From 3ed67342c70a0c1579eabc52ba1d1097dab467f0 Mon Sep 17 00:00:00 2001
From: Margherita Mutarelli <86382379+daisymut@users.noreply.github.com>
Date: Mon, 18 Nov 2024 15:14:07 +0100
Subject: [PATCH] small fixes
---
.nf-core.yml | 2 +-
assets/email_template.html | 2 +-
conf/test_comparison.config | 31 +++++++++++++++++++++++++++++++
nextflow_schema.json | 2 +-
4 files changed, 34 insertions(+), 3 deletions(-)
create mode 100644 conf/test_comparison.config
diff --git a/.nf-core.yml b/.nf-core.yml
index fc9908a..ce358ac 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -7,7 +7,7 @@ org_path: null
repository_type: pipeline
template:
author: Margherita Mutarelli, Lucio Di Filippo
- description: analysis pipeline for SAMMY-seq
+ description: Analysis pipeline for SAMMY-seq
force: false
is_nfcore: true
name: sammyseq
diff --git a/assets/email_template.html b/assets/email_template.html
index b98c389..07d48ea 100644
--- a/assets/email_template.html
+++ b/assets/email_template.html
@@ -4,7 +4,7 @@
-
+
nf-core/sammyseq Pipeline Report
diff --git a/conf/test_comparison.config b/conf/test_comparison.config
new file mode 100644
index 0000000..2d4315c
--- /dev/null
+++ b/conf/test_comparison.config
@@ -0,0 +1,31 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ Nextflow config file for running minimal tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ Defines input files and everything required to run a fast and simple pipeline test.
+
+ Use as follows:
+ nextflow run nf-core/sammyseq -profile test, --outdir
+
+----------------------------------------------------------------------------------------
+*/
+
+process {
+ resourceLimits = [
+ cpus: 4,
+ memory: '15.GB',
+ time: '1.h'
+ ]
+}
+
+params {
+ config_profile_name = 'Test profile'
+ config_profile_description = 'Minimal test dataset to check pipeline function'
+
+ // Input data
+ input = 'https://genome.isasi.cnr.it/biocomp/test-datasets/sammyseq/testdata/chr22/samplesheet_test_github_chr22_tinier.csv'
+ comparisonFile = 'https://genome.isasi.cnr.it/biocomp/test-datasets/sammyseq/testdata/chr22/samplesheet_test_github_chr22_tinier.csv'
+
+ // Genome references
+ fasta = 'https://genome.isasi.cnr.it/biocomp/test-datasets/sammyseq/testdata/chr22/chr22.fa'
+}
diff --git a/nextflow_schema.json b/nextflow_schema.json
index d09cfd8..5710e9e 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -2,7 +2,7 @@
"$schema": "https://json-schema.org/draft/2020-12/schema",
"$id": "https://raw.githubusercontent.com/nf-core/sammyseq/master/nextflow_schema.json",
"title": "nf-core/sammyseq pipeline parameters",
- "description": "analysis pipeline for SAMMY-seq",
+ "description": "Analysis pipeline for SAMMY-seq",
"type": "object",
"$defs": {
"input_output_options": {