Merge pull request #795 from nf-core/test_tsv-to-test

Test tsv to test

Author: jfy133

.github/workflows/ci.yml

@@ -62,91 +62,91 @@ jobs:
           if [[ $NXF_VER = '' ]]; then sleep 1200; fi
       - name: BASIC Run the basic pipeline with directly supplied single-end FASTQ
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --input 'data/testdata/Mammoth/fastq/*_R1_*.fq.gz' --single_end
+          nextflow run ${GITHUB_WORKSPACE} -profile test_direct,docker --input 'data/testdata/Mammoth/fastq/*_R1_*.fq.gz' --single_end
       - name: BASIC Run the basic pipeline with directly supplied paired-end FASTQ
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --input 'data/testdata/Mammoth/fastq/*_{R1,R2}_*tengrand.fq.gz'
+          nextflow run ${GITHUB_WORKSPACE} -profile test_direct,docker --input 'data/testdata/Mammoth/fastq/*_{R1,R2}_*tengrand.fq.gz'
       - name: BASIC Run the basic pipeline with supplied --input BAM
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --input 'data/testdata/Mammoth/bam/*_R1_*.bam' --bam --single_end
+          nextflow run ${GITHUB_WORKSPACE} -profile test_direct,docker --input 'data/testdata/Mammoth/bam/*_R1_*.bam' --bam --single_end
       - name: BASIC Run the basic pipeline with the test profile with, PE/SE, bwa aln
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --save_reference
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --save_reference
       - name: REFERENCE Basic workflow, with supplied indices
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --bwa_index 'results/reference_genome/bwa_index/BWAIndex/' --fasta_index 'https://github.com/nf-core/test-datasets/blob/eager/reference/Mammoth/Mammoth_MT_Krause.fasta.fai' 
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --bwa_index 'results/reference_genome/bwa_index/BWAIndex/' --fasta_index 'https://github.com/nf-core/test-datasets/blob/eager/reference/Mammoth/Mammoth_MT_Krause.fasta.fai' 
       - name: REFERENCE Run the basic pipeline with FastA reference with `fna` extension
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_fna,docker
       - name: REFERENCE Test with zipped reference input
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --fasta 'https://github.com/nf-core/test-datasets/raw/eager/reference/Mammoth/Mammoth_MT_Krause.fasta.gz'
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --fasta 'https://github.com/nf-core/test-datasets/raw/eager/reference/Mammoth/Mammoth_MT_Krause.fasta.gz'
       - name: FASTP Test fastp complexity filtering
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --complexity_filter_poly_g
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --complexity_filter_poly_g
       - name: ADAPTERREMOVAL Test skip paired end collapsing
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --skip_collapse
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --skip_collapse
       - name: ADAPTERREMOVAL Test paired end collapsing but no trimming
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_pretrim,docker --skip_trim
       - name: ADAPTERREMOVAL Run the basic pipeline with paired end data without adapterRemoval
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --skip_adapterremoval
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --skip_adapterremoval
       - name: ADAPTERREMOVAL Run the basic pipeline with preserve5p end option
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --preserve5p
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --preserve5p
       - name: ADAPTERREMOVAL Run the basic pipeline with merged only option
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --mergedonly
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --mergedonly
       - name: ADAPTERREMOVAL Run the basic pipeline with preserve5p end and merged reads only options
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --preserve5p --mergedonly
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --preserve5p --mergedonly
       - name: ADAPTER LIST Run the basic pipeline using an adapter list
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --clip_adapters_list 'https://github.com/nf-core/test-datasets/raw/eager/databases/adapters/adapter-list.txt'
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --clip_adapters_list 'https://github.com/nf-core/test-datasets/raw/eager/databases/adapters/adapter-list.txt'
       - name: ADAPTER LIST Run the basic pipeline using an adapter list, skipping adapter removal
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --clip_adapters_list 'https://github.com/nf-core/test-datasets/raw/eager/databases/adapters/adapter-list.txt' --skip_adapterremoval 
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --clip_adapters_list 'https://github.com/nf-core/test-datasets/raw/eager/databases/adapters/adapter-list.txt' --skip_adapterremoval 
       - name: POST_AR_FASTQ_TRIMMING Run the basic pipeline post-adapterremoval FASTQ trimming
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_post_ar_trimming
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_post_ar_trimming
       - name: POST_AR_FASTQ_TRIMMING Run the basic pipeline post-adapterremoval FASTQ trimming, but skip adapterremoval
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_post_ar_trimming --skip_adapterremoval
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_post_ar_trimming --skip_adapterremoval
       - name: MAPPER_CIRCULARMAPPER Test running with CircularMapper
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --mapper 'circularmapper' --circulartarget 'NC_007596.2'
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --mapper 'circularmapper' --circulartarget 'NC_007596.2'
       - name: MAPPER_BWAMEM Test running with BWA Mem
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --mapper 'bwamem'
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --mapper 'bwamem'
       - name: MAPPER_BT2 Test running with BowTie2
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --mapper 'bowtie2' --bt2_alignmode 'local' --bt2_sensitivity 'sensitive' --bt2n 1 --bt2l 16 --bt2_trim5 1 --bt2_trim3 1
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --mapper 'bowtie2' --bt2_alignmode 'local' --bt2_sensitivity 'sensitive' --bt2n 1 --bt2l 16 --bt2_trim5 1 --bt2_trim3 1
       - name: HOST_REMOVAL_FASTQ Run the basic pipeline with output unmapped reads as fastq
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_complex,docker --hostremoval_input_fastq
       - name: BAM_FILTERING Run basic mapping pipeline with mapping quality filtering, and unmapped export
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_bam_filtering --bam_mapping_quality_threshold 37  --bam_unmapped_type 'fastq'
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_bam_filtering --bam_mapping_quality_threshold 37  --bam_unmapped_type 'fastq'
       - name: BAM_FILTERING Run basic mapping pipeline with post-mapping length filtering
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --clip_readlength 0 --run_bam_filtering --bam_filter_minreadlength 50
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --clip_readlength 0 --run_bam_filtering --bam_filter_minreadlength 50
       - name: PRESEQ Run basic mapping pipeline with different preseq mode
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --preseq_mode 'lc_extrap' --preseq_maxextrap 10000 --preseq_bootstrap 10
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --preseq_mode 'lc_extrap' --preseq_maxextrap 10000 --preseq_bootstrap 10
       - name: DEDUPLICATION Test with dedup
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --dedupper 'dedup' --dedup_all_merged
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --dedupper 'dedup' --dedup_all_merged
       - name: BEDTOOLS Test bedtools feature annotation
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_bedtools_coverage --anno_file 'https://github.com/nf-core/test-datasets/raw/eager/reference/Mammoth/Mammoth_MT_Krause.gff3'
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_bedtools_coverage --anno_file 'https://github.com/nf-core/test-datasets/raw/eager/reference/Mammoth/Mammoth_MT_Krause.gff3'
       - name: GENOTYPING_HC Test running GATK HaplotypeCaller
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_fna,docker --run_genotyping --genotyping_tool 'hc' --gatk_hc_out_mode 'EMIT_ALL_ACTIVE_SITES' --gatk_hc_emitrefconf 'BP_RESOLUTION'
       - name: GENOTYPING_FB Test running FreeBayes
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_genotyping --genotyping_tool 'freebayes'
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_genotyping --genotyping_tool 'freebayes'
       - name: GENOTYPING_PC Test running pileupCaller
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_humanbam,docker --run_genotyping --genotyping_tool 'pileupcaller'
@@ -155,25 +155,25 @@ jobs:
           nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_humanbam,docker --run_genotyping --genotyping_tool 'angsd'
       - name: GENOTYPING_BCFTOOLS Test running FreeBayes with bcftools stats turned on
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_genotyping --genotyping_tool 'freebayes' --run_bcftools_stats
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_genotyping --genotyping_tool 'freebayes' --run_bcftools_stats
       - name: SKIPPING Test checking all skip steps work i.e. input bam, skipping straight to genotyping
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_bam,docker --skip_fastqc --skip_adapterremoval --skip_deduplication --skip_qualimap --skip_preseq --skip_damage_calculation --run_genotyping --genotyping_tool 'freebayes'
       - name: TRIMBAM Test bamutils works alone
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_trim_bam
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_trim_bam
       - name: PMDTOOLS Test PMDtools works alone
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_pmdtools
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_pmdtools
       - name: GENOTYPING_UG AND MULTIVCFANALYZER Test running GATK UnifiedGenotyper and MultiVCFAnalyzer, additional VCFS
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_genotyping --genotyping_tool 'ug' --gatk_ug_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer --additional_vcf_files 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/testdata/Mammoth/vcf/JK2772_CATCAGTGAGTAGA_L008_R1_001.fastq.gz.tengrand.fq.combined.fq.mapped_rmdup.bam.unifiedgenotyper.vcf.gz' --write_allele_frequencies
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_genotyping --genotyping_tool 'ug' --gatk_ug_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer --additional_vcf_files 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/testdata/Mammoth/vcf/JK2772_CATCAGTGAGTAGA_L008_R1_001.fastq.gz.tengrand.fq.combined.fq.mapped_rmdup.bam.unifiedgenotyper.vcf.gz' --write_allele_frequencies
       - name: COMPLEX LANE/LIBRARY MERGING Test running lane and library merging prior to GATK UnifiedGenotyper and running MultiVCFAnalyzer
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_complex,docker --run_genotyping --genotyping_tool 'ug' --gatk_ug_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer
       - name: GENOTYPING_UG ON TRIMMED BAM Test
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_genotyping --run_trim_bam --genotyping_source 'trimmed' --genotyping_tool 'ug' --gatk_ug_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP'
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_genotyping --run_trim_bam --genotyping_source 'trimmed' --genotyping_tool 'ug' --gatk_ug_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP'
       - name: BAM_INPUT Run the basic pipeline with the bam input profile, skip AdapterRemoval as no convertBam
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_bam,docker --skip_adapterremoval
@@ -187,17 +187,17 @@ jobs:
           for i in index0.idx ref.db ref.idx ref.inf table0.db table0.idx taxonomy.idx taxonomy.map taxonomy.tre; do wget https://github.com/nf-core/test-datasets/raw/eager/databases/malt/"$i" -P databases/malt/; done
       - name: METAGENOMIC Run the basic pipeline but with unmapped reads going into MALT
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_bam_filtering  --bam_unmapped_type 'fastq' --run_metagenomic_screening --metagenomic_tool 'malt' --database "/home/runner/work/eager/eager/databases/malt/" --malt_sam_output
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_bam_filtering  --bam_unmapped_type 'fastq' --run_metagenomic_screening --metagenomic_tool 'malt' --database "/home/runner/work/eager/eager/databases/malt/" --malt_sam_output
       - name: METAGENOMIC Run the basic pipeline but low-complexity filtered reads going into MALT
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_bam_filtering  --bam_unmapped_type 'fastq' --run_metagenomic_screening --metagenomic_tool 'malt' --database "/home/runner/work/eager/eager/databases/malt/" --metagenomic_complexity_filter
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_bam_filtering  --bam_unmapped_type 'fastq' --run_metagenomic_screening --metagenomic_tool 'malt' --database "/home/runner/work/eager/eager/databases/malt/" --metagenomic_complexity_filter
       - name: MALTEXTRACT Download resource files
         run: |
             mkdir -p databases/maltextract
             for i in ncbi.tre ncbi.map; do wget https://github.com/rhuebler/HOPS/raw/0.33/Resources/"$i" -P databases/maltextract/; done
       - name: MALTEXTRACT Basic with MALT plus MaltExtract
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_bam_filtering  --bam_unmapped_type 'fastq' --run_metagenomic_screening --metagenomic_tool 'malt' --database "/home/runner/work/eager/eager/databases/malt" --run_maltextract --maltextract_ncbifiles "/home/runner/work/eager/eager/databases/maltextract/" --maltextract_taxon_list 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/testdata/Mammoth/maltextract/MaltExtract_list.txt' 
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_bam_filtering  --bam_unmapped_type 'fastq' --run_metagenomic_screening --metagenomic_tool 'malt' --database "/home/runner/work/eager/eager/databases/malt" --run_maltextract --maltextract_ncbifiles "/home/runner/work/eager/eager/databases/maltextract/" --maltextract_taxon_list 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/testdata/Mammoth/maltextract/MaltExtract_list.txt' 
       - name: METAGENOMIC Run the basic pipeline but with unmapped reads going into Kraken
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_kraken,docker --run_bam_filtering  --bam_unmapped_type 'fastq'
@@ -212,4 +212,4 @@ jobs:
           nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_humanbam,docker --skip_fastqc --skip_adapterremoval --skip_deduplication --skip_qualimap --skip_preseq --skip_damage_calculation --run_mtnucratio
       - name: RESCALING Run basic pipeline with basic pipeline but with mapDamage rescaling of BAM files. Note this will be slow
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_mapdamage_rescaling --run_genotyping --genotyping_tool hc --genotyping_source 'rescaled'
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --run_mapdamage_rescaling --run_genotyping --genotyping_tool hc --genotyping_source 'rescaled'

CHANGELOG.md

@@ -25,6 +25,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - Fixed issue where MultiVCFAnalyzer would not pick up newly generated VCF files, when specifying additional VCF files.
 - [#790](https://github.com/nf-core/eager/issues/790) Fixed kraken2 report file-name collision when sample names have `.` in them
 - [#792](https://github.com/nf-core/eager/issues/792) Fixed java error messages for AdapterRemovalFixPrefix being hidden in output
+- [#794](https://github.com/nf-core/eager/issues/794) Aligned default test profile with nf-core standards (`test_tsv` is now `test`)
 
 ### `Dependencies`
 

README.md

@@ -35,7 +35,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
 3. Download the pipeline and test it on a minimal dataset with a single command:
 
     ```bash
-    nextflow run nf-core/eager -profile test_tsv,<docker/singularity/podman/shifter/charliecloud/conda/institute>
+    nextflow run nf-core/eager -profile test,<docker/singularity/podman/shifter/charliecloud/conda/institute>
     ```
 
     > Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile <institute>` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.

conf/test.config

@@ -4,12 +4,11 @@
  * -------------------------------------------------
  * Defines bundled input files and everything required
  * to run a fast and simple test. Use as follows:
- *   nextflow run nf-core/eager -profile test,<docker/singularity>
+ * nextflow run nf-core/eager -profile test, docker (or singularity, or conda)
  */
 
 includeConfig 'test_resources.config'
 
-
 params {
   config_profile_name = 'Test profile'
   config_profile_description = 'Minimal test dataset to check pipeline function'
@@ -19,9 +18,7 @@ params {
   max_time = 48.h
   genome = false
   //Input data
-  single_end = false
+  input = 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/testdata/Mammoth/mammoth_design_fastq.tsv'
   // Genome references
   fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/reference/Mammoth/Mammoth_MT_Krause.fasta'
-  // Ignore `--input` as otherwise the parameter validation will throw an error
-  schema_ignore_params = 'genomes,input_paths,input'
 }