From f2ba840f22f13384f6df0dcacefd19948c385555 Mon Sep 17 00:00:00 2001 From: nsharp2 Date: Thu, 9 Feb 2023 20:31:10 +0000 Subject: [PATCH 1/3] docker image updated --- processes/miqscore16s.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/processes/miqscore16s.nf b/processes/miqscore16s.nf index 028b0b2..2f45f0d 100644 --- a/processes/miqscore16s.nf +++ b/processes/miqscore16s.nf @@ -5,7 +5,7 @@ params.reverse_primer_length = 24 params.amplicon_length = 510 process miqscore16s { - container 'zymoweb/miqscore16spublic:latest' + container 'zymoresearch/miqscore16s' publishDir "${params.publish_dir}", mode: 'copy' input: @@ -28,4 +28,4 @@ process miqscore16s { python3 /opt/miqscore16s/analyzeStandardReads.py mv /data/output/*.html ./ """ -} \ No newline at end of file +} From 449eeb5c4b3b4b9b9e925a5ebed3859967e55faf Mon Sep 17 00:00:00 2001 From: nsharp2 Date: Thu, 9 Feb 2023 20:32:20 +0000 Subject: [PATCH 2/3] docker image updated with tag --- processes/miqscore16s.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/processes/miqscore16s.nf b/processes/miqscore16s.nf index 2f45f0d..a74c7cd 100644 --- a/processes/miqscore16s.nf +++ b/processes/miqscore16s.nf @@ -5,7 +5,7 @@ params.reverse_primer_length = 24 params.amplicon_length = 510 process miqscore16s { - container 'zymoresearch/miqscore16s' + container 'zymoresearch/miqscore16s:latest' publishDir "${params.publish_dir}", mode: 'copy' input: From 040474110ce73e7071c680318946bf7fec382aa1 Mon Sep 17 00:00:00 2001 From: nsharp2 Date: Thu, 9 Feb 2023 21:15:23 +0000 Subject: [PATCH 3/3] aladdin-miqScore renamed to aladdin-miqScore16S --- README.md | 4 ++-- main.nf | 10 +++++----- nextflow.config | 6 +++--- nextflow_schema.json | 6 +++--- 4 files changed, 13 insertions(+), 13 deletions(-) diff --git a/README.md b/README.md index 39a7530..515b8d3 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,2 @@ -# 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 diff --git a/main.nf b/main.nf index 72d56a4..033d231 100644 --- a/main.nf +++ b/main.nf @@ -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. */ @@ -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 @@ -85,8 +85,8 @@ workflow.onComplete { log.info "Number of successfully ran process(es) : ${workflow.stats.succeedCount}" } if(workflow.success){ - log.info "[miqScore] Pipeline completed successfully" + log.info "[miqScore16S] Pipeline completed successfully" } else { - log.info "[miqScore] Pipeline completed with errors" + log.info "[miqScore16S] Pipeline completed with errors" } -} \ No newline at end of file +} diff --git a/nextflow.config b/nextflow.config index 049b613..b9b9876 100644 --- a/nextflow.config +++ b/nextflow.config @@ -1,6 +1,6 @@ /* * ------------------------------------------------- - * Aladdin miqScore Nextflow config file + * Aladdin miqScore16S Nextflow config file * ------------------------------------------------- */ @@ -62,9 +62,9 @@ dag { } manifest { - name = 'Zymo-Research/aladdin-miqScore' + name = 'Zymo-Research/aladdin-miqScore16S' author = 'Zhenfeng Liu' - homePage = 'https://github.com/Zymo-Research/aladdin-miqScore' + homePage = 'https://github.com/Zymo-Research/aladdin-miqScore16S' description = 'Nextflow pipeline to run MIQ score calculator.' mainScript = 'main.nf' nextflowVersion = '>=20.07.1' diff --git a/nextflow_schema.json b/nextflow_schema.json index 43a9a7e..bf35978 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1,7 +1,7 @@ { "$schema": "http://json-schema.org/draft-07/schema", - "$id": "https://raw.githubusercontent.com/Zymo-Research/aladdin-miqScore/main/nextflow_schema.json", - "title": "Zymo-Research/aladdin-miqScore pipeline parameters", + "$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, @@ -131,4 +131,4 @@ "$ref": "#/definitions/generic_options" } ] -} \ No newline at end of file +}