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chksum_xam_to_interleaved_fq.cwl
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chksum_xam_to_interleaved_fq.cwl
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#!/usr/bin/env cwl-runner
class: Workflow
id: "chksum-xam-to-interleaved-fq-workflow"
label: "A CGP workflow to generate checksum and interleaved fastq from a [Cr|B]am file"
cwlVersion: v1.0
requirements:
- class: StepInputExpressionRequirement
- class: InlineJavascriptRequirement
- class: MultipleInputFeatureRequirement
- class: ScatterFeatureRequirement
inputs:
xam_in:
type: File
doc: "The [B|Cr]am file to import."
put_address:
type: string?
doc: "Optional PUT address to send JSON results of checksums"
put_headers:
type: string[]?
doc: "Optional headers to send with JSON results"
cram_ref_url:
type: string
doc: "URL path to use as cram reference e.g. 'https://www.ebi.ac.uk/ena/cram/md5/%s'"
default: "https://www.ebi.ac.uk/ena/cram/md5/%s"
outputs:
chksum_json:
type: File
outputSource: chksum/chksum_json
chksum_put_server_response:
type: ["null", File]
outputSource: chksum/server_response
interleaved_fastq_out:
type:
type: array
items: File
doc: "Array of gzipped interleaved fastq files, one per read group in xam_in"
outputSource: xam_to_interleaved_fq/ifastqs_out
results_manifest:
type: File
outputSource: manifest_string_to_file/outfile
steps:
chksum:
in:
in_file:
source: xam_in
put_address:
source: put_address
put_headers:
source: put_headers
ignore_all_curl_exits:
valueFrom: $(true)
out: [chksum_json, server_response]
run: https://raw.githubusercontent.com/cancerit/dockstore-cgp-chksum/0.4.1/Dockstore.cwl
xam_to_interleaved_fq:
in:
xam_in:
source: xam_in
ref_path:
source: cram_ref_url
out: [ifastqs_out, rg_info_json]
run: https://raw.githubusercontent.com/cancerit/dockstore-samtools-biobambam2/0.0.4/cwls/xam_to_interleaved_by_rg.cwl
out_chksum:
in:
in_file:
source: xam_to_interleaved_fq/ifastqs_out
scatter: [in_file]
scatterMethod: dotproduct
out: [chksum_json] #An array of chksums directly relating to the input array of interleaved fastq files
run: https://raw.githubusercontent.com/cancerit/dockstore-cgp-chksum/0.4.1/Dockstore.cwl
results_manifest_string:
in:
input_files:
source: [xam_in]
linkMerge: merge_flattened
input_chksum_results:
source: [chksum/chksum_json]
linkMerge: merge_flattened
output_files:
source: xam_to_interleaved_fq/ifastqs_out
output_chksum_results:
source: out_chksum/chksum_json
output_rg_info_file:
source: xam_to_interleaved_fq/rg_info_json
out: [out_string]
run: results_manifest.cwl
manifest_string_to_file:
in:
in_string:
source: [results_manifest_string/out_string]
out: [outfile]
run: string_to_file.cwl
doc: |
A workflow to generate checksums of [B|Cr]am files and interleaved FastQs derived from them. See the [workflow-seq-import](https://github.com/cancerit/workflow-seq-import) website for more information.
$schemas:
- http://schema.org/docs/schema_org_rdfa.html
$namespaces:
s: http://schema.org/
s:codeRepository: https://github.com/cancerit/workflow-seq-import
s:license: https://spdx.org/licenses/AGPL-3.0
s:author:
- class: s:Person
s:identifier: https://orcid.org/0000-0002-0407-0386
s:email: mailto:drj@sanger.ac.uk
s:name: David Jones
dct:creator:
foaf:name: David Jones
foaf:mbox: "genservhelp@sanger.ac.uk"