expand([
- 'MG.R1.uniq.trimmed.{f}.fq',
- 'MG.R2.uniq.trimmed.{f}.fq',
- 'MG.SE.uniq.trimmed.{f}.fq'], f=config['human_filtering']['filter']), dir=P_OUT)
+ 'MG.R1.trimmed.{f}.fq',
+ 'MG.R2.trimmed.{f}.fq',
+ 'MG.SE.trimmed.{f}.fq'], f=config['human_filtering']['filter']), dir=P_OUT)
benchmark:
"%s/benchmarks/PREPROCESSING_MG_FILTER_HG.json" % P_OUT
shell:
diff --git a/rules/Preprocessing/master.rules b/rules/Preprocessing/master.rules
index 36ca9cdf046ba4aec0ef2d3e4a7b58513c9414e2..8d3003a209e93beb71f0cbafe70d4aa2b97d5d6e 100644
--- a/rules/Preprocessing/master.rules
+++ b/rules/Preprocessing/master.rules
@@ -28,12 +28,12 @@ def preprocessing_output_files():
def preprocessed_mg(target, dir=P_OUT):
if config['preprocessing_filtering']:
# with human filtering ON
- return '{dir}/MG.{target}.uniq.trimmed.{f}.fq'.format(
+ return '{dir}/MG.{target}.trimmed.{f}.fq'.format(
f=config['human_filtering']['filter'],
dir=dir,
target=target)
# with human filtering OFF
- return '{dir}/MG.{target}.uniq.trimmed.fq'.format(dir=dir, target=target)
+ return '{dir}/MG.{target}.trimmed.fq'.format(dir=dir, target=target)
def preprocessed_mt(target, dir=P_OUT):