---
layout: default
navsection: userguide
-title: "Writing a CWL workflow"
+title: "Developing workflows with CWL"
...
+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
+
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
{% include 'what_is_cwl' %}
{% include 'tutorial_expectations' %}
-h2. Registering a CWL workflow
-
-Use @--create-workflow@ to register a CWL workflow with Arvados.
+h2. Developing workflows
-The following examples assume that you have prepared to run arvados-cwl-runner tool as explained in the "Using Common Workflow Language":{{site.baseurl}}/user/topics/running-workflow-command-line.html.textile.liquid page.
+For an introduction and and detailed documentation about writing CWL, see the "CWL User Guide":https://www.commonwl.org/user_guide and the "CWL Specification":http://commonwl.org/v1.2 .
-{% include 'register_cwl_workflow' %}
+See "Writing Portable High-Performance Workflows":{{site.baseurl}}/user/cwl/cwl-style.html and "Arvados CWL Extensions":{{site.baseurl}}/user/cwl/cwl-extensions.html for additional information about using CWL on Arvados.
-h2. Running a CWL workflow
+See "Repositories of CWL Tools and Workflows":https://www.commonwl.org/#Repositories_of_CWL_Tools_and_Workflows for links to repositories of existing tools for reuse.
-h3. Running a workflow at command prompt
+See "Software for working with CWL":https://www.commonwl.org/#Software_for_working_with_CWL for links to software tools to help create CWL documents.
-Not yet implemented
+h2. Using cwltool
-h3. Running a workflow using Workbench
+When developing a workflow, it is often helpful to run it on the local host to avoid the overhead of submitting to the cluster. To execute a workflow only on the local host (without submitting jobs to an Arvados cluster) you can use the @cwltool@ command. Note that when using @cwltool@ you must have the input data accessible on the local file system using either @arv-mount@ or @arv-get@ to fetch the data from Keep.
-The workflow can also be executed using Workbench. Go to the Workbench Dashboard and click the <span class="btn btn-sm btn-primary"><i class="fa fa-fw fa-gear"></i> Run a process...</span> button and select the desired workflow.
+<notextile>
+<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arv-get 2463fa9efeb75e099685528b3b9071e0+438/ .</span>
+156 MiB / 156 MiB 100.0%
+~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arv-get ae480c5099b81e17267b7445e35b4bc7+180/ .</span>
+23 MiB / 23 MiB 100.0%
+~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">cwltool bwa-mem-input.yml bwa-mem-input-local.yml</span>
+cwltool 1.0.20160629140624
+[job bwa-mem.cwl] /home/example/arvados/doc/user/cwl/bwa-mem$ docker \
+ run \
+ -i \
+ --volume=/home/example/arvados/doc/user/cwl/bwa-mem/19.fasta.ann:/var/lib/cwl/job979368791_bwa-mem/19.fasta.ann:ro \
+ --volume=/home/example/arvados/doc/user/cwl/bwa-mem/HWI-ST1027_129_D0THKACXX.1_1.fastq:/var/lib/cwl/job979368791_bwa-mem/HWI-ST1027_129_D0THKACXX.1_1.fastq:ro \
+ --volume=/home/example/arvados/doc/user/cwl/bwa-mem/19.fasta.sa:/var/lib/cwl/job979368791_bwa-mem/19.fasta.sa:ro \
+ --volume=/home/example/arvados/doc/user/cwl/bwa-mem/19.fasta.amb:/var/lib/cwl/job979368791_bwa-mem/19.fasta.amb:ro \
+ --volume=/home/example/arvados/doc/user/cwl/bwa-mem/19.fasta.pac:/var/lib/cwl/job979368791_bwa-mem/19.fasta.pac:ro \
+ --volume=/home/example/arvados/doc/user/cwl/bwa-mem/HWI-ST1027_129_D0THKACXX.1_2.fastq:/var/lib/cwl/job979368791_bwa-mem/HWI-ST1027_129_D0THKACXX.1_2.fastq:ro \
+ --volume=/home/example/arvados/doc/user/cwl/bwa-mem/19.fasta.bwt:/var/lib/cwl/job979368791_bwa-mem/19.fasta.bwt:ro \
+ --volume=/home/example/arvados/doc/user/cwl/bwa-mem:/var/spool/cwl:rw \
+ --volume=/tmp/tmpgzyou9:/tmp:rw \
+ --workdir=/var/spool/cwl \
+ --read-only=true \
+ --log-driver=none \
+ --user=1001 \
+ --rm \
+ --env=TMPDIR=/tmp \
+ --env=HOME=/var/spool/cwl \
+ biodckr/bwa \
+ bwa \
+ mem \
+ -t \
+ 1 \
+ -R \
+ '@RG ID:arvados_tutorial PL:illumina SM:HWI-ST1027_129' \
+ /var/lib/cwl/job979368791_bwa-mem/19.fasta \
+ /var/lib/cwl/job979368791_bwa-mem/HWI-ST1027_129_D0THKACXX.1_1.fastq \
+ /var/lib/cwl/job979368791_bwa-mem/HWI-ST1027_129_D0THKACXX.1_2.fastq > /home/example/arvados/doc/user/cwl/bwa-mem/HWI-ST1027_129_D0THKACXX.1_1.sam
+[M::bwa_idx_load_from_disk] read 0 ALT contigs
+[M::process] read 100000 sequences (10000000 bp)...
+[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 4745, 1, 0)
+[M::mem_pestat] skip orientation FF as there are not enough pairs
+[M::mem_pestat] analyzing insert size distribution for orientation FR...
+[M::mem_pestat] (25, 50, 75) percentile: (154, 181, 214)
+[M::mem_pestat] low and high boundaries for computing mean and std.dev: (34, 334)
+[M::mem_pestat] mean and std.dev: (185.63, 44.88)
+[M::mem_pestat] low and high boundaries for proper pairs: (1, 394)
+[M::mem_pestat] skip orientation RF as there are not enough pairs
+[M::mem_pestat] skip orientation RR as there are not enough pairs
+[M::mem_process_seqs] Processed 100000 reads in 9.848 CPU sec, 9.864 real sec
+[main] Version: 0.7.12-r1039
+[main] CMD: bwa mem -t 1 -R @RG ID:arvados_tutorial PL:illumina SM:HWI-ST1027_129 /var/lib/cwl/job979368791_bwa-mem/19.fasta /var/lib/cwl/job979368791_bwa-mem/HWI-ST1027_129_D0THKACXX.1_1.fastq /var/lib/cwl/job979368791_bwa-mem/HWI-ST1027_129_D0THKACXX.1_2.fastq
+[main] Real time: 10.061 sec; CPU: 10.032 sec
+Final process status is success
+{
+ "aligned_sam": {
+ "size": 30738959,
+ "path": "/home/example/arvados/doc/user/cwl/bwa-mem/HWI-ST1027_129_D0THKACXX.1_1.sam",
+ "checksum": "sha1$0c668cca45fef02397bb5302880526d300ee4dac",
+ "class": "File"
+ }
+}
+</code></pre>
+</notextile>
+If you get the error @JavascriptException: Long-running script killed after 20 seconds.@ this may be due to the Dockerized Node.js engine taking too long to start. You may address this by installing Node.js locally (run @apt-get install nodejs@ on Debian or Ubuntu) or by specifying a longer timeout with the @--eval-timeout@ option. For example, run the workflow with @cwltool --eval-timeout=40@ for a 40-second timeout.
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