Fix files in conf directory

fifthguy · May 11, 2021 · 90b98e3 · 90b98e3
1 parent 6a8da1e
commit 90b98e3
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Showing 8 changed files with 97 additions and 102 deletions.
diff --git a/.editorconfig b/.editorconfig
@@ -8,9 +8,6 @@ trim_trailing_whitespace = true
 indent_size = 4
 indent_style = space
 
-[*.{yml,yaml}]
-indent_size = 2
-
 # These files are edited upstream in nf-core/modules
 [/modules/nf-core/**]
 charset = unset

diff --git a/conf/test.config b/conf/test.config
@@ -8,26 +8,26 @@
  */
 
 params {
-  config_profile_name        = 'Test profile'
-  config_profile_description = 'Minimal test dataset to check pipeline function'
+    config_profile_name        = 'Test profile'
+    config_profile_description = 'Minimal test dataset to check pipeline function'
 
-  // Limit resources so that this can run on GitHub Actions
-  max_cpus   = 2
-  max_memory = 6.GB
-  max_time   = 6.h
+    // Limit resources so that this can run on GitHub Actions
+    max_cpus   = 2
+    max_memory = 6.GB
+    max_time   = 6.h
 
-  // Input data to test amplicon analysis
-  input              = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'
-  platform           = 'illumina'
-  protocol           = 'amplicon'
-  primer_set         = 'artic'
-  primer_set_version = 1
+    // Input data to test amplicon analysis
+    input              = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'
+    platform           = 'illumina'
+    protocol           = 'amplicon'
+    primer_set         = 'artic'
+    primer_set_version = 1
 
-  // Genome references
-  genome     = 'MN908947.3'
-  kraken2_db = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/kraken2/kraken2_hs22.tar.gz'
+    // Genome references
+    genome     = 'MN908947.3'
+    kraken2_db = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/kraken2/kraken2_hs22.tar.gz'
 
-  // Other pipeline options
-  callers    = 'ivar,bcftools'
-  assemblers = 'spades,unicycler,minia'
+    // Other pipeline options
+    callers    = 'ivar,bcftools'
+    assemblers = 'spades,unicycler,minia'
 }
diff --git a/conf/test_full.config b/conf/test_full.config
@@ -8,20 +8,20 @@
  */
 
 params {
-  config_profile_name        = 'Full test profile'
-  config_profile_description = 'Full test dataset to check pipeline function'
+    config_profile_name        = 'Full test profile'
+    config_profile_description = 'Full test dataset to check pipeline function'
 
-  // Input data for full test of amplicon analysis
-  input              = 's3://nf-core-awsmegatests/viralrecon/input_data/210212_K00102_0557_AHKN3LBBXY/samplesheet.csv'
-  platform           = 'illumina'
-  protocol           = 'amplicon'
-  primer_set         = 'artic'
-  primer_set_version = 3
+    // Input data for full test of amplicon analysis
+    input              = 's3://nf-core-awsmegatests/viralrecon/input_data/210212_K00102_0557_AHKN3LBBXY/samplesheet.csv'
+    platform           = 'illumina'
+    protocol           = 'amplicon'
+    primer_set         = 'artic'
+    primer_set_version = 3
 
-  // Genome references
-  genome = 'MN908947.3'
+    // Genome references
+    genome = 'MN908947.3'
 
-  // Other pipeline options
-  callers    = 'ivar,bcftools'
-  assemblers = 'spades,unicycler,minia'
+    // Other pipeline options
+    callers    = 'ivar,bcftools'
+    assemblers = 'spades,unicycler,minia'
 }
diff --git a/conf/test_full_nanopore.config b/conf/test_full_nanopore.config
@@ -8,21 +8,20 @@
  */
 
 params {
-  config_profile_name        = 'Full test profile for nanopore data'
-  config_profile_description = 'Full test dataset to check pipeline function'
+    config_profile_name        = 'Full test profile for nanopore data'
+    config_profile_description = 'Full test dataset to check pipeline function'
 
-  // Input data for full test of amplicon analysis
-  platform           = 'nanopore'
-  input              = 's3://nf-core-awsmegatests/viralrecon/input_data/20210205_1526_X4_FAP51364_21fa8135/samplesheet.csv'
-  fastq_dir          = 's3://nf-core-awsmegatests/viralrecon/input_data/20210205_1526_X4_FAP51364_21fa8135/fastq_pass/'
-  fast5_dir          = 's3://nf-core-awsmegatests/viralrecon/input_data/20210205_1526_X4_FAP51364_21fa8135/fast5_pass/'
-  sequencing_summary = 's3://nf-core-awsmegatests/viralrecon/input_data/20210205_1526_X4_FAP51364_21fa8135/sequencing_summary.txt'
-
-  // Genome references
-  genome             = 'MN908947.3'
-  primer_set_version = 3
-
-  // Other parameters
-  artic_minion_medaka_model = 's3://nf-core-awsmegatests/viralrecon/input_data/20210205_1526_X4_FAP51364_21fa8135/r941_min_high_g360_model.hdf5'
+    // Input data for full test of amplicon analysis
+    platform           = 'nanopore'
+    input              = 's3://nf-core-awsmegatests/viralrecon/input_data/20210205_1526_X4_FAP51364_21fa8135/samplesheet.csv'
+    fastq_dir          = 's3://nf-core-awsmegatests/viralrecon/input_data/20210205_1526_X4_FAP51364_21fa8135/fastq_pass/'
+    fast5_dir          = 's3://nf-core-awsmegatests/viralrecon/input_data/20210205_1526_X4_FAP51364_21fa8135/fast5_pass/'
+    sequencing_summary = 's3://nf-core-awsmegatests/viralrecon/input_data/20210205_1526_X4_FAP51364_21fa8135/sequencing_summary.txt'
+
+    // Genome references
+    genome             = 'MN908947.3'
+    primer_set_version = 3
 
+    // Other parameters
+    artic_minion_medaka_model = 's3://nf-core-awsmegatests/viralrecon/input_data/20210205_1526_X4_FAP51364_21fa8135/r941_min_high_g360_model.hdf5'
 }
diff --git a/conf/test_full_sispa.config b/conf/test_full_sispa.config
@@ -8,18 +8,18 @@
  */
 
 params {
-  config_profile_name        = 'Full test profile'
-  config_profile_description = 'Full test dataset to check pipeline function'
+    config_profile_name        = 'Full test profile'
+    config_profile_description = 'Full test dataset to check pipeline function'
 
-  // Input data for full test of SISPA/metagenomics analysis
-  input    = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_full_illumina_sispa.csv'
-  platform = 'illumina'
-  protocol = 'metagenomic'
+    // Input data for full test of SISPA/metagenomics analysis
+    input    = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_full_illumina_sispa.csv'
+    platform = 'illumina'
+    protocol = 'metagenomic'
 
-  // Genome references
-  genome = 'MN908947.3'
+    // Genome references
+    genome = 'MN908947.3'
 
-  // Other pipeline options
-  callers    = 'ivar,bcftools'
-  assemblers = 'spades,unicycler,minia'
+    // Other pipeline options
+    callers    = 'ivar,bcftools'
+    assemblers = 'spades,unicycler,minia'
 }
diff --git a/conf/test_nanopore.config b/conf/test_nanopore.config
@@ -8,26 +8,25 @@
  */
 
 params {
-  config_profile_name        = 'Test profile'
-  config_profile_description = 'Minimal test dataset to check pipeline function for Nanopore data'
+    config_profile_name        = 'Test profile'
+    config_profile_description = 'Minimal test dataset to check pipeline function for Nanopore data'
 
-  // Limit resources so that this can run on GitHub Actions
-  max_cpus   = 2
-  max_memory = 6.GB
-  max_time   = 6.h
+    // Limit resources so that this can run on GitHub Actions
+    max_cpus   = 2
+    max_memory = 6.GB
+    max_time   = 6.h
 
-  // Input data to test nanopore analysis
-  platform           = 'nanopore'
-  input              = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_nanopore.csv'
-  fastq_dir          = 's3://nf-core-awsmegatests/viralrecon/input_data/minion_test/fastq_pass/'
-  fast5_dir          = 's3://nf-core-awsmegatests/viralrecon/input_data/minion_test/fast5_pass/'
-  sequencing_summary = 's3://nf-core-awsmegatests/viralrecon/input_data/minion_test/sequencing_summary.txt'
-
-  // Genome references
-  genome             = 'MN908947.3'
-  primer_set_version = 3
+    // Input data to test nanopore analysis
+    platform           = 'nanopore'
+    input              = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_nanopore.csv'
+    fastq_dir          = 's3://nf-core-awsmegatests/viralrecon/input_data/minion_test/fastq_pass/'
+    fast5_dir          = 's3://nf-core-awsmegatests/viralrecon/input_data/minion_test/fast5_pass/'
+    sequencing_summary = 's3://nf-core-awsmegatests/viralrecon/input_data/minion_test/sequencing_summary.txt'
 
-  // Other parameters
-  artic_minion_medaka_model = 's3://nf-core-awsmegatests/viralrecon/input_data/minion_test/r941_min_high_g360_model.hdf5'
+    // Genome references
+    genome             = 'MN908947.3'
+    primer_set_version = 3
 
+    // Other parameters
+    artic_minion_medaka_model = 's3://nf-core-awsmegatests/viralrecon/input_data/minion_test/r941_min_high_g360_model.hdf5'
 }
diff --git a/conf/test_sispa.config b/conf/test_sispa.config
@@ -8,24 +8,24 @@
  */
 
 params {
-  config_profile_name        = 'Test profile'
-  config_profile_description = 'Minimal test dataset to check pipeline function'
+    config_profile_name        = 'Test profile'
+    config_profile_description = 'Minimal test dataset to check pipeline function'
 
-  // Limit resources so that this can run on GitHub Actions
-  max_cpus   = 2
-  max_memory = 6.GB
-  max_time   = 6.h
+    // Limit resources so that this can run on GitHub Actions
+    max_cpus   = 2
+    max_memory = 6.GB
+    max_time   = 6.h
 
-  // Input data to test SISPA/metagenomics analysis
-  input    = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_sispa.csv'
-  platform = 'illumina'
-  protocol = 'metagenomic'
+    // Input data to test SISPA/metagenomics analysis
+    input    = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_sispa.csv'
+    platform = 'illumina'
+    protocol = 'metagenomic'
 
-  // Genome references
-  genome     = 'MN908947.3'
-  kraken2_db = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/kraken2/kraken2_hs22.tar.gz'
+    // Genome references
+    genome     = 'MN908947.3'
+    kraken2_db = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/kraken2/kraken2_hs22.tar.gz'
 
-  // Other pipeline options
-  callers    = 'ivar,bcftools'
-  assemblers = 'spades,unicycler,minia'
+    // Other pipeline options
+    callers    = 'ivar,bcftools'
+    assemblers = 'spades,unicycler,minia'
 }
diff --git a/conf/test_sra.config b/conf/test_sra.config
@@ -8,14 +8,14 @@
  */
 
 params {
-  config_profile_name        = 'Test profile'
-  config_profile_description = 'Minimal test dataset to check pipeline function'
+    config_profile_name        = 'Test profile'
+    config_profile_description = 'Minimal test dataset to check pipeline function'
 
-  // Limit resources so that this can run on GitHub Actions
-  max_cpus   = 2
-  max_memory = 6.GB
-  max_time   = 6.h
+    // Limit resources so that this can run on GitHub Actions
+    max_cpus   = 2
+    max_memory = 6.GB
+    max_time   = 6.h
 
-  // Input data to test SRA download functionality using SISPA/metagenomics data
-  public_data_ids = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_sra.csv'
+    // Input data to test SRA download functionality using SISPA/metagenomics data
+    public_data_ids = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_sra.csv'
 }