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Merge pull request #4 from Zymo-Research/aladdin-miqScore16S
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aladdin-miqScore renamed to aladdin-miqScore16S
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nsharp2 authored Feb 9, 2023
2 parents 6ab5955 + 0404741 commit a5ecd5c
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4 changes: 2 additions & 2 deletions README.md
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# aladdin-miqScore
Nextflow pipeline that calculates MIQ score. Compatible with Aladdin platform
# aladdin-miqScore16S
Nextflow pipeline that calculates MIQ 16S score. Compatible with Aladdin platform
10 changes: 5 additions & 5 deletions main.nf
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@@ -1,6 +1,6 @@
#!/usr/bin/env nextflow
/*
A nextflow pipeline to calculate MIQ score, that is compatible with Aladdin platform.
A nextflow pipeline to calculate MIQ 16S score, that is compatible with Aladdin platform.
This is essentially a wrapper to run the code in MIQ score public repos, plus code to interact with Aladdin platform.
*/

Expand Down Expand Up @@ -32,7 +32,7 @@ design = setup_channel(params.design, "design CSV file", true, "")
/*
* COLLECT SUMMARY & LOG
*/
log.info "Aladdin miqScore v${workflow.manifest.version}"
log.info "Aladdin miqScore16S v${workflow.manifest.version}"
def summary = collect_summary(params, workflow)
log.info summary.collect { k,v -> "${k.padRight(21)}: $v" }.join("\n")
// Save workflow summary plain text
Expand Down Expand Up @@ -85,8 +85,8 @@ workflow.onComplete {
log.info "Number of successfully ran process(es) : ${workflow.stats.succeedCount}"
}
if(workflow.success){
log.info "[miqScore] Pipeline completed successfully"
log.info "[miqScore16S] Pipeline completed successfully"
} else {
log.info "[miqScore] Pipeline completed with errors"
log.info "[miqScore16S] Pipeline completed with errors"
}
}
}
6 changes: 3 additions & 3 deletions nextflow.config
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@@ -1,6 +1,6 @@
/*
* -------------------------------------------------
* Aladdin miqScore Nextflow config file
* Aladdin miqScore16S Nextflow config file
* -------------------------------------------------
*/

Expand Down Expand Up @@ -62,9 +62,9 @@ dag {
}

manifest {
name = 'Zymo-Research/aladdin-miqScore'
name = 'Zymo-Research/aladdin-miqScore16S'
author = 'Zhenfeng Liu'
homePage = 'https://github.com/Zymo-Research/aladdin-miqScore'
homePage = 'https://github.com/Zymo-Research/aladdin-miqScore16S'
description = 'Nextflow pipeline to run MIQ score calculator.'
mainScript = 'main.nf'
nextflowVersion = '>=20.07.1'
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6 changes: 3 additions & 3 deletions nextflow_schema.json
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@@ -1,7 +1,7 @@
{
"$schema": "http://json-schema.org/draft-07/schema",
"$id": "https://raw.githubusercontent.com/Zymo-Research/aladdin-miqScore/main/nextflow_schema.json",
"title": "Zymo-Research/aladdin-miqScore pipeline parameters",
"$id": "https://raw.githubusercontent.com/Zymo-Research/aladdin-miqScore16S/main/nextflow_schema.json",
"title": "Zymo-Research/aladdin-miqScore16S pipeline parameters",
"description": "Nextflow pipeline for calculating MIQ scores, part of the Aladdin Bioinformatics Platform pipeline catalog",
"single_sample": true,
"group_comparison": false,
Expand Down Expand Up @@ -131,4 +131,4 @@
"$ref": "#/definitions/generic_options"
}
]
}
}
4 changes: 2 additions & 2 deletions processes/miqscore16s.nf
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Expand Up @@ -5,7 +5,7 @@ params.reverse_primer_length = 24
params.amplicon_length = 510

process miqscore16s {
container 'zymoweb/miqscore16spublic:latest'
container 'zymoresearch/miqscore16s:latest'
publishDir "${params.publish_dir}", mode: 'copy'

input:
Expand All @@ -28,4 +28,4 @@ process miqscore16s {
python3 /opt/miqscore16s/analyzeStandardReads.py
mv /data/output/*.html ./
"""
}
}

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