Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

clonal_threshold accepts multiple values in nextflow_schema.json #293

Merged
merged 5 commits into from
Dec 22, 2023
Merged

clonal_threshold accepts multiple values in nextflow_schema.json #293

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
65a1e89
clonal_threshold validation uses JSON schema format
adamrtalbot Dec 21, 2023
2915e70
cheat linter with extra 'type' entry
adamrtalbot Dec 21, 2023
17470ca
fix docker emulation
ggabernet Dec 22, 2023
adbdd1a
fix schema linting
ggabernet Dec 22, 2023
35463cb
making @maxulysse happy
ggabernet Dec 22, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
### `Fixed`

- Removed optional output from FilterQuality to not fail silently
- clonal_threshold is validated to be 'auto' or number greater than zero

### `Dependencies`

Expand Down
2 changes: 1 addition & 1 deletion nextflow.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -190,7 +190,7 @@ profiles {
}
docker {
docker.enabled = true
docker.userEmulation = true
docker.runOptions = '-u $(id -u):$(id -g)'
conda.enabled = false
singularity.enabled = false
podman.enabled = false
Expand Down
15 changes: 12 additions & 3 deletions nextflow_schema.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -61,7 +61,7 @@
"type": "string",
"fa_icon": "fas fa-flask",
"description": "Protocol used for the V(D)J amplicon sequencing library generation.",
"enum": ["specific_pcr_umi", "specific_pcr", "dt_5p_race", "dt_5p_race_umi"],
"enum": ["dt_5p_race", "dt_5p_race_umi", "specific_pcr", "specific_pcr_umi"],
"help_text": "Available protocols are:\n- `specific_pcr_umi`: RT-PCR using transcript-specific primers containing UMIs.\n- `specific_pcr`: RT-PCR using transcript-specific primers.\n- `dt_5p_race_umi`: 5\u2019-RACE PCR using oligo-dT primers and template switch primers containing UMI.\n- `dt_5p_race`: 5\u2019-RACE PCR (i.e. RT is followed by a template switch (TS) step) using oligo-dT primers."
},
"race_linker": {
Expand Down Expand Up @@ -167,7 +167,6 @@
},
"adapter_fasta": {
"type": "string",
"default": "None",
"fa_icon": "fas fa-file",
"description": "Fasta file with adapter sequences to be trimmed."
},
Expand Down Expand Up @@ -235,7 +234,7 @@
"type": "string",
"default": "cut",
"description": "Masking mode for the pRESTO MaskPrimer step. Available: cut, mask, trim, tag.",
"enum": ["cut", "mask", "trim", "tag"],
"enum": ["cut", "mask", "tag", "trim"],
"help_text": "The primer masking modes will perform the following actions:\n\n* `cut`: remove both the primer region and the preceding sequence.\n* `mask`: replace the primer region with Ns and remove the preceding sequence.\n* `trim`: remove the region preceding the primer, but leave the primer region intact.\n* `tag`: leave the input sequence unmodified.",
"fa_icon": "fas fa-mask"
},
Expand Down Expand Up @@ -335,6 +334,16 @@
"default": "",
"properties": {
"clonal_threshold": {
"oneOf": [
{
"type": "string",
"enum": ["auto"]
},
{
"type": "number",
"minimum": 0
}
],
"type": ["string", "number"],
"default": "auto",
"fa_icon": "fab fa-pagelines",
Expand Down
Loading