Dsl2 new test configs

conf/test.config

@@ -18,31 +18,49 @@ process {
     ]
 }
 
+// TO DO: Change name to test.config once migration is complete.
 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'
 
     // 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  = params.pipelines_testdata_base_path + 'eager/testdata/Mammoth/samplesheet_v3.tsv'
+    input                           = params.pipelines_testdata_base_path + 'eager/testdata/Mammoth/samplesheet_v3.tsv'
 
     // Genome references
-    fasta = params.pipelines_testdata_base_path + 'eager/reference/Mammoth/Mammoth_MT_Krause.fasta'
+    fasta                           = params.pipelines_testdata_base_path + 'eager/reference/Mammoth/Mammoth_MT_Krause.fasta'
+
+    // Preprocessing
+    preprocessing_tool              = 'adapterremoval'
 
     // Sharding FASTQ
-    run_fastq_sharding                    = true
-    fastq_shard_size                      = 5000
+    run_fastq_sharding              = true
+    fastq_shard_size                = 5000
+
+    // Mapping
+    mapping_tool                    = 'bwaaln'
+    skip_qualimap                   = false
 
     // BAM filtering
-    run_bamfiltering                      = true
-    bamfiltering_minreadlength            = 30
-    bamfiltering_mappingquality           = 37
+    run_bamfiltering                = true
+    bamfiltering_minreadlength      = 30
+    bamfiltering_mappingquality     = 37
+    deduplication_tool              = 'markduplicates'
+
+    // PreSeq
+    mapstats_preseq_mode            = 'c_curve'
+
+    // Damage calculation
+    damagecalculation_tool          = 'damageprofiler'
+    skip_qualimap                   = false
 
-    // Map Stats
-    run_bedtools_coverage                 = true
-    mapstats_bedtools_featurefile         = params.pipelines_testdata_base_path + 'eager/reference/Mammoth/Mammoth_MT_Krause.gff3'
+    // Genotyping
+    run_genotyping                  = true
+    genotyping_source               = 'raw'
+    genotyping_tool                 = 'ug'
 
     // Metagenomic screening
-    run_metagenomics                      = false
+    run_metagenomics                = true
+    metagenomics_profiling_tool     = 'metaphlan'
+    metagenomics_profiling_database = params.pipelines_testdata_base_path + 'eager/databases/metaphlan/metaphlan4_database.tar.gz'
+    metagenomics_run_postprocessing = true
 }

conf/test_humanpopgen.config

@@ -0,0 +1,64 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    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/eager -profile test_humanpopgen,<docker/singularity> --outdir <OUTDIR>
+
+----------------------------------------------------------------------------------------
+*/
+
+process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '1.h'
+    ]
+
+    // To avoid pipeline failure due to not having X reads and to not have overcrowded datasets in the test
+    withName: ANGSD_CONTAMINATION {
+        errorStrategy  = { task.exitStatus in [134] ? 'ignore' : 'finish' }
+    }
+}
+
+params {
+    config_profile_name                = 'Test human popgen profile'
+    config_profile_description         = 'Minimal test dataset to check pipeline function'
+
+    // Input data
+    input                              = params.pipelines_testdata_base_path + 'eager/testdata/Human/human_design_bam_eager3.tsv'
+
+    // Genome references
+    fasta                              = params.pipelines_testdata_base_path + 'eager/reference/Human/hs37d5_chr21-MT.fa.gz'
+
+    // Mapping
+    mapping_tool                       = 'bowtie2'
+    convert_inputbam                    = true
+
+    // BAM filtering
+    run_bamfiltering                   = true
+    bamfiltering_minreadlength         = 30
+    bamfiltering_mappingquality        = 37
+
+    // Damage
+    damagecalculation_tool             = 'mapdamage'
+    run_trim_bam                       = true
+
+    // Contamination
+    run_mtnucratio                     = true
+    run_contamination_estimation_angsd = true
+
+    // Genotyping
+    genotyping_tool                    = 'pileupcaller'
+    run_genotyping                     = true
+    genotyping_source                  = 'trimmed'
+    genotyping_pileupcaller_bedfile    = params.pipelines_testdata_base_path + 'eager/reference/Human/1240K.pos.list_hs37d5.0based.bed.gz'
+    genotyping_pileupcaller_snpfile    = params.pipelines_testdata_base_path + 'eager/reference/Human/1240K_covered_in_JK2067_downsampled_s0.1.numeric_chromosomes.snp'
+
+    //Sex Determination
+    run_sexdeterrmine                  = true
+    sexdeterrmine_bedfile              = params.pipelines_testdata_base_path + 'eager/reference/Human/1240K.pos.list_hs37d5.0based.bed.gz'
+
+}

conf/test_microbial.config

@@ -0,0 +1,65 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    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/eager -profile test_microbial,<docker/singularity> --outdir <OUTDIR>
+
+----------------------------------------------------------------------------------------
+*/
+
+process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '1.h'
+    ]
+}
+
+params {
+    config_profile_name             = 'Test microbial profile'
+    config_profile_description      = 'Minimal test dataset to check pipeline function'
+
+    // Input data
+    input                           = params.pipelines_testdata_base_path + 'eager/testdata/Mammoth/samplesheet_PE_only_v3.tsv'
+
+    // Genome references
+    fasta_sheet                     = params.pipelines_testdata_base_path + 'eager/reference/reference_sheet_multiref.csv'
+
+    // Host Removal
+    run_host_removal                   = true
+
+    // Preprocessing
+    sequencing_qc_tool              = 'falco'
+    preprocessing_excludeunmerged   = true
+
+    // Mapping
+    mapping_tool                    = 'circularmapper'
+
+    // BAM filtering
+    deduplication_tool              = "dedup"
+    run_bamfiltering                = true
+    bamfiltering_minreadlength      = 30
+    bamfiltering_mappingquality     = 37
+
+    // Metagenomics
+    run_metagenomics                = true
+    metagenomics_profiling_tool     = 'krakenuniq'
+    metagenomics_profiling_database = params.pipelines_testdata_base_path + 'eager/databases/krakenuniq/testdb-krakenuniq.tar.gz'
+    run_host_removal                = true
+
+    // Manipulate Damage
+    run_mapdamage_rescaling         = true
+
+    // Bedtools coverage
+    run_bedtools_coverage           = true
+
+    // Genotyping
+    run_genotyping                  = true
+    genotyping_source               = 'rescaled'
+    genotyping_tool                 = 'freebayes'
+
+
+}