From d46ddd972c2fc2c3ce0e7fe03b3ad42a4821332a Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Tue, 5 Apr 2022 11:04:30 +0200 Subject: [PATCH] Expand tests and fix schema after review --- .github/workflows/ci.yml | 8 ++++++++ conf/test.config | 13 +++++++------ nextflow.config | 2 +- nextflow_schema.json | 3 ++- 4 files changed, 18 insertions(+), 8 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index b8975b5..79148f0 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -29,8 +29,16 @@ jobs: - NXF_VER: "" NXF_EDGE: "1" parameters: + - "--longread_clip false" + - "--shortread_clip false" - "--shortread_clipmerge_tool fastp" + - "--shortread_clipmerge_tool fastp --shortread_clipmerge_mergepairs --shortread_clipmerge_excludeunmerged" + - "--shortread_clipmerge_tool fastp --shortread_clipmerge_mergepairs" - "--shortread_clipmerge_tool adapterremoval" + - "--shortread_clipmerge_tool adapterremoval --shortread_clipmerge_mergepairs --shortread_clipmerge_excludeunmerged" + - "--shortread_clipmerge_tool adapterremoval --shortread_clipmerge_mergepairs" + - "--shortread_complexityfilter_tool bbduk" + - "--shortread_complexityfilter_tool prinseq" steps: - name: Check out pipeline code diff --git a/conf/test.config b/conf/test.config index ff92fe7..bdad2c1 100644 --- a/conf/test.config +++ b/conf/test.config @@ -22,11 +22,12 @@ params { // Input data // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets // TODO nf-core: Give any required params for the test so that command line flags are not needed - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv' - databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv' - run_kraken2 = true - run_malt = true - run_metaphlan3 = true - shortread_clipmerge = true + input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv' + databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv' + run_kraken2 = true + run_malt = true + run_metaphlan3 = true + shortread_clipmerge = true + longread_clip = false shortread_complexityfilter = true } diff --git a/nextflow.config b/nextflow.config index cd81f08..e6d6307 100644 --- a/nextflow.config +++ b/nextflow.config @@ -51,7 +51,7 @@ params { max_cpus = 16 max_time = '240.h' - // Databaess + // Databases databases = null // FASTQ preprocessing diff --git a/nextflow_schema.json b/nextflow_schema.json index bec9ea4..6f6125e 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -328,7 +328,8 @@ }, "shortread_complexityfilter_prinseqplusplus_mode": { "type": "string", - "default": "entropy" + "default": "entropy", + "enum": ["entropy", "dust"] }, "shortread_complexityfilter_prinseqplusplus_dustscore": { "type": "number",