-
phac-nml/iridanextexample v${version}
+
phac-nml/gasnomenclature v${version}
Run Name: $runName
<% if (!success){
out << """
-
phac-nml/iridanextexample execution completed unsuccessfully!
+
phac-nml/gasnomenclature execution completed unsuccessfully!
The exit status of the task that caused the workflow execution to fail was: $exitStatus.
The full error message was:
${errorReport}
@@ -27,7 +27,7 @@
phac-nml/iridanextexample execution co
} else {
out << """
- phac-nml/iridanextexample execution completed successfully!
+ phac-nml/gasnomenclature execution completed successfully!
"""
}
@@ -44,8 +44,8 @@ Pipeline Configuration:
-phac-nml/iridanextexample
-
https://github.com/phac-nml/iridanextexample
+
phac-nml/gasnomenclature
+
https://github.com/phac-nml/gasnomenclature
diff --git a/assets/email_template.txt b/assets/email_template.txt
index 0c55e86..19c2e43 100644
--- a/assets/email_template.txt
+++ b/assets/email_template.txt
@@ -4,15 +4,15 @@
|\\ | |__ __ / ` / \\ |__) |__ } {
| \\| | \\__, \\__/ | \\ |___ \\`-._,-`-,
`._,._,'
- phac-nml/iridanextexample v${version}
+ phac-nml/gasnomenclature v${version}
----------------------------------------------------
Run Name: $runName
<% if (success){
- out << "## phac-nml/iridanextexample execution completed successfully! ##"
+ out << "## phac-nml/gasnomenclature execution completed successfully! ##"
} else {
out << """####################################################
-## phac-nml/iridanextexample execution completed unsuccessfully! ##
+## phac-nml/gasnomenclature execution completed unsuccessfully! ##
####################################################
The exit status of the task that caused the workflow execution to fail was: $exitStatus.
The full error message was:
@@ -35,5 +35,5 @@ Pipeline Configuration:
<% out << summary.collect{ k,v -> " - $k: $v" }.join("\n") %>
--
-phac-nml/iridanextexample
-https://github.com/phac-nml/iridanextexample
+phac-nml/gasnomenclature
+https://github.com/phac-nml/gasnomenclature
diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml
index a50a571..87069b2 100644
--- a/assets/methods_description_template.yml
+++ b/assets/methods_description_template.yml
@@ -1,11 +1,11 @@
id: "nf-core-iridanext-methods-description"
description: "Suggested text and references to use when describing pipeline usage within the methods section of a publication."
-section_name: "phac-nml/iridanextexample Methods Description"
-section_href: "https://github.com/phac-nml/iridanextexample"
+section_name: "phac-nml/gasnomenclature Methods Description"
+section_href: "https://github.com/phac-nml/gasnomenclature"
plot_type: "html"
data: |
Methods
-
Data was processed using phac-nml/iridanextexample v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.
+
Data was processed using phac-nml/gasnomenclature v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.
The pipeline was executed with Nextflow v${workflow.nextflow.version} (Di Tommaso et al., 2017) with the following command:
${workflow.commandLine}
${tool_citations}
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index cc1689a..1d064f5 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,13 +1,13 @@
report_comment: >
- This report has been generated by the
phac-nml/iridanextexample
+ This report has been generated by the
phac-nml/gasnomenclature
analysis pipeline. For information about how to interpret these results, please see the
-
documentation.
+
documentation.
report_section_order:
- "phac-nml-iridanextexample-methods-description":
+ "phac-nml-gasnomenclature-methods-description":
order: -1000
software_versions:
order: -1001
- "phac-nml-iridanextexample-summary":
+ "phac-nml-gasnomenclature-summary":
order: -1002
export_plots: true
diff --git a/assets/schema_input.json b/assets/schema_input.json
index b1dd3fc..7068f08 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -1,7 +1,7 @@
{
"$schema": "http://json-schema.org/draft-07/schema",
- "$id": "https://raw.githubusercontent.com/phac-nml/iridanextexample/main/assets/schema_input.json",
- "title": "phac-nml/iridanextexample pipeline - params.input schema",
+ "$id": "https://raw.githubusercontent.com/phac-nml/gasnomenclature/main/assets/schema_input.json",
+ "title": "phac-nml/gasnomenclature pipeline - params.input schema",
"description": "Schema for the file provided with params.input",
"type": "array",
"items": {
diff --git a/assets/slackreport.json b/assets/slackreport.json
index 350c725..60e64ca 100644
--- a/assets/slackreport.json
+++ b/assets/slackreport.json
@@ -3,7 +3,7 @@
{
"fallback": "Plain-text summary of the attachment.",
"color": "<% if (success) { %>good<% } else { %>danger<%} %>",
- "author_name": "phac-nml/iridanextexample v${version} - ${runName}",
+ "author_name": "phac-nml/gasnomenclature v${version} - ${runName}",
"author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico",
"text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>",
"fields": [
diff --git a/conf/base.config b/conf/base.config
index 503b044..f12b332 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -1,6 +1,6 @@
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- phac-nml/iridanextexample Nextflow base config file
+ phac-nml/gasnomenclature Nextflow base config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
A 'blank slate' config file, appropriate for general use on most high performance
compute environments. Assumes that all software is installed and available on
diff --git a/conf/test.config b/conf/test.config
index 52f31db..0e0b591 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -5,7 +5,7 @@
Defines input files and everything required to run a fast and simple pipeline test.
Use as follows:
- nextflow run phac-nml/iridanextexample -profile test,
--outdir
+ nextflow run phac-nml/gasnomenclature -profile test, --outdir
----------------------------------------------------------------------------------------
*/
@@ -20,5 +20,5 @@ params {
max_time = '1.h'
// Input data
- input = 'https://raw.githubusercontent.com/phac-nml/iridanextexample/main/assets/samplesheet.csv'
+ input = 'https://raw.githubusercontent.com/phac-nml/gasnomenclature/main/assets/samplesheet.csv'
}
diff --git a/conf/test_full.config b/conf/test_full.config
index 319becf..c8b5764 100644
--- a/conf/test_full.config
+++ b/conf/test_full.config
@@ -5,7 +5,7 @@
Defines input files and everything required to run a full size pipeline test.
Use as follows:
- nextflow run phac-nml/iridanextexample -profile test_full, --outdir
+ nextflow run phac-nml/gasnomenclature -profile test_full, --outdir
----------------------------------------------------------------------------------------
*/
@@ -15,5 +15,5 @@ params {
config_profile_description = 'Full test dataset to check pipeline function'
// Input data for full size test
- input = 'https://raw.githubusercontent.com/phac-nml/iridanextexample/main/assets/samplesheet.csv'
+ input = 'https://raw.githubusercontent.com/phac-nml/gasnomenclature/main/assets/samplesheet.csv'
}
diff --git a/docs/README.md b/docs/README.md
index db77372..1935d67 100644
--- a/docs/README.md
+++ b/docs/README.md
@@ -1,6 +1,6 @@
-# phac-nml/iridanextexample: Documentation
+# phac-nml/gasnomenclature: Documentation
-The phac-nml/iridanextexample documentation is split into the following pages:
+The phac-nml/gasnomenclature documentation is split into the following pages:
- [Usage](usage.md)
- An overview of how the pipeline works, how to run it and a description of all of the different command-line flags.
diff --git a/docs/output.md b/docs/output.md
index 69a1069..817c382 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -1,4 +1,4 @@
-# phac-nml/iridanextexample: Output
+# phac-nml/gasnomenclature: Output
## Introduction
diff --git a/docs/run-wes-example.json b/docs/run-wes-example.json
index 7807de1..13acb46 100644
--- a/docs/run-wes-example.json
+++ b/docs/run-wes-example.json
@@ -13,6 +13,6 @@
"engine": "nextflow",
"execute_loc": "azure"
},
- "workflow_url": "https://github.com/phac-nml/iridanextexample",
+ "workflow_url": "https://github.com/phac-nml/gasnomenclature",
"workflow_attachment": ""
}
diff --git a/docs/usage.md b/docs/usage.md
index ff2ccc4..4fbd758 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -1,4 +1,4 @@
-# phac-nml/iridanextexample: Usage
+# phac-nml/gasnomenclature: Usage
## Introduction
@@ -62,7 +62,7 @@ Do not use `-c ` to specify parameters as this will result in errors. Cust
The above pipeline run specified with a params file in yaml format:
```bash
-nextflow run phac-nml/iridanextexample -profile docker -params-file params.yaml
+nextflow run phac-nml/gasnomenclature -profile docker -params-file params.yaml
```
with `params.yaml` containing:
@@ -79,7 +79,7 @@ You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-c
It is a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since.
-First, go to the [phac-nml/iridanextexample page](https://github.com/phac-nml/iridanextexample) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag.
+First, go to the [phac-nml/gasnomenclature page](https://github.com/phac-nml/gasnomenclature) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag.
This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future.
diff --git a/main.nf b/main.nf
index cd2ba58..8b9894a 100644
--- a/main.nf
+++ b/main.nf
@@ -1,9 +1,9 @@
#!/usr/bin/env nextflow
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- phac-nml/iridanextexample
+ phac-nml/gasnomenclature
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- Github : https://github.com/phac-nml/iridanextexample
+ Github : https://github.com/phac-nml/gasnomenclature
----------------------------------------------------------------------------------------
*/
@@ -39,10 +39,10 @@ WorkflowMain.initialise(workflow, params, log, args)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
-include { IRIDANEXT } from './workflows/iridanextexample'
+include { IRIDANEXT } from './workflows/gasnomenclature'
//
-// WORKFLOW: Run main phac-nml/iridanextexample analysis pipeline
+// WORKFLOW: Run main phac-nml/gasnomenclature analysis pipeline
//
workflow PHACNML_IRIDANEXT {
IRIDANEXT ()
diff --git a/modules.json b/modules.json
index 3f7b665..4a918c9 100644
--- a/modules.json
+++ b/modules.json
@@ -1,6 +1,6 @@
{
- "name": "phac-nml/iridanextexample",
- "homePage": "https://github.com/phac-nml/iridanextexample",
+ "name": "phac-nml/gasnomenclature",
+ "homePage": "https://github.com/phac-nml/gasnomenclature",
"repos": {
"https://github.com/nf-core/modules.git": {
"modules": {
diff --git a/modules/local/gas/call/main.nf b/modules/local/gas/call/main.nf
new file mode 100644
index 0000000..1fe2c64
--- /dev/null
+++ b/modules/local/gas/call/main.nf
@@ -0,0 +1,37 @@
+
+
+process GAS_CALL{
+ label "process_high"
+ tag "Calling: ${meta.id}"
+
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/genomic_address_service%3A0.1.1--pyh7cba7a3_1' :
+ 'quay.io/biocontainers/genomic_address_service:0.1.1--pyh7cba7a3_1' }"
+
+
+ input:
+ tuple val(meta), path(reference_clusters), path(distances)
+
+ output:
+ tuple val(meta), path("${prefix}/results.{text,parquet}"), emit: distances, optional: true
+ tuple val(meta), path("${prefix}/thresholds.json"), emit: thresholds
+ tuple val(meta), path("${prefix}/run.json"), emit: run
+ path "versions.yml", emit: versions
+
+ script:
+ // Need to add more args for gas call below
+ prefix = meta.id
+ """
+ gas call --dists $distances \\
+ --rclusters $reference_clusters \\
+ --outdir ${prefix} \\
+ --threshold ${params.gm_thresholds} \\
+ --delimeter ${params.gm_delimiter}
+
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ genomic_address_service: \$( gas call -V | sed -e "s/gas//g" )
+ END_VERSIONS
+ """
+
+}
diff --git a/modules/local/profile_dists/main.nf b/modules/local/profile_dists/main.nf
new file mode 100644
index 0000000..2e48a02
--- /dev/null
+++ b/modules/local/profile_dists/main.nf
@@ -0,0 +1,61 @@
+process PROFILE_DISTS{
+ label "process_high"
+ tag "Pairwise Distance Generation: ${meta.id}"
+
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/profile_dists%3A1.0.0--pyh7cba7a3_0' :
+ 'quay.io/biocontainers/profile_dists:1.0.0--pyh7cba7a3_0' }"
+
+ input:
+ tuple val(meta), path(query), path(ref)
+ val mapping_format
+ path(mapping_file)
+ path(columns)
+
+
+ output:
+ tuple val(meta), path("${prefix}_${mapping_format}/allele_map.json"), emit: allele_map
+ tuple val(meta), path("${prefix}_${mapping_format}/query_profile.{text,parquet}"), emit: query_profile
+ tuple val(meta), path("${prefix}_${mapping_format}/ref_profile.{text,parquet}"), emit: ref_profile
+ tuple val(meta), path("${prefix}_${mapping_format}/results.{text,parquet}"), emit: results
+ tuple val(meta), path("${prefix}_${mapping_format}/run.json"), emit: run
+ path "versions.yml", emit: versions
+
+
+ script:
+ def args = ""
+
+ if(mapping_file){
+ args = args + "--mapping_file $mapping_file"
+ }
+ if(columns){
+ args = args + " --columns $columns"
+ }
+ if(params.pd_force){
+ args = args + " --force"
+ }
+ if(params.pd_skip){
+ args = args + " --skip"
+ }
+ if(params.pd_count_missing){
+ args = args + " --count_missing"
+ }
+ // --match_threshold $params.profile_dists.match_thresh \\
+ prefix = meta.id
+ """
+ profile_dists --query $query --ref $ref $args --outfmt $mapping_format \\
+ --distm $params.pd_distm \\
+ --file_type $params.pd_file_type \\
+ --missing_thresh $params.pd_missing_threshold \\
+ --sample_qual_thresh $params.pd_sample_quality_threshold \\
+ --max_mem ${task.memory.toGiga()} \\
+ --cpus ${task.cpus} \\
+ -o ${prefix}_${mapping_format}
+
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ profile_dists: \$( profile_dists -V | sed -e "s/profile_dists//g" )
+ END_VERSIONS
+ """
+
+}
diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf
index 5fb6717..6c1c1f4 100644
--- a/modules/local/samplesheet_check.nf
+++ b/modules/local/samplesheet_check.nf
@@ -17,7 +17,7 @@ process SAMPLESHEET_CHECK {
when:
task.ext.when == null || task.ext.when
- script: // This script is bundled with the pipeline, in phac-nml/iridanextexample/bin/
+ script: // This script is bundled with the pipeline, in phac-nml/gasnomenclature/bin/
"""
check_samplesheet.py \\
$samplesheet \\
diff --git a/nextflow.config b/nextflow.config
index bba34c0..cdd6d74 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -1,6 +1,6 @@
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- phac-nml/iridanextexample Nextflow config file
+ phac-nml/gasnomenclature Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
@@ -195,13 +195,13 @@ dag {
}
manifest {
- name = 'phac-nml/iridanextexample'
- author = """Aaron Petkau and Eric Marinier"""
- homePage = 'https://github.com/phac-nml/iridanextexample'
- description = """IRIDA Next Example Pipeline"""
+ name = 'phac-nml/gasnomenclature'
+ author = """Matthew Wells, Aaron Petkau, Eric Marinier and Kyla Cochrane"""
+ homePage = 'https://github.com/phac-nml/gasnomenclature'
+ description = """Gas Nomenclature assignment pipeline"""
mainScript = 'main.nf'
nextflowVersion = '!>=23.04.0'
- version = '1.0.3'
+ version = 'v0.0.1dev'
doi = ''
defaultBranch = 'main'
}
diff --git a/nextflow_schema.json b/nextflow_schema.json
index f26142a..8639c86 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -1,7 +1,7 @@
{
"$schema": "http://json-schema.org/draft-07/schema",
- "$id": "https://raw.githubusercontent.com/phac-nml/iridanextexample/main/nextflow_schema.json",
- "title": "phac-nml/iridanextexample pipeline parameters",
+ "$id": "https://raw.githubusercontent.com/phac-nml/gasnomenclature/main/nextflow_schema.json",
+ "title": "phac-nml/gasnomenclature pipeline parameters",
"description": "IRIDA Next Example Pipeline",
"type": "object",
"definitions": {