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Correct namespaces #97

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b5666a9
Correct SevenBridges namespace
stain Oct 21, 2019
4c46a70
Include foaf/dct namespaces
stain Oct 21, 2019
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4 changes: 4 additions & 0 deletions CRAM-no-header-md5sum/CRAM_md5sum_checker_wrapper.cwl
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@@ -1,6 +1,10 @@
cwlVersion: v1.0
class: Workflow

$namespaces:
dct: http://purl.org/dc/terms/
foaf: http://xmlns.com/foaf/0.1/

dct:creator:
'@id': https://orcid.org/0000-0001-5173-4627
foaf:name: Walter Shands
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4 changes: 4 additions & 0 deletions CRAM-no-header-md5sum/md5sum/CRAM_md5sum.cwl
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@@ -1,6 +1,10 @@
cwlVersion: v1.0
class: Workflow

$namespaces:
dct: http://purl.org/dc/terms/
foaf: http://xmlns.com/foaf/0.1/

dct:creator:
'@id': https://orcid.org/0000-0001-5173-4627
foaf:name: Walter Shands
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2 changes: 1 addition & 1 deletion aligner/sbg-alignment-cwl/steps/align.cwl
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@@ -1,7 +1,7 @@
class: CommandLineTool
cwlVersion: v1.0
$namespaces:
sbg: 'https://sevenbridges.com'
sbg: 'https://sevenbridges.com/'
id: marko_zecevic_topmed_alignment_topmed_align_0
baseCommand:
- chmod
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2 changes: 1 addition & 1 deletion aligner/sbg-alignment-cwl/steps/alignment-validation.cwl
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@@ -1,7 +1,7 @@
class: CommandLineTool
cwlVersion: v1.0
$namespaces:
sbg: 'https://sevenbridges.com'
sbg: 'https://sevenbridges.com/'
id: alignment_validation
baseCommand:
- '{'
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2 changes: 1 addition & 1 deletion aligner/sbg-alignment-cwl/steps/post-align.cwl
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@@ -1,7 +1,7 @@
class: CommandLineTool
cwlVersion: v1.0
$namespaces:
sbg: 'https://sevenbridges.com'
sbg: 'https://sevenbridges.com/'
id: marko_zecevic_topmed_alignment_topmed_post_align_3
baseCommand:
- samtools
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2 changes: 1 addition & 1 deletion aligner/sbg-alignment-cwl/steps/pre-align.cwl
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@@ -1,7 +1,7 @@
class: CommandLineTool
cwlVersion: v1.0
$namespaces:
sbg: 'https://sevenbridges.com'
sbg: 'https://sevenbridges.com/'
id: marko_zecevic_validation_app_topmed_alignment_topmed_pre_align_7
baseCommand:
- samtools
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2 changes: 1 addition & 1 deletion aligner/sbg-alignment-cwl/steps/samtools-sort.cwl
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@@ -1,7 +1,7 @@
class: CommandLineTool
cwlVersion: v1.0
$namespaces:
sbg: 'https://sevenbridges.com'
sbg: 'https://sevenbridges.com/'
id: marko_zecevic_topmed_alignment_samtools_sort_0
baseCommand:
- samtools
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5 changes: 4 additions & 1 deletion aligner/sbg-alignment-cwl/topmed-alignment-checker.cwl
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Expand Up @@ -4,7 +4,10 @@ id: topmed_alignment_checker
doc: Checker for the TopMed alignment workflow.
label: TOPMed Alignment - checker
$namespaces:
sbg: 'https://sevenbridges.com'
sbg: 'https://sevenbridges.com/'
dct: http://purl.org/dc/terms/
foaf: http://xmlns.com/foaf/0.1/

inputs:
- id: reference_genome
'sbg:fileTypes': 'FA, FASTA'
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4 changes: 3 additions & 1 deletion aligner/sbg-alignment-cwl/topmed-alignment.cwl
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Expand Up @@ -8,7 +8,9 @@ doc: >-
Wrapper Author: Marko Zecevic (marko.zecevic@sbgenomics.com)
label: TOPMed Alignment
$namespaces:
sbg: 'https://sevenbridges.com'
sbg: 'https://sevenbridges.com/'
dct: http://purl.org/dc/terms/
foaf: http://xmlns.com/foaf/0.1/
inputs:
- id: input_file
'sbg:fileTypes': CRAM
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4 changes: 4 additions & 0 deletions aligner/topmed-cwl/workflow/alignment_workflow.cwl
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Expand Up @@ -174,3 +174,7 @@ steps:
reference: indexed_reference_fasta
input_bam: SortBam/output_sorted_bam
out: [output]

$namespaces:
dct: http://purl.org/dc/terms/
foaf: http://xmlns.com/foaf/0.1/
2 changes: 1 addition & 1 deletion ...ant-caller/sbg-variant-caller-cwl/steps/topmed_freeze3_calling/topmed_freeze3_calling.cwl
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Expand Up @@ -374,4 +374,4 @@ requirements:
return files.reverse();
};
$namespaces:
sbg: 'https://sevenbridges.com'
sbg: 'https://sevenbridges.com/'
2 changes: 1 addition & 1 deletion variant-caller/sbg-variant-caller-cwl/steps/verifybamid/verifybamid.cwl
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Expand Up @@ -194,4 +194,4 @@ requirements:
return files.reverse();
};
$namespaces:
sbg: 'https://sevenbridges.com'
sbg: 'https://sevenbridges.com/'
4 changes: 3 additions & 1 deletion variant-caller/sbg-variant-caller-cwl/topmed_freeze3_calling/topmed_freeze3_calling.cwl
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Expand Up @@ -541,7 +541,9 @@ hints:
'sbg:appVersion':
- v1.0
$namespaces:
sbg: 'https://sevenbridges.com'
sbg: 'https://sevenbridges.com/'
foaf: http://xmlns.com/foaf/0.1/
dct: http://purl.org/dc/terms/
'sbg:revision': 25
'sbg:latestRevision': 25
'sbg:projectName': TOPMed Freeze 3a Variant Calling Pipeline
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5 changes: 1 addition & 4 deletions variant-caller/sbg-variant-caller-cwl/topmed_variant_calling_pipeline.cwl
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Expand Up @@ -151,8 +151,5 @@ steps:
requirements:
- class: InlineJavascriptRequirement
$namespaces:
sbg: 'https://sevenbridges.com'
'dct:creator':
'foaf:mbox': 'mailto:vladimir.obucina@sbgenomics.com'
'foaf:name': Vladimir Obucina
sbg: 'https://sevenbridges.com/'

6 changes: 3 additions & 3 deletions ...nt-caller-cwl/variant-caller-cwl-checker/ConcordanceTest/concordance_checker_workflow.cwl
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Expand Up @@ -120,7 +120,7 @@ steps:
https://igor.sbgenomics.com/ns/brood/images/vladimir_obucina/topmed-freeze-3a-variant-calling-pipeline/gatkconcordance/1.png
'sbg:sbgMaintained': false
$namespaces:
sbg: 'https://sevenbridges.com'
sbg: 'https://sevenbridges.com/'
'sbg:modifiedBy': vladimir_obucina
'sbg:appVersion':
- v1.0
Expand Down Expand Up @@ -210,7 +210,7 @@ steps:
https://igor.sbgenomics.com/ns/brood/images/vladimir_obucina/topmed-freeze-3a-variant-calling-pipeline/gatkconcordancechecker/2.png
'sbg:sbgMaintained': false
$namespaces:
sbg: 'https://sevenbridges.com'
sbg: 'https://sevenbridges.com/'
'sbg:modifiedBy': vladimir_obucina
'sbg:appVersion':
- v1.0
Expand Down Expand Up @@ -253,7 +253,7 @@ requirements: []
'sbg:appVersion':
- v1.0
$namespaces:
sbg: 'https://sevenbridges.com'
sbg: 'https://sevenbridges.com/'
'sbg:revision': 4
'sbg:revisionsInfo':
- 'sbg:revision': 0
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2 changes: 1 addition & 1 deletion ...er/sbg-variant-caller-cwl/variant-caller-cwl-checker/ConcordanceTest/gatk_concordance.cwl
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Expand Up @@ -61,7 +61,7 @@ requirements:
'sbg:appVersion':
- v1.0
$namespaces:
sbg: 'https://sevenbridges.com'
sbg: 'https://sevenbridges.com/'
'sbg:revision': 1
'sbg:revisionsInfo':
- 'sbg:revision': 0
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2 changes: 1 addition & 1 deletion ...ariant-caller-cwl/variant-caller-cwl-checker/ConcordanceTest/gatk_concordance_checker.cwl
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Expand Up @@ -51,7 +51,7 @@ requirements:
'sbg:appVersion':
- v1.0
$namespaces:
sbg: 'https://sevenbridges.com'
sbg: 'https://sevenbridges.com/'
'sbg:revision': 2
'sbg:revisionsInfo':
- 'sbg:revision': 0
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2 changes: 1 addition & 1 deletion ...caller/sbg-variant-caller-cwl/variant-caller-cwl-checker/topmed-variantcaller-checker.cwl
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Expand Up @@ -175,4 +175,4 @@ requirements:
read_and_compare_vcfs_from_tar_gz(test_vcf, truth_vcf)
- class: InlineJavascriptRequirement
$namespaces:
sbg: 'https://sevenbridges.com'
sbg: 'https://sevenbridges.com/'
2 changes: 1 addition & 1 deletion ...ller/sbg-variant-caller-cwl/variant-caller-cwl-checker/topmed_freeze3_calling_checker.cwl
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Expand Up @@ -85,4 +85,4 @@ steps:
requirements:
- class: SubworkflowFeatureRequirement
$namespaces:
sbg: 'https://sevenbridges.com'
sbg: 'https://sevenbridges.com/'
2 changes: 1 addition & 1 deletion variant-caller/sbg-variant-caller-cwl/verifybamid/verifybamid.cwl
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Expand Up @@ -253,7 +253,7 @@ requirements:
'sbg:modifiedBy': vladimir_obucina
'sbg:revisionNotes': 'UPDATE: GRCh37 instead of hg19'
$namespaces:
sbg: 'https://sevenbridges.com'
sbg: 'https://sevenbridges.com/'
'sbg:cmdPreview': >-
export PATH=$PATH:/VerifyBamID/bin/ && VerifyBamID --UDPath
/VerifyBamID/resource/1000g.phase3.100k.b37.vcf.gz.dat.UD --BedPath
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