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fix wfmash_sparse_map parameter #152

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merged 9 commits into from
Sep 21, 2023
Merged

fix wfmash_sparse_map parameter #152

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a1f8072
fix wfmash_sparse_map parameter
subwaystation Sep 21, 2023
16bcbcc
add wfmash_sparse_map test
subwaystation Sep 21, 2023
6538720
try linter fix
subwaystation Sep 21, 2023
dc5495a
try fix
subwaystation Sep 21, 2023
2904385
add wfmash_sparse_map to ignored params
subwaystation Sep 21, 2023
2570fd5
revert to string theory
subwaystation Sep 21, 2023
a2a4fe4
remove ignore parameter --wfmash_sparse_map
subwaystation Sep 21, 2023
7575ba1
update tests, add pattern
subwaystation Sep 21, 2023
90ebc5d
update CI, fix linting error
subwaystation Sep 21, 2023
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23 changes: 23 additions & 0 deletions .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -128,6 +128,29 @@ jobs:
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }}

wfmash_sparse_map:
name: Run pipeline with wfmash_sparse_map parameters
# Only run on push if this is the nf-core dev branch (merged PRs)
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/pangenome') }}"
runs-on: ubuntu-latest
strategy:
matrix:
parameters:
- "--wfmash_sparse_map auto"
- "--wfmash_sparse_map 0.5"
steps:
- name: Check out pipeline code
uses: actions/checkout@v3

- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
with:
version: "23.04.0"

- name: Run pipeline with test data and wfmash_only parameters
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }}

communities:
name: Run pipeline with community parameters
# Only run on push if this is the nf-core dev branch (merged PRs)
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8 changes: 4 additions & 4 deletions conf/modules.config
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Expand Up @@ -15,10 +15,10 @@ def generate_wfmash_sparse_map_cmd() {
def wfmash_sparse_map_cmd = ""
if (params.wfmash_sparse_map == "auto") {
def n = params.n_haplotypes
def x = Math.log(n)/n * 10
wfmash_sparse_map_frac = 1
if (x < 1) {
def wfmash_sparse_map_frac = x
def x = Math.log(n)/n * 10.0
wfmash_sparse_map_frac = 1.0
if (x < 1.0) {
wfmash_sparse_map_frac = x
}
wfmash_sparse_map_cmd = "-x ${wfmash_sparse_map_frac}"
} else {
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2 changes: 1 addition & 1 deletion nextflow.config
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Expand Up @@ -101,7 +101,7 @@ params {

// Schema validation default options
validationFailUnrecognisedParams = false
validationLenientMode = false
validationLenientMode = true
validationSchemaIgnoreParams = 'genomes'
validationShowHiddenParams = false
validate_params = true
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19 changes: 6 additions & 13 deletions nextflow_schema.json
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Expand Up @@ -54,7 +54,7 @@
"properties": {
"wfmash_map_pct_id": {
"type": "number",
"default": 90,
"default": 90.0,
"description": "Percent identity in the wfmash mashmap step.",
"help_text": "Use `mash dist` or `mash triangle` to explore the typical level of divergence between the sequences in your input (see https://pggb.readthedocs.io/en/latest/rst/tutorials/divergence_estimation.html#divergence-estimation for more information). Convert this to an approximate percent identity and provide it as --wfmash_map_pct_id <PCT>. A list of examples can be found at https://github.com/pangenome/pggb#example-builds-for-diverse-species."
},
Expand All @@ -81,9 +81,10 @@
"description": "Ignore the top % most-frequent kmers."
},
"wfmash_sparse_map": {
"type": "number",
"default": "1.0",
"description": "Keep this fraction of mappings (\"auto\" for giant component heuristic)."
"default": 1.0,
"description": "Keep this fraction of mappings (\"auto\" for giant component heuristic).",
"type": "string",
"pattern": "(auto|[01]\\.\\d+)"
},
"wfmash_merge_segments": {
"type": "boolean",
Expand Down Expand Up @@ -136,7 +137,7 @@
},
"seqwish_sparse_factor": {
"type": "number",
"default": 0,
"default": 0.0,
"description": "Keep this randomly selected fraction of input matches."
},
"seqwish_temp_dir": {
Expand Down Expand Up @@ -360,14 +361,12 @@
"type": "boolean",
"description": "Display help text.",
"fa_icon": "fas fa-question-circle",
"default": false,
"hidden": true
},
"version": {
"type": "boolean",
"description": "Display version and exit.",
"fa_icon": "fas fa-question-circle",
"default": false,
"hidden": true
},
"publish_dir_mode": {
Expand All @@ -391,7 +390,6 @@
"type": "boolean",
"description": "Send plain-text email instead of HTML.",
"fa_icon": "fas fa-remove-format",
"default": false,
"hidden": true
},
"max_multiqc_email_size": {
Expand All @@ -406,7 +404,6 @@
"type": "boolean",
"description": "Do not use coloured log outputs.",
"fa_icon": "fas fa-palette",
"default": false,
"hidden": true
},
"hook_url": {
Expand Down Expand Up @@ -445,31 +442,27 @@
"type": "boolean",
"fa_icon": "far fa-eye-slash",
"description": "Show all params when using `--help`",
"default": false,
"hidden": true,
"help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
},
"validationFailUnrecognisedParams": {
"type": "boolean",
"fa_icon": "far fa-check-circle",
"description": "Validation of parameters fails when an unrecognised parameter is found.",
"default": false,
"hidden": true,
"help_text": "By default, when an unrecognised parameter is found, it returns a warinig."
},
"validationLenientMode": {
"type": "boolean",
"fa_icon": "far fa-check-circle",
"description": "Validation of parameters in lenient more.",
"default": false,
"hidden": true,
"help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)."
},
"show_hidden_params": {
"type": "boolean",
"fa_icon": "far fa-check-circle",
"description": "Do we want to display hidden parameters?",
"default": false,
"hidden": true,
"help_text": "Do we want to display hidden parameters?"
},
Expand Down