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Update rnasum input parameters #480

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merged 3 commits into from
Apr 5, 2024
Merged

Update rnasum input parameters #480

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9f3c6fb
update rnasum input parameters
skanwal Apr 4, 2024
17a8d0f
update bindings
skanwal Apr 4, 2024
e9d5eec
move arguments to params and other param updates
skanwal Apr 5, 2024
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11 changes: 4 additions & 7 deletions config/project.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -10,8 +10,7 @@ projects:
linked_projects:
- dc8e6ba9-b744-437b-b070-4cf014694b3d
- c9173925-a838-4394-9fc6-61cb93c252a1
tenant_id:
YXdzLXVzLXBsYXRmb3JtOjEwMDAwNTM3OjBiYTU5YWUxLWZkYWUtNDNiYS1hM2I1LTRkMzY3YTQzYWJkNQ
tenant_id: YXdzLXVzLXBsYXRmb3JtOjEwMDAwNTM3OjBiYTU5YWUxLWZkYWUtNDNiYS1hM2I1LTRkMzY3YTQzYWJkNQ
tools:
- name: samtools-merge
path: samtools-merge
Expand Down Expand Up @@ -474,7 +473,7 @@ projects:
- name: 0.5.0
path: 0.5.0/rnasum__0.5.0.cwl
ica_workflow_version_name: 0.5.0
modification_time: 2024-01-04T01:02:49UTC
modification_time: 2024-04-04T02:32:11UTC
run_instances: []
- name: samtools-stats
path: samtools-stats
Expand Down Expand Up @@ -1056,8 +1055,7 @@ projects:
- 20b42a71-1ebc-4e7b-b659-313f2f4524c3
- c9173925-a838-4394-9fc6-61cb93c252a1
- dc8e6ba9-b744-437b-b070-4cf014694b3d
tenant_id:
YXdzLXVzLXBsYXRmb3JtOjEwMDAwNTM3OjBiYTU5YWUxLWZkYWUtNDNiYS1hM2I1LTRkMzY3YTQzYWJkNQ
tenant_id: YXdzLXVzLXBsYXRmb3JtOjEwMDAwNTM3OjBiYTU5YWUxLWZkYWUtNDNiYS1hM2I1LTRkMzY3YTQzYWJkNQ
tools:
- name: dragen-build-reference-tarball
path: dragen-build-reference-tarball
Expand Down Expand Up @@ -3315,8 +3313,7 @@ projects:
production: false
linked_projects:
- 30f09dfb-10e3-43b4-9056-07c8623b96a3
tenant_id:
YXdzLXVzLXBsYXRmb3JtOjEwMDAwNTM3OjBiYTU5YWUxLWZkYWUtNDNiYS1hM2I1LTRkMzY3YTQzYWJkNQ
tenant_id: YXdzLXVzLXBsYXRmb3JtOjEwMDAwNTM3OjBiYTU5YWUxLWZkYWUtNDNiYS1hM2I1LTRkMzY3YTQzYWJkNQ
tools:
- name: custom-create-tso500-samplesheet
path: custom-create-tso500-samplesheet
Expand Down
2 changes: 1 addition & 1 deletion config/tool.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -453,7 +453,7 @@ tools:
md5sum: 8b05e1c40c2ff0befb56df0b31560c04
- name: 0.5.0
path: 0.5.0/rnasum__0.5.0.cwl
md5sum: dc500a423a94d396bfd84155570779e7
md5sum: 796c913d5ca9630fe96eae4dc4b93308
categories: []
- name: samtools-stats
path: samtools-stats
Expand Down
55 changes: 52 additions & 3 deletions tools/rnasum/0.5.0/rnasum__0.5.0.cwl
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Expand Up @@ -53,28 +53,63 @@ arguments:

inputs:
# Input folders
dragen_transcriptome_directory:
dragen_wts_dir:
label: dragen transcriptome directory
doc: |
Location of the results from Dragen RNA-seq pipeline
type: Directory?
inputBinding:
prefix: "--dragen_wts_dir"
arriba_directory:
dragen_fusions:
label: dragen fusions
doc: |
Location of the fusion output from Dragen RNA-seq pipeline
type: File?
inputBinding:
prefix: "--dragen_fusions"
salmon:
label: salmom
doc: |
Location of the quantification output from salmon
type: File?
inputBinding:
prefix: "--salmon"
arriba_dir:
label: arriba directory
doc: |
Location of the arriba outputs directory
type: Directory?
inputBinding:
prefix: "--arriba_dir"
arriba_pdf:
label: arriba pdf
doc: |
Location of the pdf output from arriba
type: File?
inputBinding:
prefix: "--arriba_pdf"
arriba_tsv:
label: arriba tsv
doc: |
Location of the tsv output from arriba
type: File?
inputBinding:
prefix: "--arriba_tsv"
umccrise_directory:
label: umccrise directory
doc: |
The umccrise output directory
type: Directory?
inputBinding:
prefix: "--umccrise"
report_directory:
manta_tsv:
label: manta tsv
doc: |
Location of the tsv output from manta
type: File?
inputBinding:
prefix: "--manta_tsv"
report_dir:
label: report dir
doc: |
Desired location for the outputs
Expand Down Expand Up @@ -128,6 +163,20 @@ inputs:
type: boolean?
inputBinding:
prefix: "--immunogram"
pcgr_tiers_tsv:
label: pcgr tiers tsv
doc: |
Location of the tsv output from pcgr
type: File?
inputBinding:
prefix: "--pcgr_tiers_tsv"
purple_gene_tsv:
label: purple gene tsv
doc: |
Location of the tsv output from purple
type: File?
inputBinding:
prefix: "--purple_gene_tsv"
pcgr_tier:
label: pcgr tier
default: 4
Expand Down