Merge pull request #35 from ENCODE-DCC/PIP-399_ATAQC

Pip 399 ataqc (2)
ENCODE-DCC · Nov 13, 2018 · ddcc810 · ddcc810
2 parents 3c87ffd + ed7cefb
commit ddcc810
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Showing 70 changed files with 1,302 additions and 2,080 deletions.
diff --git a/.gitignore b/.gitignore
@@ -113,3 +113,4 @@ cromwell*.jar
 output_*.json
 test_genome*
 test_sample*
+tmp
diff --git a/Jenkinsfile b/Jenkinsfile
@@ -40,9 +40,9 @@ pipeline {
 				                slackSend "The images will be tagged as $TAG"
 
                                 // pull the cache template image (the image is going to stay pretty much the same so it is no need to be dynamic)
-                                sh "docker pull quay.io/encode-dcc/chip-seq-pipeline:v1.1"
+                                sh "docker pull quay.io/encode-dcc/chip-seq-pipeline:v1.1.1"
                                 sh "docker login -u=${QUAY_USER} -p=${QUAY_PASS} quay.io"
-                                sh "docker build --cache-from quay.io/encode-dcc/chip-seq-pipeline:v1.1 -f docker_image/Dockerfile -t chip-seq-pipeline ."
+                                sh "docker build --cache-from quay.io/encode-dcc/chip-seq-pipeline:v1.1.1 -f docker_image/Dockerfile -t chip-seq-pipeline ."
                                 sh "docker tag chip-seq-pipeline $TAG"
                                 sh "docker push $TAG"
                                 sh "docker logout"
@@ -57,9 +57,9 @@ pipeline {
                                 slackSend (color: '#7CFC00', message: "started job: ${env.JOB_NAME}, build number ${env.BUILD_NUMBER} on branch: ${env.BRANCH_NAME}.")
                                 slackSend "The images will be tagged as quay.io/encode-dcc/chip-seq-pipeline:latest"
                                 // pull the cache template image (the image is going to stay pretty much the same so it is no need to be dynamic)
-                                sh "docker pull quay.io/encode-dcc/chip-seq-pipeline:v1.1"
+                                sh "docker pull quay.io/encode-dcc/chip-seq-pipeline:v1.1.1"
                                 sh "docker login -u=${QUAY_USER} -p=${QUAY_PASS} quay.io"
-                                sh "docker build --cache-from quay.io/encode-dcc/chip-seq-pipeline:v1.1 -f docker_image/Dockerfile -t chip-seq-pipeline ."
+                                sh "docker build --cache-from quay.io/encode-dcc/chip-seq-pipeline:v1.1.1 -f docker_image/Dockerfile -t chip-seq-pipeline ."
                                 sh "docker tag chip-seq-pipeline quay.io/encode-dcc/chip-seq-pipeline:latest"
                                 sh "docker push quay.io/encode-dcc/chip-seq-pipeline:latest"
                                 sh "docker logout"
@@ -69,7 +69,7 @@ pipeline {
                 stage('Run-Task-Level-Tests-Non-Master'){
                         agent {label 'slave-w-docker-cromwell-60GB-ebs'} 
                         steps{
-                                sh "cd test/test_task && git clone https://github.com/ENCODE-DCC/chip-seq-pipeline-test-data"
+                                sh "cd test/test_task && rm -rf chip-seq-pipeline-test-data && git clone https://github.com/ENCODE-DCC/chip-seq-pipeline-test-data"
                                 sh """cd test/test_task
                                       ./test.sh test_bam2ta.wdl test_bam2ta.json $TAG
                                       python -c "import sys; import json; data=json.loads(sys.stdin.read()); sys.exit(int(not data[u'match_overall']))" < test_bam2ta.result.json

diff --git a/backends/backend.conf b/backends/backend.conf
@@ -18,12 +18,10 @@ backend {
           String? slurm_account
           String? slurm_extra_param
           String singularity_container
-          String? singularity_options
-          String singularity_command = "exec"
-          String? singularity_command_options
+          String? singularity_bindpath
         """
         submit = """
-          sbatch \
+          ls ${singularity_container} $(echo ${singularity_bindpath} | tr , ' ') 1>/dev/null && (sbatch \
           --export=ALL \
           -J ${job_name} \
           -D ${cwd} \
@@ -38,7 +36,7 @@ backend {
           ${"--account " + slurm_account} \
           ${"--gres gpu:" + gpu} \
           ${slurm_extra_param} \
-          --wrap "chmod u+x ${script} && SINGULARITY_BINDPATH=$(echo ${cwd} | sed 's/cromwell-executions/\n/g' | head -n1) singularity ${singularity_options} ${singularity_command} ${singularity_command_options} --home ${cwd} ${if defined(gpu) then "--nv" else ""}  ${singularity_container} ${script}"
+          --wrap "chmod u+x ${script} && SINGULARITY_BINDPATH=$(echo ${cwd} | sed 's/cromwell-executions/\n/g' | head -n1),${singularity_bindpath} singularity exec --home ${cwd} ${if defined(gpu) then '--nv' else ''} ${singularity_container} ${script}")
         """
         kill = "scancel ${job_id}"
         check-alive = "squeue -j ${job_id}"
@@ -60,12 +58,10 @@ backend {
           String? sge_queue
           String? sge_extra_param
           String singularity_container
-          String? singularity_options
-          String singularity_command = "exec"
-          String? singularity_command_options
+          String? singularity_bindpath
         """
         submit = """
-          echo "chmod u+x ${script} && SINGULARITY_BINDPATH=$(echo ${cwd} | sed 's/cromwell-executions/\n/g' | head -n1) singularity ${singularity_options} ${singularity_command} ${singularity_command_options} --home ${cwd} ${if defined(gpu) then "--nv" else ""}   ${singularity_container} ${script}" | qsub \
+          ls ${singularity_container} $(echo ${singularity_bindpath} | tr , ' ') 1>/dev/null && (echo "chmod u+x ${script} && SINGULARITY_BINDPATH=$(echo ${cwd} | sed 's/cromwell-executions/\n/g' | head -n1),${singularity_bindpath} singularity exec --home ${cwd} ${if defined(gpu) then '--nv' else ''} ${singularity_container} ${script}" | qsub \
           -S /bin/sh \
           -terse \
           -b n \
@@ -81,7 +77,7 @@ backend {
           ${"-q " + sge_queue} \
           ${"-l gpu=" + gpu} \
           ${sge_extra_param} \
-          -V
+          -V)
         """
         kill = "qdel ${job_id}"
         check-alive = "qstat -j ${job_id}"
@@ -92,19 +88,15 @@ backend {
     singularity {
       actor-factory = "cromwell.backend.impl.sfs.config.ConfigBackendLifecycleActorFactory"
       config {
-        script-epilogue = "sleep 30 && sync"
+        script-epilogue = "sleep 5 && sync"
         concurrent-job-limit = 10
         runtime-attributes = """
           Int? gpu
           String singularity_container
-          String? singularity_options
-          String singularity_command = "exec"
-          String? singularity_command_options
+          String? singularity_bindpath
         """
         submit = """
-          chmod u+x ${script} && SINGULARITY_BINDPATH=$(echo ${cwd} | sed 's/cromwell-executions/\n/g' | head -n1) singularity ${singularity_options} \
-          ${singularity_command} ${singularity_command_options} --home ${cwd} ${if defined(gpu) then "--nv" else ""} \
-          ${singularity_container} ${script} & echo $!
+          ls ${singularity_container} $(echo ${singularity_bindpath} | tr , ' ') 1>/dev/null && (chmod u+x ${script} && SINGULARITY_BINDPATH=$(echo ${cwd} | sed 's/cromwell-executions/\n/g' | head -n1),${singularity_bindpath} singularity exec --home ${cwd} ${if defined(gpu) then '--nv' else ''} ${singularity_container} ${script} & echo $! && disown)
         """
         job-id-regex = "(\\d+)"
         check-alive = "ps -ef | grep -v grep | grep ${job_id}" 

diff --git a/chip.wdl b/chip.wdl
@@ -691,6 +691,8 @@ workflow chip {
 		paired_end = paired_end,
 		pipeline_type = pipeline_type,
 		peak_caller = peak_caller_,
+		macs2_cap_num_peak = macs2_cap_num_peak,
+		macs2_cap_num_peak = spp_cap_num_peak,		
 		idr_thresh = idr_thresh,
 		flagstat_qcs = bwa.flagstat_qc,
 		nodup_flagstat_qcs = filter.flagstat_qc,
@@ -985,7 +987,7 @@ task xcor {
 		#@docker : "quay.io/encode-dcc/atac-seq-pipeline:v1"
 		cpu : select_first([cpu,2])
 		memory : "${select_first([mem_mb,'16000'])} MB"
-		time : select_first([time_hr,6])
+		time : select_first([time_hr,24])
 		disks : select_first([disks,"local-disk 100 HDD"])
 	}
 }
@@ -1087,6 +1089,7 @@ task macs2 {
 		File npeak = glob("*[!.][!b][!f][!i][!l][!t].narrowPeak.gz")[0]
 		File bfilt_npeak = glob("*.bfilt.narrowPeak.gz")[0]
 		File bfilt_npeak_bb = glob("*.bfilt.narrowPeak.bb")[0]
+		Array[File] bfilt_npeak_hammock = glob("*.bfilt.narrowPeak.hammock.gz*")
 		File sig_pval = if select_first([make_signal,false]) then glob("*.pval.signal.bigwig")[0] else glob("null")[0]
 		File sig_fc = if select_first([make_signal,false]) then glob("*.fc.signal.bigwig")[0] else glob("null")[0]
 		File frip_qc = glob("*.frip.qc")[0]
@@ -1125,6 +1128,7 @@ task spp {
 		File rpeak = glob("*[!.][!b][!f][!i][!l][!t].regionPeak.gz")[0]
 		File bfilt_rpeak = glob("*.bfilt.regionPeak.gz")[0]
 		File bfilt_rpeak_peak_bb = glob("*.bfilt.regionPeak.bb")[0]
+		Array[File] bfilt_rpeak_hammock = glob("*.bfilt.regionPeak.hammock.gz*")
 		File frip_qc = glob("*.frip.qc")[0]
 	}
 	runtime {
@@ -1171,6 +1175,7 @@ task idr {
 		File idr_peak = glob("*[!.][!b][!f][!i][!l][!t]."+peak_type+".gz")[0]
 		File bfilt_idr_peak = glob("*.bfilt."+peak_type+".gz")[0]
 		File bfilt_idr_peak_bb = glob("*.bfilt."+peak_type+".bb")[0]
+		Array[File] bfilt_idr_peak_hammock = glob("*.bfilt."+peak_type+".hammock.gz*")
 		File idr_plot = glob("*.txt.png")[0]
 		File idr_unthresholded_peak = glob("*.txt.gz")[0]
 		File idr_log = glob("*.log")[0]
@@ -1215,6 +1220,7 @@ task overlap {
 		File overlap_peak = glob("*[!.][!b][!f][!i][!l][!t]."+peak_type+".gz")[0]
 		File bfilt_overlap_peak = glob("*.bfilt."+peak_type+".gz")[0]
 		File bfilt_overlap_peak_bb = glob("*.bfilt."+peak_type+".bb")[0]
+		Array[File] bfilt_overlap_peak_hammock = glob("*.bfilt."+peak_type+".hammock.gz*")
 		File frip_qc = if defined(ta) then glob("*.frip.qc")[0] else glob("null")[0]
 	}
 	runtime {
@@ -1247,10 +1253,12 @@ task reproducibility {
 			${"--chrsz " + chrsz}
 	}
 	output {
-		File optimal_peak = glob("optimal_peak.gz")[0]
-		File conservative_peak = glob("conservative_peak.gz")[0]
+		File optimal_peak = glob("optimal_peak.*.gz")[0]
+		File conservative_peak = glob("conservative_peak.*.gz")[0]
 		File optimal_peak_bb = glob("optimal_peak.*.bb")[0]
 		File conservative_peak_bb = glob("conservative_peak.*.bb")[0]
+		Array[File] optimal_peak_hammock = glob("optimal_peak.*.hammock.gz*")
+		Array[File] conservative_peak_hammock = glob("conservative_peak.*.hammock_gz*")
 		File reproducibility_qc = glob("*reproducibility.qc")[0]
 	}
 	runtime {
@@ -1270,9 +1278,12 @@ task qc_report {
 	String? desc # description for sample
 	#String? encode_accession_id	# ENCODE accession ID of sample
 	# workflow params
+	Int? multimapping
 	Boolean paired_end
 	String pipeline_type
 	String peak_caller
+	Int? macs2_cap_num_peak
+	Int? spp_cap_num_peak
 	Float idr_thresh
 	# QCs
 	Array[File]? flagstat_qcs
@@ -1315,11 +1326,14 @@ task qc_report {
 
 	command {
 		python $(which encode_qc_report.py) \
-			${"--name '" + name + "'"} \
-			${"--desc '" + desc + "'"} \
+			${"--name '" + sub(select_first([name,""]),"'","_") + "'"} \
+			${"--desc '" + sub(select_first([desc,""]),"'","_") + "'"} \
+			${"--multimapping " + multimapping} \
 			${if paired_end then "--paired-end" else ""} \
 			--pipeline-type ${pipeline_type} \
 			--peak-caller ${peak_caller} \
+			${"--macs2-cap-num-peak " + macs2_cap_num_peak} \
+			${"--spp-cap-num-peak " + spp_cap_num_peak} \
 			--idr-thresh ${idr_thresh} \
 			--flagstat-qcs ${sep=' ' flagstat_qcs} \
 			--nodup-flagstat-qcs ${sep=' ' nodup_flagstat_qcs} \

diff --git a/conda/install_dependencies.sh b/conda/install_dependencies.sh
@@ -64,6 +64,11 @@ source activate ${CONDA_ENV}
   echo "export PYTHONNOUSERSITE=True" >> ${CONDA_ACTIVATE_SH}
   echo "unset OPENBLAS_NUM_THREADS MKL_NUM_THREADS PYTHONNOUSERSITE" > ${CONDA_DEACTIVATE_SH}
 
+  # to prevent conflict between Conda's R and global(local) R
+  echo "export R_HOME=${CONDA_LIB}/R" >> ${CONDA_ACTIVATE_SH}
+  echo "export R_LIBS=${CONDA_LIB}/R/library" >> ${CONDA_ACTIVATE_SH}
+  echo "unset R_HOME R_LIBS" > ${CONDA_DEACTIVATE_SH}
+
   # hack around the need for both python2 and python3 in the same environment
   CONDA_BIN="${CONDA_PREFIX}/bin"
   cd ${CONDA_BIN}

diff --git a/conda/requirements.txt b/conda/requirements.txt
@@ -42,3 +42,4 @@ deeptools ==2.5.4 #2.2.3 does not support plotFingerprint --outQualityMetrics
 pybigwig==0.3.11
 #openssl ==1.0.2g-0
 phantompeakqualtools ==1.2
+tabix==0.2.6
diff --git a/conda/requirements_py3.txt b/conda/requirements_py3.txt
@@ -10,3 +10,4 @@ java-jdk ==8.0.92
 libgcc==5.2.0 # this does not work with MacOS...
 matplotlib ==1.5.1
 ncurses ==6.1
+tabix==0.2.6
diff --git a/docker_image/Dockerfile b/docker_image/Dockerfile
@@ -37,13 +37,9 @@ RUN apt-get update && apt-get install -y \
     r-base-core \
     default-jre \
     apt-transport-https \
+    tabix \
 && rm -rf /var/lib/apt/lists/*
 
-# Make directory for all softwares
-RUN mkdir /software
-WORKDIR /software
-ENV PATH="/software:${PATH}"
-
 # Install Intel MKL for BLAS
 RUN wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2019.PUB && apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS-2019.PUB && rm -rf GPG-PUB-KEY-INTEL-SW-PRODUCTS-2019.PUB && sh -c 'echo deb https://apt.repos.intel.com/mkl all main > /etc/apt/sources.list.d/intel-mkl.list' && apt-get update && apt-get install intel-mkl-64bit-2018.0-033 -y && rm -rf /var/lib/apt/lists/*
 ENV LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/opt/intel/compilers_and_libraries_2018.0.128/linux/mkl/lib/intel64_lin
@@ -52,10 +48,14 @@ ENV LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/opt/intel/compilers_and_libraries_2018.0
 RUN pip install --no-cache-dir common python-dateutil cython==0.27.3 && \
     pip3 install --no-cache-dir common python-dateutil cython==0.27.3
 
+# Make directory for all softwares
+RUN mkdir /software
+WORKDIR /software
+ENV PATH="/software:${PATH}"
+
 # Install numpy 1.11.3 (python2/3, linked with MKL)
-COPY docker_image/numpy/site.cfg .
-RUN git clone --branch v1.11.3 https://github.com/numpy/numpy && \
-    cd numpy && cp ../site.cfg . && python setup.py install && python3 setup.py install && cd ../ && rm -rf numpy*
+RUN git clone --branch v1.11.3 https://github.com/numpy/numpy && cd numpy && \
+    /bin/bash -c 'echo -e "[mkl]\nlibrary_dirs = /opt/intel/compilers_and_libraries_2018/linux/mkl/lib/intel64\ninclude_dirs = /opt/intel/compilers_and_libraries_2018/linux/mkl/include\nmkl_libs = mkl_rt\nlapack_libs =" > site.cfg' && python setup.py install && python3 setup.py install && cd ../ && rm -rf numpy*
 
 # Install scipy 1.0.0 (python2/3)
 RUN git clone --branch v1.0.0 --single-branch https://github.com/scipy/scipy && \
@@ -92,7 +92,7 @@ RUN wget https://github.com/broadinstitute/picard/releases/download/2.10.6/picar
 RUN wget https://github.com/lomereiter/sambamba/releases/download/v0.6.6/sambamba_v0.6.6_linux.tar.bz2 && tar -xvjf sambamba_v0.6.6_linux.tar.bz2 && mv sambamba_v0.6.6 sambamba && rm -rf sambamba_*
 
 # Install R packages
-RUN echo "r <- getOption('repos'); r['CRAN'] <- 'http://cran.us.r-project.org'; options(repos = r);" > ~/.Rprofile && \
+RUN echo "r <- getOption('repos'); r['CRAN'] <- 'http://cran.r-project.org'; options(repos = r);" > ~/.Rprofile && \
     Rscript -e "install.packages('snow')" && \
     Rscript -e "install.packages('snowfall')" && \
     Rscript -e "install.packages('bitops')" && \
@@ -127,6 +127,9 @@ RUN pip install --no-cache-dir pyfaidx==0.4.7.1
 # Install UCSC tools (Kent utils) latest for peak2bigbed conversion
 RUN wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bedToBigBed && chmod +x bedToBigBed
 
+# Install bgzip/tabix for Wash U browser track (hammock type)
+#RUN apt-get update && apt-get install -y tabix && rm -rf /var/lib/apt/lists/*
+
 # Prevent conflict with locally installed python outside of singularity container
 ENV PYTHONNOUSERSITE=True
 

diff --git a/docs/dev.md b/docs/dev.md
@@ -9,7 +9,7 @@ Run the following command line locally to build out DX workflows for this pipeli
 
 ```
 # version
-VER=v1.1
+VER=v1.1.1
 
 # general
 java -jar ~/dxWDL-0.77.jar compile chip.wdl -project "ENCODE Uniform Processing Pipelines" -extras workflow_opts/docker.json -f -folder /ChIP-seq2/workflows/$VER/general -defaults examples/dx/template_general.json
@@ -33,7 +33,7 @@ java -jar ~/dxWDL-0.77.jar compile chip.wdl -project "ENCODE Uniform Processing
 ## DX Azure
 ```
 # version
-VER=v1.1
+VER=v1.1.1
 
 # general
 java -jar ~/dxWDL-0.77.jar compile chip.wdl -project "ENCODE Uniform Processing Pipelines Azure" -extras workflow_opts/docker.json -f -folder /ChIP-seq2/workflows/$VER/general -defaults examples/dx_azure/template_general.json

diff --git a/docs/input.md b/docs/input.md
@@ -202,6 +202,6 @@ Walltime (`time`) settings (for SGE and SLURM only).
 * `"chip.bwa.time_hr"` : (optional) Walltime for `bwa` (default: 48).
 * `"chip.filter.time_hr"` : (optional) Walltime for `filter` (default: 24).
 * `"chip.bam2ta.time_hr"` : (optional) Walltime for `bam2ta` (default: 6).
-* `"chip.xcor.time_hr"` : (optional) Walltime for `xcor` (default: 6).
+* `"chip.xcor.time_hr"` : (optional) Walltime for `xcor` (default: 24).
 * `"chip.macs2_time_hr"` : (optional) Walltime for `macs2` (default: 24).
 
diff --git a/docs/tutorial_dx_web.md b/docs/tutorial_dx_web.md
@@ -41,16 +41,16 @@ This document describes instruction for the item 2).
 1. DNANexus allows only one copy of a workflow per project. The example workflow in the previous section is pre-built for the subsampled test sample [ENCSR936XTK](https://www.encodeproject.org/experiments/ENCSR936XTK/) with all parameters defined already.
 
 2. Copy one of the following workflows according to the platform you have chosen for your project (AWS or Azure).
-* [AWS general](https://platform.dnanexus.com/projects/BKpvFg00VBPV975PgJ6Q03v6/data/ChIP-seq2/workflows/v1.1/general) without pre-defined reference genome.
-* [AWS hg38](https://platform.dnanexus.com/projects/BKpvFg00VBPV975PgJ6Q03v6/data/ChIP-seq2/workflows/v1.1/hg38) with pre-defined hg38 reference genome.
-* [AWS hg19](https://platform.dnanexus.com/projects/BKpvFg00VBPV975PgJ6Q03v6/data/ChIP-seq2/workflows/v1.1/hg19) with pre-defined hg38 reference genome.
-* [AWS mm10](https://platform.dnanexus.com/projects/BKpvFg00VBPV975PgJ6Q03v6/data/ChIP-seq2/workflows/v1.1/mm10) with pre-defined mm10 reference genome.
-* [AWS mm9](https://platform.dnanexus.com/projects/BKpvFg00VBPV975PgJ6Q03v6/data/ChIP-seq2/workflows/v1.1/mm9) with pre-defined mm9 reference genome.
-* [Azure general](https://platform.dnanexus.com/projects/F6K911Q9xyfgJ36JFzv03Z5J/data/ChIP-seq2/workflows/v1.1/general) without pre-defined reference genome.
-* [Azure hg38](https://platform.dnanexus.com/projects/F6K911Q9xyfgJ36JFzv03Z5J/data/ChIP-seq2/workflows/v1.1/hg38) with pre-defined hg38 reference genome.
-* [Azure hg19](https://platform.dnanexus.com/projects/F6K911Q9xyfgJ36JFzv03Z5J/data/ChIP-seq2/workflows/v1.1/hg19) with pre-defined hg38 reference genome.
-* [Azure mm10](https://platform.dnanexus.com/projects/F6K911Q9xyfgJ36JFzv03Z5J/data/ChIP-seq2/workflows/v1.1/mm10) with pre-defined mm10 reference genome.
-* [Azure mm9](https://platform.dnanexus.com/projects/F6K911Q9xyfgJ36JFzv03Z5J/data/ChIP-seq2/workflows/v1.1/mm9) with pre-defined mm9 reference genome.
+* [AWS general](https://platform.dnanexus.com/projects/BKpvFg00VBPV975PgJ6Q03v6/data/ChIP-seq2/workflows/v1.1.1/general) without pre-defined reference genome.
+* [AWS hg38](https://platform.dnanexus.com/projects/BKpvFg00VBPV975PgJ6Q03v6/data/ChIP-seq2/workflows/v1.1.1/hg38) with pre-defined hg38 reference genome.
+* [AWS hg19](https://platform.dnanexus.com/projects/BKpvFg00VBPV975PgJ6Q03v6/data/ChIP-seq2/workflows/v1.1.1/hg19) with pre-defined hg38 reference genome.
+* [AWS mm10](https://platform.dnanexus.com/projects/BKpvFg00VBPV975PgJ6Q03v6/data/ChIP-seq2/workflows/v1.1.1/mm10) with pre-defined mm10 reference genome.
+* [AWS mm9](https://platform.dnanexus.com/projects/BKpvFg00VBPV975PgJ6Q03v6/data/ChIP-seq2/workflows/v1.1.1/mm9) with pre-defined mm9 reference genome.
+* [Azure general](https://platform.dnanexus.com/projects/F6K911Q9xyfgJ36JFzv03Z5J/data/ChIP-seq2/workflows/v1.1.1/general) without pre-defined reference genome.
+* [Azure hg38](https://platform.dnanexus.com/projects/F6K911Q9xyfgJ36JFzv03Z5J/data/ChIP-seq2/workflows/v1.1.1/hg38) with pre-defined hg38 reference genome.
+* [Azure hg19](https://platform.dnanexus.com/projects/F6K911Q9xyfgJ36JFzv03Z5J/data/ChIP-seq2/workflows/v1.1.1/hg19) with pre-defined hg38 reference genome.
+* [Azure mm10](https://platform.dnanexus.com/projects/F6K911Q9xyfgJ36JFzv03Z5J/data/ChIP-seq2/workflows/v1.1.1/mm10) with pre-defined mm10 reference genome.
+* [Azure mm9](https://platform.dnanexus.com/projects/F6K911Q9xyfgJ36JFzv03Z5J/data/ChIP-seq2/workflows/v1.1.1/mm9) with pre-defined mm9 reference genome.
 
 3. Click on the DX workflow `chip`.