added WDL2CWL conversion examples #80
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mr-c
requested changes
May 14, 2020
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Thank you @ambarishK for starting this. The layout needs to match the repository layout, so please pull everything up from the WDL2CWL_example. Did you test the conversion from WDL?
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| #!/usr/bin/env cwl-runner | |||
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| #!/usr/bin/env cwl-runner | |||
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ngsap2@ubuntu:~$ sudo docker run -v /var/run/docker.sock:/var/run/docker.sock -v "$PWD":"$PWD" -w="$PWD" commonworkflowlanguage/cwltool Ambarish_Kumar_SOP-GATK-SAR-CoV-2.cwl Ambarish_Kumar_SOP-GATK-SAR-CoV-2_inputs.yml
INFO /usr/local/bin/cwltool 2.0.20200107113851
INFO Resolved 'Ambarish_Kumar_SOP-GATK-SAR-CoV-2.cwl' to 'file:///home/ngsap2/Ambarish_Kumar_SOP-GATK-SAR-CoV-2.cwl'
tools/picard/picard_MarkDuplicates.cwl:24:3: object id `tools/picard/picard_MarkDuplicates.cwl#alignments` previously defined
ERROR Tool definition failed validation:
Ambarish_Kumar_SOP-GATK-SAR-CoV-2.cwl:83:12: Workflow step output 'bam_duprem' does not correspond
to
tools/picard/picard_MarkDuplicates.cwl:101:1: tool output (expected 'alignments', 'log',
'metrics')
Ambarish_Kumar_SOP-GATK-SAR-CoV-2.cwl:81:5: Step is missing required parameters 'alignments',
'alignments_are_sorted', 'remove_duplicates'
```
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| #!/usr/bin/env cwl-runner | |||
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| #!/usr/bin/env cwl-runner | |||
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| #!/usr/bin/env cwl-runner | |||
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ngsap2@ubuntu:~$ sudo docker run -v /var/run/docker.sock:/var/run/docker.sock -v "$PWD":"$PWD" -w="$PWD" commonworkflowlanguage/cwltool /home/ngsap2/tools/bowtie2/bowtie2_build.cwl -c /home/ngsap2/testdata16march/ebola_ref.fasta --bt2_index_base eb
INFO /usr/local/bin/cwltool 2.0.20200107113851
INFO Resolved '/home/ngsap2/tools/bowtie2/bowtie2_build.cwl' to 'file:///home/ngsap2/tools/bowtie2/bowtie2_build.cwl'
ERROR testdata16march/ebola_ref.fasta:1:1: while scanning a block scalar
testdata16march/ebola_ref.fasta:1:2: expected chomping or indentation indicators, but found 'g'
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| #!/usr/bin/env cwl-runner | |||
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Please use existing tool descriptions, such as https://github.com/common-workflow-library/bio-cwl-tools/blob/release/samtools/samtools_index.cwl
| "arguments": [ | ||
| { | ||
| "shellQuote": false, | ||
| "valueFrom": "samtools index $(inputs.inputBAM.path)samtools mpileup -B -f $(inputs.ReferenceGenome.path) $(inputs.inputBAM.path) > $(inputs.sampleName).mpileup" |
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Did you test this? I think a | is missing.
wdl2cwl is a very old tool, I'm not sure if it ever worked.
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| #!/usr/bin/env cwl-runner | |||
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|
Okay, the directory is restructured, but there are still many tool descriptions for tools that have descriptions for. So you need to try out the existing descriptions and either (1) propose changes or (2) motivate why a new description is needed. Examples of (1) are : extra flag, additional output capture. Examples of (2) are: additional subcommand or fundamentally different mode of operation using an already described (sub)command. |
mr-c
reviewed
May 15, 2020
bowtie2/AlignmentDocker.cwl
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| arguments: | ||
| valueFrom: bowtie2-build $(inputs.ReferenceGenome.path) $(inputs.index) bowtie2 -q -x $(inputs.index) -1 $(inputs.leftFastq.path) -2 $(inputs.rightFastq.path) -S $(inputs.sampleName).sam | ||
| shellQuote: false |
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Suggested change
| arguments: | |
| valueFrom: bowtie2-build $(inputs.ReferenceGenome.path) $(inputs.index) bowtie2 -q -x $(inputs.index) -1 $(inputs.leftFastq.path) -2 $(inputs.rightFastq.path) -S $(inputs.sampleName).sam | |
| shellQuote: false | |
| arguments: | |
| valueFrom: bowtie2-build $(inputs.ReferenceGenome.path) $(inputs.index) | bowtie2 -q -x $(inputs.index) -1 $(inputs.leftFastq.path) -2 $(inputs.rightFastq.path) -S $(inputs.sampleName).sam | |
| shellQuote: false |
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Piped bowtie2-build and bowtie2.
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Please validate the change.
There is error.
(env) ngsap2@ubuntu:~$ cwl-runner alignmentDocker.cwl
INFO /home/ngsap2/.local/bin/cwl-runner 3.0.20200324120055
INFO Resolved 'alignmentDocker.cwl' to 'file:///home/ngsap2/alignmentDocker.cwl'
ERROR Tool definition failed validation:
alignmentDocker.cwl:14:24: mapping values are not allowed here
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I have run cwl-format and cwltool --validate for AlignmentDocker.cwl. But cwltool run fails. Error is below.
ngsap2@ubuntu:~$ sudo docker run -v /var/run/docker.sock:/var/run/docker.sock -v "$PWD":"$PWD" -w="$PWD" commonworkflowlanguage/cwltool /home/ngsap2/samtoolsDocker/AlignmentDockerNew.cwl --leftFastq /home/ngsap2/Downloads/testdata16march/ebola_mut_reads1.fq --rightFastq /home/ngsap2/Downloads/testdata16march/ebola_mut_reads2.fq --ReferenceGenome /home/ngsap2/Downloads/testdata16march/ebola_ref.fasta --sampleName ebola --index eb --docker comics/bowtie2
INFO /usr/local/bin/cwltool 2.0.20200107113851
INFO Resolved '/home/ngsap2/samtoolsDocker/AlignmentDockerNew.cwl' to 'file:///home/ngsap2/samtoolsDocker/AlignmentDockerNew.cwl'
INFO ['docker', 'pull', 'docker']
Using default tag: latest
latest: Pulling from library/docker
cbdbe7a5bc2a: Pulling fs layer
6f4c731d6eb3: Pulling fs layer
5d79d4ac3cd0: Pulling fs layer
65de10866d6a: Pulling fs layer
ffd69ed7f17f: Pulling fs layer
07ba9e5a2fa6: Pulling fs layer
75478c283dd2: Pulling fs layer
ffd69ed7f17f: Waiting
07ba9e5a2fa6: Waiting
75478c283dd2: Waiting
65de10866d6a: Waiting
5d79d4ac3cd0: Verifying Checksum
5d79d4ac3cd0: Download complete
cbdbe7a5bc2a: Verifying Checksum
cbdbe7a5bc2a: Download complete
6f4c731d6eb3: Verifying Checksum
6f4c731d6eb3: Download complete
cbdbe7a5bc2a: Pull complete
ffd69ed7f17f: Download complete
07ba9e5a2fa6: Verifying Checksum
07ba9e5a2fa6: Download complete
6f4c731d6eb3: Pull complete
5d79d4ac3cd0: Pull complete
75478c283dd2: Verifying Checksum
75478c283dd2: Download complete
65de10866d6a: Verifying Checksum
65de10866d6a: Download complete
65de10866d6a: Pull complete
ffd69ed7f17f: Pull complete
07ba9e5a2fa6: Pull complete
75478c283dd2: Pull complete
Digest: sha256:8c119115801ae96e1f55b2ccb69cc84537c79eea057a00f363df0196f3d09fd4
Status: Downloaded newer image for docker:latest
INFO [job AlignmentDocker] /tmp/jx5vfv7x$ docker \
run \
-i \
--volume=/tmp/jx5vfv7x:/BScJye:rw \
--volume=/tmp/e3m0q78a:/tmp:rw \
--volume=/home/ngsap2/Downloads/testdata16march/ebola_mut_reads1.fq:/var/lib/cwl/stgfeed78c8-d5f0-4802-9b1d-d8e9ab026a04/ebola_mut_reads1.fq:ro \
--volume=/home/ngsap2/Downloads/testdata16march/ebola_mut_reads2.fq:/var/lib/cwl/stg425eea77-c9d2-44d6-b616-53e511a4b32d/ebola_mut_reads2.fq:ro \
--volume=/home/ngsap2/Downloads/testdata16march/ebola_ref.fasta:/var/lib/cwl/stg5c94f135-a5af-4a66-8fe8-fb0d1541a958/ebola_ref.fasta:ro \
--workdir=/BScJye \
--read-only=true \
--user=0:0 \
--rm \
--env=TMPDIR=/tmp \
--env=HOME=/BScJye \
--cidfile=/tmp/b66i6_y0/20200517054753-879463.cid \
docker \
/bin/sh \
-c \
bowtie2-build /var/lib/cwl/stg5c94f135-a5af-4a66-8fe8-fb0d1541a958/ebola_ref.fasta eb | bowtie2 -q -x eb -1 /var/lib/cwl/stgfeed78c8-d5f0-4802-9b1d-d8e9ab026a04/ebola_mut_reads1.fq -2 /var/lib/cwl/stg425eea77-c9d2-44d6-b616-53e511a4b32d/ebola_mut_reads2.fq -S ebola.sam
/bin/sh: bowtie2-build: not found
/bin/sh: bowtie2: not found
INFO [job AlignmentDocker] Max memory used: 0MiB
ERROR [job AlignmentDocker] Job error:
("Error collecting output for parameter 'rawSAM':\nsamtoolsDocker/AlignmentDockerNew.cwl:31:5: Did not find output file with glob pattern: '['ebola.sam']'", {})
WARNING [job AlignmentDocker] completed permanentFail
{}
WARNING Final process status is permanentFail
mr-c
reviewed
May 15, 2020
bowtie2/AlignmentDocker.cwl
Outdated
Comment on lines
13
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| dockerPull: docker |
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Suggested change
| -class: DockerRequirement | |
| dockerPull: docker | |
| - class: DockerRequirement | |
| dockerPull: docker |
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Made the changes.
Now the error is into arguments section.
https://github.com/ambarishK/bio-cwl-tools/blob/release/bowtie2/AlignmentDocker.cwl
(env) ngsap2@ubuntu:~$ cwl-runner alignmentDocker.cwl
INFO /home/ngsap2/.local/bin/cwl-runner 3.0.20200324120055
INFO Resolved 'alignmentDocker.cwl' to 'file:///home/ngsap2/alignmentDocker.cwl'
ERROR Tool definition failed validation:
alignmentDocker.cwl:7:5: Object `alignmentDocker.cwl` is not valid because
tried `CommandLineTool` but
alignmentDocker.cwl:104:5: the `arguments` field is not valid because
value is a CommentedMap, expected null or array of <string or
Expression or CommandLineBinding>
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cwl-format and cwltool --validate is complete but cwltool run fails. Error is posted in above comment.
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This is my pull request for WDL2CWL conversion example.
Will fix #79