Merge pull request #13 from nf-core/dev

Syncing

.travis.yml

@@ -34,60 +34,60 @@ install:
   - sudo apt-get install npm && npm install -g markdownlint-cli
 
 env:
-  - NXF_VER='19.04.0' # Specify a minimum NF version that should be tested and work
-  - NXF_VER='' # Plus: get the latest NF version and check that it works
+  - NXF_VER='19.04.0' NXF_ANSI_LOG=0 RUN_NAME="eager-${TRAVIS_PULL_REQUEST_BRANCH}-${TRAVIS_JOB_NUMBER}" TOWER='' # Specify a minimum NF version that should be tested and work
+  - NXF_VER='' NXF_ANSI_LOG=0 RUN_NAME="eager-${TRAVIS_PULL_REQUEST_BRANCH}-${TRAVIS_JOB_NUMBER}" TOWER='-with-tower' TOWER_ACCESS_TOKEN="1c1f493bc2703472d6f1b9f6fb9e9d117abab7b1" NXF_ANSI_LOG=0 # Plus: get the latest NF version and check that it works
 
 script:
   # Lint the pipeline code
   - nf-core lint ${TRAVIS_BUILD_DIR}
   # REFERENCE: Run the basic pipeline with the test profile
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "eager-basic" -profile test,docker --pairedEnd --saveReference
+  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-basic" -profile test,docker --pairedEnd --saveReference $TOWER
   # REFERENCE: Run the basic pipeline with single end data (pretending its single end actually) and all prepared index files
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "eager-singleEnd" -profile test,docker --singleEnd 
+  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-singleEnd" -profile test,docker --singleEnd $TOWER
   # REFERENCE: Run the basic pipeline with FastA reference with `fna` extension
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "eager-fna_ref" -profile test_fna,docker --pairedEnd --saveReference
+  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-fna_ref" -profile test_fna,docker --pairedEnd --saveReference $TOWER
   # REFERENCE: Test using pre-computed indices from a separate run beforehand
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "eager-preindex_ref" -profile test_fna,docker --pairedEnd --bwa_index results/reference_genome/bwa_index/BWAIndex/Mammoth_MT_Krause.fna --fasta_index results/reference_genome/fasta_index/Mammoth_MT_Krause.fna.fai --seq_dict results/reference_genome/seq_dict/Mammoth_MT_Krause.dict 
+  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-preindex_ref" -profile test_fna,docker --pairedEnd --bwa_index results/reference_genome/bwa_index/BWAIndex/Mammoth_MT_Krause.fna --fasta_index results/reference_genome/fasta_index/Mammoth_MT_Krause.fna.fai --seq_dict results/reference_genome/seq_dict/Mammoth_MT_Krause.dict $TOWER
   # REFERENCE: Test with zipped reference input
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "eager-gz_ref" -profile test,docker --pairedEnd --fasta 'https://github.com/jfy133/test-datasets/raw/eager/reference/Mammoth/Mammoth_MT_Krause.fasta.gz'
-  # FASTP: Run the same pipeline testing optional step: fastp, complexity 
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "eager-fastp" -profile test,docker --pairedEnd --complexity_filter
+  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-gz_ref" -profile test,docker --pairedEnd --fasta 'https://github.com/jfy133/test-datasets/raw/eager/reference/Mammoth/Mammoth_MT_Krause.fasta.gz' $TOWER
+  # FASTP: Run the same pipeline testing optional steps of fastp, complexity 
+  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-fastp" -profile test,docker --pairedEnd --complexity_filter $TOWER
   # ADAPTERREMOVAL: Run the basic pipeline with paired end data without collapsing
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "eager-skip_collapse" -profile test,docker --pairedEnd --skip_collapse
+  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-skip_collapse" -profile test,docker --pairedEnd --skip_collapse $TOWER
   # ADAPTERREMOVAL: Run the basic pipeline with paired end data without trimming, but still merge
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "eager-pretrim" -profile test_pretrim,docker --pairedEnd --skip_trim 
+  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-pretrim" -profile test_pretrim,docker --pairedEnd --skip_trim $TOWER
   # ADAPTERREMOVAL: Run the basic pipeline with paired end data without adapterRemoval
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "eager-skip_adapterremoval" -profile test,docker --pairedEnd --skip_adapterremoval
+  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-skip_adapterremoval" -profile test,docker --pairedEnd --skip_adapterremoval $TOWER
   # ADAPTERREMOVAL: Run the basic pipeline with preserve5p end option
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "eager-preserve5p" -profile test,docker --pairedEnd --preserve5p
+  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-preserve5p" -profile test,docker --pairedEnd --preserve5p $TOWER
   # ADAPTERREMOVAL: Run the basic pipeline with merged only option
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "eager-mergedonly" -profile test,docker --pairedEnd --mergedonly
+  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-mergedonly" -profile test,docker --pairedEnd --mergedonly $TOWER
   # ADAPTERREMOVAL: Run the basic pipeline with preserve5p end and merged reads only options
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "eager-preserve5p_mergedonly" -profile test,docker --pairedEnd --preserve5p --mergedonly
+  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-preserve5p_mergedonly" -profile test,docker --pairedEnd --preserve5p --mergedonly $TOWER
   # MAPPER_CIRCULARMAPPER: Test running with CircularMapper
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "eager-circularmapper" -profile test,docker --pairedEnd --mapper 'circularmapper' --circulartarget 'NC_007596.2'
+  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-circularmapper" -profile test,docker --pairedEnd --mapper 'circularmapper' --circulartarget 'NC_007596.2' $TOWER
   # MAPPER_BWAMEM: Test running with BWA Mem
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "eager-bwa_mem" -profile test,docker --pairedEnd --mapper 'bwamem'
+  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-bwa_mem" -profile test,docker --pairedEnd --mapper 'bwamem' $TOWER
   # STRIP_FASTQ: Run the basic pipeline with output unmapped reads as fastq
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "eager-stripfastq" -profile test,docker --pairedEnd --strip_input_fastq
+  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-stripfastq" -profile test,docker --pairedEnd --strip_input_fastq $TOWER
   # BAM_FILTERING: Run basic mapping pipeline with mapping quality filtering, and unmapped export
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "eager-unmapped_export" -profile test,docker --pairedEnd --run_bam_filtering --bam_mapping_quality_threshold 37 --bam_discard_umapped --bam_unmapped_type 'fastq'
+  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-unmapped_export" -profile test,docker --pairedEnd --run_bam_filtering --bam_mapping_quality_threshold 37 --bam_discard_umapped --bam_unmapped_type 'fastq' $TOWER
   # GENOTYPING_HC: Test running GATK HaplotypeCaller
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "eager-haplotypercaller" -profile test_fna,docker --pairedEnd  --dedupper 'dedup' --run_genotyping --genotyping_tool 'hc' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_hc_emitrefconf 'BP_RESOLUTION'
+  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-haplotypercaller" -profile test_fna,docker --pairedEnd  --dedupper 'dedup' --run_genotyping --genotyping_tool 'hc' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_hc_emitrefconf 'BP_RESOLUTION' $TOWER
   # GENOTYPING_FB: Test running FreeBayes
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "eager-freebayes" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_genotyping --genotyping_tool 'freebayes'
+  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-freebayes" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_genotyping --genotyping_tool 'freebayes' $TOWER
   # SKIPPING: Test checking all skip steps work i.e. input bam, skipping straight to genotyping
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "eager-skipping_logic" -profile test_bam,docker --bam --singleEnd --skip_fastqc --skip_adapterremoval --skip_mapping --skip_deduplication --skip_qualimap --skip_preseq --skip_damage_calculation --run_genotyping --genotyping_tool 'freebayes'
+  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-skipping_logic" -profile test_bam,docker --bam --singleEnd --skip_fastqc --skip_adapterremoval --skip_mapping --skip_deduplication --skip_qualimap --skip_preseq --skip_damage_calculation --run_genotyping --genotyping_tool 'freebayes' $TOWER
   # TRIM_BAM/PMD/GENOTYPING_UG/MULTIVCFANALYZER: Test running PMDTools, TrimBam, GATK UnifiedGenotyper and MultiVCFAnalyzer
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "eager-pmd_trimbam_unifiedgenotyper_multivcfanalyzer" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_trim_bam --run_pmdtools --run_genotyping --genotyping_source 'trimmed' --genotyping_tool 'ug' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer
+  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-pmd_trimbam_unifiedgenotyper_multivcfanalyzer" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_trim_bam --run_pmdtools --run_genotyping --genotyping_source 'trimmed' --genotyping_tool 'ug' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer $TOWER
   # GENOTYPING_UG/PMD/MULTIVCFANALYZER: Test running GATK UnifiedGenotyper and MultiVCFAnalyzer, additional VCFS
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "eager-multivcfanalyzer_additionalvcfs" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_genotyping --genotyping_tool 'ug' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer --additional_vcf_files 'https://raw.githubusercontent.com/jfy133/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 ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-multivcfanalyzer_additionalvcfs" -profile test,docker --pairedEnd  --dedupper 'dedup' --run_genotyping --genotyping_tool 'ug' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer --additional_vcf_files 'https://raw.githubusercontent.com/jfy133/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 $TOWER
   # BAM_INPUT: Run the basic pipeline with the bam input profile, skip AdapterRemoval as no convertBam
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "eager-baminput_noConvertBam" -profile test_bam,docker --bam --skip_adapterremoval --run_convertbam
+  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-baminput_noConvertBam" -profile test_bam,docker --bam --skip_adapterremoval --run_convertbam $TOWER
   # BAM_INPUT: Run the basic pipeline with the bam input profile, convert to FASTQ for adapterremoval test and downstream
-  - nextflow run ${TRAVIS_BUILD_DIR} -name "eager-baminput_convertbam_basic" -profile test_bam,docker --bam --run_convertbam
+  - nextflow run ${TRAVIS_BUILD_DIR} -name "$RUN_NAME-baminput_convertbam_basic" -profile test_bam,docker --bam --run_convertbam $TOWER
   # [DISABLED UNTIL BED FILE AVAILABLE - 2h RUN TIME WITHOUT] - SEXDETERMINAION: Run the basic pipeline with the bam input profile, but don't convert BAM, skip everything but sex determination
-  #- nextflow run ${TRAVIS_BUILD_DIR} -profile test_humanbam,docker --bam --skip_fastqc --skip_adapterremoval --skip_mapping --skip_deduplication --skip_qualimap --singleEnd --run_sexdeterrmine
+  #- nextflow run ${TRAVIS_BUILD_DIR} -profile test_humanbam,docker --bam --skip_fastqc --skip_adapterremoval --skip_mapping --skip_deduplication --skip_qualimap --singleEnd --run_sexdeterrmine $TOWER
   # [DISABLED UNTIL SMALL HUMAN REFERENCE AVALIABLE - REQUIRES HUMAN FASTA] - NUCLEAR INPUT
-  #- nextflow run ${TRAVIS_BUILD_DIR} -profile test_humanbam,docker --bam --skip_fastqc --skip_adapterremoval --skip_mapping --skip_deduplication --skip_qualimap --singleEnd --run_nuclearcontamination
+  #- nextflow run ${TRAVIS_BUILD_DIR} -profile test_humanbam,docker --bam --skip_fastqc --skip_adapterremoval --skip_mapping --skip_deduplication --skip_qualimap --singleEnd --run_nuclearcontamination $TOWER
 

conf/test.config

@@ -23,8 +23,3 @@ params {
   // Genome references
   fasta = 'https://raw.githubusercontent.com/jfy133/test-datasets/eager/reference/Mammoth/Mammoth_MT_Krause.fasta'
 }
-
-tower {
-  accessToken = '1c1f493bc2703472d6f1b9f6fb9e9d117abab7b1'
-  enabled = true
-}

conf/test_bam.config

@@ -21,8 +21,3 @@ params {
   // Genome references
   fasta = 'https://raw.githubusercontent.com/jfy133/test-datasets/eager/reference/Mammoth/Mammoth_MT_Krause.fasta'
 }
-
-tower {
-  accessToken = '1c1f493bc2703472d6f1b9f6fb9e9d117abab7b1'
-  enabled = true
-}

conf/test_fna.config

@@ -23,8 +23,3 @@ params {
   // Genome references
   fasta = 'https://raw.githubusercontent.com/jfy133/test-datasets/eager/reference/Mammoth/Mammoth_MT_Krause.fna'
 }
-
-tower {
-  accessToken = '1c1f493bc2703472d6f1b9f6fb9e9d117abab7b1'
-  enabled = true
-}

conf/test_humanbam.config

@@ -21,8 +21,3 @@ params {
   // Genome references
   fasta = 'https://raw.githubusercontent.com/jfy133/test-datasets/eager/reference/Mammoth/Mammoth_MT_Krause.fasta'
 }
-
-tower {
-  accessToken = '1c1f493bc2703472d6f1b9f6fb9e9d117abab7b1'
-  enabled = true
-}

conf/test_pretrim.config

@@ -22,8 +22,3 @@ params {
   // Genome references
   fasta = 'https://raw.githubusercontent.com/jfy133/test-datasets/eager/reference/Mammoth/Mammoth_MT_Krause.fasta'
 }
-
-tower {
-  accessToken = '1c1f493bc2703472d6f1b9f6fb9e9d117abab7b1'
-  enabled = true
-}