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More tutorial testing, tutorial updates.
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‎docs/_writing_dependencies_containers_cwl.rst‎

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@@ -53,6 +53,8 @@ to check if a tool contains only best-practice ``requirement`` tags. The ``lint`
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command can also be fed the ``--biocontainers`` flag to check if a
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BioContainers_ container has been registered that is compatible with that tool.
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.. include:: _writing_containers_linter_explain.rst
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The Conda exercises project template has an example tool (``exercise3``) that we
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can use to demonstrate ``--biocontainers``. If you are continuing from the Conda
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tutorial, simply move to ``../exercise3`` otherwise using ``planemo project_init``
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.. INFO: BioContainer best-practice container found [quay.io/biocontainers/seqtk:1.2--1].
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Failed linting
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.. include:: _writing_containers_linter_explain.rst
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::
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$ planemo test --biocontainers seqtk_seq.cwl

‎docs/tests/tests_conda_cwl.sh‎

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#!/bin/bash
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SCRIPTS_DIRECTORY="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
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PROJECT_DIRECTORY="${SCRIPTS_DIRECTORY}/../.."
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set -o xtrace
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set -e
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shopt -s expand_aliases # Needed for conda_env test
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# Preconditions:
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# - seqtk not on PATH
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# - seqtk_example doesn't exist and in home directory
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# - conda_exercises doesn't exist in home directory.
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# - seqtk environment is absent
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echo "Setup completed seqtk example"
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# TODO: project_init once in master branch
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# planemo project_init --template=seqtk_complete_cwl seqtk_example
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cp -r $PROJECT_DIRECTORY/project_templates/seqtk_complete_cwl seqtk_example
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planemo project_init --template=seqtk_complete_cwl seqtk_example
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cd seqtk_example
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echo "Check conda_requirements - should see them linting properly"
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cd
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# TODO: project_init once in master branch
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# planemo project_init --template conda_exercises_cwl conda_exercises
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cp -r $PROJECT_DIRECTORY/project_templates/conda_exercises_cwl conda_exercises
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planemo project_init --template conda_exercises_cwl conda_exercises
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cd conda_exercises/exercise_1
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ls

‎docs/tests/tests_docker_cwl.sh‎

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#!/bin/bash
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SCRIPTS_DIRECTORY="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
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PROJECT_DIRECTORY="${SCRIPTS_DIRECTORY}/../.."
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set -o xtrace
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set -e
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# Preconditions
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# - seqtk not on PATH
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# - Planemo installed
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# - seqtk_example directory doesn't exist in the home directory.
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# - conda_exercises directory doesn't exist in the home directory.
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# - conda_answers directory doesn't exist in the home directory.
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# - conda_testing directory doesn't exist in the home directory
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# - docker running and sudo-less access available via the docker command.
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cd
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rm -rf conda_exercises
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rm -rf conda_answers_cwl
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rm -rf conda_testing
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echo "Setup completed seqtk example"
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# TODO: project_init once in master branch
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# planemo project_init --template=conda_exercies_cwl conda_exercies
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cp -r $PROJECT_DIRECTORY/project_templates/conda_exercies_cwl conda_exercies
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planemo project_init --template=conda_exercies_cwl conda_exercies
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cd conda_exercies
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cd conda_exercises/exercise_3
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echo "We should see biocontainer found for this tool, but not a Docker container"
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planemo lint --biocontainers seqtk_seq.cwl | true
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echo "This should pass and we should see container was used."
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planemo test --biocontainers --engine cwltool seqtk_seq.cwl
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planemo test --biocontainers seqtk_seq.cwl
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echo "This should fail without biocontainers"
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planemo test seqtk_seq.cwl
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cd ..
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echo "Run seqtk exercise answers"
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planemo project_init --template=conda_answers_cwl conda_answers
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cd conda_answers/exercise_3
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planemo lint --biocontainers seqtk_seq.cwl
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planemo test seqtk_seq.cwl
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planemo project_init --template=conda_testing_cwl conda_testing
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cd conda_testing/
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echo "Should show quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:03dc1d2818d9de56938078b8b78b82d967c1f820-0 is built"

‎project_templates/conda_answers_cwl/exercise_3/seqtk_seq.cwl‎

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#!/usr/bin/env cwl-runner
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cwlVersion: 'v1.0'
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class: CommandLineTool
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id: "seqtk_seq"
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label: "Convert to FASTA (seqtk)"
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hints:
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DockerRequirement:
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dockerPull: quay.io/biocontainers/seqtk:1.2--1
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SoftwareRequirement:
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packages:
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- package: seqtk
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version:
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- "1.2"
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inputs:
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input1:
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type: File
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doc: |
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Input FASTA file.
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inputBinding:
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position: 1
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prefix: "-a"
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outputs:
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output1:
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type: File
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outputBinding:
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glob: out
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baseCommand:
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- "seqtk"
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- "seq"
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arguments: []
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stdout: out
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doc: |
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Usage: seqtk seq [options] <in.fq>|<in.fa>
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Options: -q INT mask bases with quality lower than INT [0]
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-X INT mask bases with quality higher than INT [255]
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-n CHAR masked bases converted to CHAR; 0 for lowercase [0]
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-l INT number of residues per line; 0 for 2^32-1 [0]
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-Q INT quality shift: ASCII-INT gives base quality [33]
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-s INT random seed (effective with -f) [11]
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-f FLOAT sample FLOAT fraction of sequences [1]
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-M FILE mask regions in BED or name list FILE [null]
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-L INT drop sequences with length shorter than INT [0]
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-c mask complement region (effective with -M)
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-r reverse complement
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-A force FASTA output (discard quality)
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-C drop comments at the header lines
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-N drop sequences containing ambiguous bases
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-1 output the 2n-1 reads only
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-2 output the 2n reads only
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-V shift quality by '(-Q) - 33'
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-U convert all bases to uppercases
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-S strip of white spaces in sequences
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$namespaces:
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s: http://schema.org/
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$schemas:
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- http://schema.org/docs/schema_org_rdfa.html
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s:mainEntity:
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class: s:SoftwareSourceCode
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s:name: seqtk
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s:about: 'Toolkit for processing sequences in FASTA/Q formats'
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s:url: https://github.com/lh3/seqtk
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s:codeRepository: https://github.com/lh3/seqtk
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s:license:
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- https://opensource.org/licenses/MIT
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s:targetProduct:
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class: s:SoftwareApplication
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s:softwareVersion: "1.2"
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s:applicationCategory: commandline tool
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s:programmingLanguage: C
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s:publication:
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- class: s:ScholarlyArticle
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id: http://dx.doi.org/10.1093/bioinformatics/bts635
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s:author:
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- class: s:Person
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s:name: "Heng Li"
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s:sameAs:
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- id: https://orcid.org/0000-0003-4874-2874
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s:downloadUrl: https://github.com/galaxyproject/planemo/blob/master/project_templates/seqtk_complete_cwl/seqtk_seq.cwl
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s:codeRepository: https://github.com/galaxyproject/planemo
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s:author:
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class: s:Person
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s:name: John Chilton
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s:email: mailto:jmchilton@gmail.com
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s:sameAs:
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- id: https://orcid.org/0000-0002-6794-0756

‎project_templates/conda_answers_cwl/exercise_3/seqtk_seq_job.yml‎

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input1:
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class: File
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path: test-data/2.fastq

‎project_templates/conda_answers_cwl/exercise_3/seqtk_seq_tests.yml‎

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- doc: test generated from example command
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job: seqtk_seq_job.json
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outputs:
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output1:
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path: test-data/2.fasta

‎project_templates/conda_answers_cwl/exercise_3/test-data/2.fasta‎

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>EAS54_6_R1_2_1_413_324
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CCCTTCTTGTCTTCAGCGTTTCTCC
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>EAS54_6_R1_2_1_540_792
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TTGGCAGGCCAAGGCCGATGGATCA
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>EAS54_6_R1_2_1_443_348
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GTTGCTTCTGGCGTGGGTGGGGGGG

‎project_templates/conda_answers_cwl/exercise_3/test-data/2.fastq‎

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@EAS54_6_R1_2_1_413_324
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CCCTTCTTGTCTTCAGCGTTTCTCC
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;;3;;;;;;;;;;;;7;;;;;;;88
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@EAS54_6_R1_2_1_540_792
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TTGGCAGGCCAAGGCCGATGGATCA
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;;;;;;;;;;;7;;;;;-;;;3;83
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@EAS54_6_R1_2_1_443_348
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GTTGCTTCTGGCGTGGGTGGGGGGG
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+EAS54_6_R1_2_1_443_348
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;;;;;;;;;;;9;7;;.7;393333

‎project_templates/conda_exercises_cwl/exercise_3/seqtk_seq_job.yml‎

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input1:
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class: File
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path: test-data/2.fastq

‎project_templates/conda_exercises_cwl/exercise_3/seqtk_seq_tests.yml‎

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- doc: test generated from example command
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job:
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input1:
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class: File
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path: test-data/2.fastq
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job: seqtk_seq_job.json
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outputs:
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output1:
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path: test-data/2.fasta

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