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‎chip.wdl

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# ENCODE DCC TF/Histone ChIP-Seq pipeline
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# Author: Jin Lee (leepc12@gmail.com)
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#CAPER docker quay.io/encode-dcc/chip-seq-pipeline:v1.2.1
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#CAPER singularity docker://quay.io/encode-dcc/chip-seq-pipeline:v1.2.1
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#CAPER docker quay.io/encode-dcc/chip-seq-pipeline:v1.2.2
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#CAPER singularity docker://quay.io/encode-dcc/chip-seq-pipeline:v1.2.2
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#CROO out_def https://storage.googleapis.com/encode-pipeline-output-definition/chip.out_def.json
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workflow chip {
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String pipeline_ver = 'v1.2.1'
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String pipeline_ver = 'v1.2.2'
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### sample name, description
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String title = 'Untitled'
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String description = 'No description'

‎docs/deprecated/tutorial_local_singularity.md

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6. Pull a singularity container for the pipeline. This will pull pipeline's docker container first and build a singularity one on `~/.singularity`.
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```bash
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$ mkdir -p ~/.singularity && cd ~/.singularity && SINGULARITY_CACHEDIR=~/.singularity SINGULARITY_PULLFOLDER=~/.singularity singularity pull --name chip-seq-pipeline-v1.2.1.simg -F docker://quay.io/encode-dcc/chip-seq-pipeline:v1.2.1
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$ mkdir -p ~/.singularity && cd ~/.singularity && SINGULARITY_CACHEDIR=~/.singularity SINGULARITY_PULLFOLDER=~/.singularity singularity pull --name chip-seq-pipeline-v1.2.2.simg -F docker://quay.io/encode-dcc/chip-seq-pipeline:v1.2.2
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```
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7. Run a pipeline for the test sample.
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```javascript
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{
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"default_runtime_attributes" : {
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"singularity_container" : "~/.singularity/chip-seq-pipeline-v1.2.1.simg",
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"singularity_container" : "~/.singularity/chip-seq-pipeline-v1.2.2.simg",
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"singularity_bindpath" : "/your/,YOUR_OWN_DATA_DIR1,YOUR_OWN_DATA_DIR2,..."
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}
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}

‎docs/deprecated/tutorial_scg.md

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```javascript
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{
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"default_runtime_attributes" : {
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"singularity_container" : "~/.singularity/chip-seq-pipeline-v1.2.1.simg",
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"singularity_container" : "~/.singularity/chip-seq-pipeline-v1.2.2.simg",
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"singularity_bindpath" : "/reference/ENCODE,/scratch,/srv/gsfs0,YOUR_OWN_DATA_DIR1,YOUR_OWN_DATA_DIR1,..."
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}
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}

‎docs/deprecated/tutorial_scg_backend.md

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5. Pull a singularity container for the pipeline. This will pull pipeline's docker container first and build a singularity one on `~/.singularity`.
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```bash
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$ sdev # SCG cluster does not allow building a container on login node
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$ mkdir -p ~/.singularity && cd ~/.singularity && SINGULARITY_CACHEDIR=~/.singularity SINGULARITY_PULLFOLDER=~/.singularity singularity pull --name chip-seq-pipeline-v1.2.1.simg -F docker://quay.io/encode-dcc/chip-seq-pipeline:v1.2.1
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$ mkdir -p ~/.singularity && cd ~/.singularity && SINGULARITY_CACHEDIR=~/.singularity SINGULARITY_PULLFOLDER=~/.singularity singularity pull --name chip-seq-pipeline-v1.2.2.simg -F docker://quay.io/encode-dcc/chip-seq-pipeline:v1.2.2
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$ exit
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```
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```javascript
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{
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"default_runtime_attributes" : {
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"singularity_container" : "~/.singularity/chip-seq-pipeline-v1.2.1.simg",
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"singularity_container" : "~/.singularity/chip-seq-pipeline-v1.2.2.simg",
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"singularity_bindpath" : "/scratch/users,/srv/gsfs0,/your/,YOUR_OWN_DATA_DIR1,YOUR_OWN_DATA_DIR1,..."
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}
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}

‎docs/deprecated/tutorial_sge.md

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7. Pull a singularity container for the pipeline. This will pull pipeline's docker container first and build a singularity one on `~/.singularity`.
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```bash
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$ mkdir -p ~/.singularity && cd ~/.singularity && SINGULARITY_CACHEDIR=~/.singularity SINGULARITY_PULLFOLDER=~/.singularity singularity pull --name chip-seq-pipeline-v1.2.1.simg -F docker://quay.io/encode-dcc/chip-seq-pipeline:v1.2.1
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$ mkdir -p ~/.singularity && cd ~/.singularity && SINGULARITY_CACHEDIR=~/.singularity SINGULARITY_PULLFOLDER=~/.singularity singularity pull --name chip-seq-pipeline-v1.2.2.simg -F docker://quay.io/encode-dcc/chip-seq-pipeline:v1.2.2
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```
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8. Run a pipeline for the test sample. If your parallel environment (PE) found from step 5) has a different name from `shm` then edit the following shell script to change the PE name.
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```javascript
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{
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"default_runtime_attributes" : {
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"singularity_container" : "~/.singularity/chip-seq-pipeline-v1.2.1.simg",
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"singularity_container" : "~/.singularity/chip-seq-pipeline-v1.2.2.simg",
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"singularity_bindpath" : "/your/,YOUR_OWN_DATA_DIR1,YOUR_OWN_DATA_DIR2,..."
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}
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}

‎docs/deprecated/tutorial_sge_backend.md

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7. Pull a singularity container for the pipeline. This will pull pipeline's docker container first and build a singularity one on `~/.singularity`.
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```bash
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$ mkdir -p ~/.singularity && cd ~/.singularity && SINGULARITY_CACHEDIR=~/.singularity SINGULARITY_PULLFOLDER=~/.singularity singularity pull --name chip-seq-pipeline-v1.2.1.simg -F docker://quay.io/encode-dcc/chip-seq-pipeline:v1.1
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$ mkdir -p ~/.singularity && cd ~/.singularity && SINGULARITY_CACHEDIR=~/.singularity SINGULARITY_PULLFOLDER=~/.singularity singularity pull --name chip-seq-pipeline-v1.2.2.simg -F docker://quay.io/encode-dcc/chip-seq-pipeline:v1.1
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```
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8. Run a pipeline for the test sample.

‎docs/deprecated/tutorial_sherlock.md

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```javascript
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{
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"default_runtime_attributes" : {
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"singularity_container" : "~/.singularity/chip-seq-pipeline-v1.2.1.simg",
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"singularity_container" : "~/.singularity/chip-seq-pipeline-v1.2.2.simg",
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"singularity_bindpath" : "/scratch,/lscratch,/oak/stanford,/home/groups/cherry/encode,/your/,YOUR_OWN_DATA_DIR1,YOUR_OWN_DATA_DIR1,..."
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}
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}

‎docs/deprecated/tutorial_sherlock_backend.md

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6. Pull a singularity container for the pipeline. This will pull pipeline's docker container first and build a singularity one on `~/.singularity`. Stanford Sherlock does not allow building a container on login nodes. Wait until you get a command prompt after `sdev`.
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```bash
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$ sdev # sherlock cluster does not allow building a container on login node
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$ mkdir -p ~/.singularity && cd ~/.singularity && SINGULARITY_CACHEDIR=~/.singularity SINGULARITY_PULLFOLDER=~/.singularity singularity pull --name chip-seq-pipeline-v1.2.1.simg -F docker://quay.io/encode-dcc/chip-seq-pipeline:v1.2.1
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$ mkdir -p ~/.singularity && cd ~/.singularity && SINGULARITY_CACHEDIR=~/.singularity SINGULARITY_PULLFOLDER=~/.singularity singularity pull --name chip-seq-pipeline-v1.2.2.simg -F docker://quay.io/encode-dcc/chip-seq-pipeline:v1.2.2
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$ exit # exit from an interactive node
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```
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```javascript
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{
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"default_runtime_attributes" : {
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"singularity_container" : "~/.singularity/chip-seq-pipeline-v1.2.1.simg",
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"singularity_container" : "~/.singularity/chip-seq-pipeline-v1.2.2.simg",
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"singularity_bindpath" : "/scratch,/oak/stanford,/your/,YOUR_OWN_DATA_DIR1,YOUR_OWN_DATA_DIR1,..."
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}
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}

‎docs/deprecated/tutorial_slurm.md

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7. Pull a singularity container for the pipeline. This will pull pipeline's docker container first and build a singularity one on `~/.singularity`.
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```bash
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$ mkdir -p ~/.singularity && cd ~/.singularity && SINGULARITY_CACHEDIR=~/.singularity SINGULARITY_PULLFOLDER=~/.singularity singularity pull --name chip-seq-pipeline-v1.2.1.simg -F docker://quay.io/encode-dcc/chip-seq-pipeline:v1.2.1
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$ mkdir -p ~/.singularity && cd ~/.singularity && SINGULARITY_CACHEDIR=~/.singularity SINGULARITY_PULLFOLDER=~/.singularity singularity pull --name chip-seq-pipeline-v1.2.2.simg -F docker://quay.io/encode-dcc/chip-seq-pipeline:v1.2.2
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```
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8. Run a pipeline for the test sample. If your cluster requires to specify any of them then add one to the command line.
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```javascript
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{
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"default_runtime_attributes" : {
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"singularity_container" : "~/.singularity/chip-seq-pipeline-v1.2.1.simg",
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"singularity_container" : "~/.singularity/chip-seq-pipeline-v1.2.2.simg",
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"singularity_bindpath" : "/your/,YOUR_OWN_DATA_DIR1,YOUR_OWN_DATA_DIR2,..."
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}
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}

‎docs/deprecated/tutorial_slurm_backend.md

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```bash
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$ mkdir -p ~/.singularity && cd ~/.singularity && SINGULARITY_CACHEDIR=~/.singularity SINGULARITY_PULLFOLDER=~/.singularity singularity pull --name chip-seq-pipeline-v1.2.1.simg -F docker://quay.io/encode-dcc/chip-seq-pipeline:v1.2.1
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$ mkdir -p ~/.singularity && cd ~/.singularity && SINGULARITY_CACHEDIR=~/.singularity SINGULARITY_PULLFOLDER=~/.singularity singularity pull --name chip-seq-pipeline-v1.2.2.simg -F docker://quay.io/encode-dcc/chip-seq-pipeline:v1.2.2
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```
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```javascript
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{
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"singularity_container" : "~/.singularity/chip-seq-pipeline-v1.2.2.simg",
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‎docs/dev.md

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## Command line for version change
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```bash
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PREV_VER=v1.2.1
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for f in $(grep -rl ${PREV_VER} --include=*.{wdl,md,sh})
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```bash
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VER=v1.2.2
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# general
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java -jar ~/dxWDL-0.77.jar compile chip.wdl -project "ENCODE Uniform Processing Pipelines" -extras workflow_opts/docker.json -f -folder /ChIP-seq2/workflows/$VER/general -defaults examples/dx/template_general.json

‎docs/tutorial_dx_web.md

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3. Move to one of the following workflow directories according to the platform you have chosen for your project (AWS or Azure). These DX workflows are pre-built with all parameters defined.
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* [AWS test workflow](https://platform.DNAnexus.com/projects/BKpvFg00VBPV975PgJ6Q03v6/data/ChIP-seq2/workflows/v1.2.1/test_ENCSR936XTK_subsampled_chr19_only)
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* [Azure test workflow](https://platform.DNAnexus.com/projects/F6K911Q9xyfgJ36JFzv03Z5J/data/ChIP-seq2/workflows/v1.2.1/test_ENCSR936XTK_subsampled_chr19_only)
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* [AWS test workflow](https://platform.DNAnexus.com/projects/BKpvFg00VBPV975PgJ6Q03v6/data/ChIP-seq2/workflows/v1.2.2/test_ENCSR936XTK_subsampled_chr19_only)
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* [Azure test workflow](https://platform.DNAnexus.com/projects/F6K911Q9xyfgJ36JFzv03Z5J/data/ChIP-seq2/workflows/v1.2.2/test_ENCSR936XTK_subsampled_chr19_only)
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4. Copy it to your project by right-clicking on the DX workflow `chip` and choose "Copy".
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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.
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2. Copy one of the following workflows according to the platform you have chosen for your project (AWS or Azure).
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* [AWS general](https://platform.DNAnexus.com/projects/BKpvFg00VBPV975PgJ6Q03v6/data/ChIP-seq2/workflows/v1.2.1/general) without pre-defined reference genome.
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* [AWS hg38](https://platform.DNAnexus.com/projects/BKpvFg00VBPV975PgJ6Q03v6/data/ChIP-seq2/workflows/v1.2.1/hg38) with pre-defined hg38 reference genome.
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* [AWS hg19](https://platform.DNAnexus.com/projects/BKpvFg00VBPV975PgJ6Q03v6/data/ChIP-seq2/workflows/v1.2.1/hg19) with pre-defined hg19 reference genome.
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* [AWS mm10](https://platform.DNAnexus.com/projects/BKpvFg00VBPV975PgJ6Q03v6/data/ChIP-seq2/workflows/v1.2.1/mm10) with pre-defined mm10 reference genome.
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* [AWS mm9](https://platform.DNAnexus.com/projects/BKpvFg00VBPV975PgJ6Q03v6/data/ChIP-seq2/workflows/v1.2.1/mm9) with pre-defined mm9 reference genome.
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* [Azure general](https://platform.DNAnexus.com/projects/F6K911Q9xyfgJ36JFzv03Z5J/data/ChIP-seq2/workflows/v1.2.1/general) without pre-defined reference genome.
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* [Azure hg38](https://platform.DNAnexus.com/projects/F6K911Q9xyfgJ36JFzv03Z5J/data/ChIP-seq2/workflows/v1.2.1/hg38) with pre-defined hg38 reference genome.
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* [Azure hg19](https://platform.DNAnexus.com/projects/F6K911Q9xyfgJ36JFzv03Z5J/data/ChIP-seq2/workflows/v1.2.1/hg19) with pre-defined hg19 reference genome.
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* [Azure mm10](https://platform.DNAnexus.com/projects/F6K911Q9xyfgJ36JFzv03Z5J/data/ChIP-seq2/workflows/v1.2.1/mm10) with pre-defined mm10 reference genome.
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* [Azure mm9](https://platform.DNAnexus.com/projects/F6K911Q9xyfgJ36JFzv03Z5J/data/ChIP-seq2/workflows/v1.2.1/mm9) with pre-defined mm9 reference genome.
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* [AWS general](https://platform.DNAnexus.com/projects/BKpvFg00VBPV975PgJ6Q03v6/data/ChIP-seq2/workflows/v1.2.2/general) without pre-defined reference genome.
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* [AWS hg38](https://platform.DNAnexus.com/projects/BKpvFg00VBPV975PgJ6Q03v6/data/ChIP-seq2/workflows/v1.2.2/hg38) with pre-defined hg38 reference genome.
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* [AWS hg19](https://platform.DNAnexus.com/projects/BKpvFg00VBPV975PgJ6Q03v6/data/ChIP-seq2/workflows/v1.2.2/hg19) with pre-defined hg19 reference genome.
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* [AWS mm10](https://platform.DNAnexus.com/projects/BKpvFg00VBPV975PgJ6Q03v6/data/ChIP-seq2/workflows/v1.2.2/mm10) with pre-defined mm10 reference genome.
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* [AWS mm9](https://platform.DNAnexus.com/projects/BKpvFg00VBPV975PgJ6Q03v6/data/ChIP-seq2/workflows/v1.2.2/mm9) with pre-defined mm9 reference genome.
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* [Azure general](https://platform.DNAnexus.com/projects/F6K911Q9xyfgJ36JFzv03Z5J/data/ChIP-seq2/workflows/v1.2.2/general) without pre-defined reference genome.
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* [Azure hg38](https://platform.DNAnexus.com/projects/F6K911Q9xyfgJ36JFzv03Z5J/data/ChIP-seq2/workflows/v1.2.2/hg38) with pre-defined hg38 reference genome.
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* [Azure hg19](https://platform.DNAnexus.com/projects/F6K911Q9xyfgJ36JFzv03Z5J/data/ChIP-seq2/workflows/v1.2.2/hg19) with pre-defined hg19 reference genome.
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* [Azure mm10](https://platform.DNAnexus.com/projects/F6K911Q9xyfgJ36JFzv03Z5J/data/ChIP-seq2/workflows/v1.2.2/mm10) with pre-defined mm10 reference genome.
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* [Azure mm9](https://platform.DNAnexus.com/projects/F6K911Q9xyfgJ36JFzv03Z5J/data/ChIP-seq2/workflows/v1.2.2/mm9) with pre-defined mm9 reference genome.
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3. Click on the DX workflow `chip`.
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‎test/test_task/test.sh

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DOCKER_IMAGE=quay.io/encode-dcc/chip-seq-pipeline:v1.2.2
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‎test/test_workflow/test_chip.sh

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DOCKER_IMAGE=quay.io/encode-dcc/chip-seq-pipeline:v1.2.2
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‎workflow_opts/docker.json

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{
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"default_runtime_attributes" : {
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"docker" : "quay.io/encode-dcc/chip-seq-pipeline:v1.2.1",
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"docker" : "quay.io/encode-dcc/chip-seq-pipeline:v1.2.2",
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"zones": "us-west1-a us-west1-b us-west1-c us-central1-c us-central1-b",
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"failOnStderr" : false,
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"continueOnReturnCode" : 0,

‎workflow_opts/scg.json

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{
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"slurm_account" : "YOUR_SLURM_ACCOUNT",
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"singularity_container" : "/reference/ENCODE/pipeline_singularity_images/chip-seq-pipeline-v1.2.1.simg",
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"singularity_container" : "/reference/ENCODE/pipeline_singularity_images/chip-seq-pipeline-v1.2.2.simg",
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"singularity_bindpath" : "/reference/ENCODE,/scratch,/srv/gsfs0"
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‎workflow_opts/sge.json

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{
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"singularity_container" : "~/.singularity/chip-seq-pipeline-v1.2.1.simg"
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"singularity_container" : "~/.singularity/chip-seq-pipeline-v1.2.2.simg"
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‎workflow_opts/sherlock.json

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{
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"singularity_container" : "/home/groups/cherry/encode/pipeline_singularity_images/chip-seq-pipeline-v1.2.1.simg",
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"singularity_container" : "/home/groups/cherry/encode/pipeline_singularity_images/chip-seq-pipeline-v1.2.2.simg",
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"singularity_bindpath" : "/scratch,/lscratch,/oak/stanford,/home/groups/cherry/encode"
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}
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}

‎workflow_opts/singularity.json

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{
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"default_runtime_attributes" : {
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"singularity_container" : "~/.singularity/chip-seq-pipeline-v1.2.1.simg"
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"singularity_container" : "~/.singularity/chip-seq-pipeline-v1.2.2.simg"
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}
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}

‎workflow_opts/slurm.json

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"default_runtime_attributes" : {
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"slurm_partition" : "YOUR_SLURM_PARTITION",
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"slurm_account" : "YOUR_SLURM_ACCOUNT",
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"singularity_container" : "~/.singularity/chip-seq-pipeline-v1.2.1.simg"
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"singularity_container" : "~/.singularity/chip-seq-pipeline-v1.2.2.simg"
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}
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}

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