From 5e18e36895ba7a63e864faad4105e14597ffcddb Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Fri, 9 Apr 2021 13:47:05 +0100 Subject: [PATCH] Update and check tests are running for all modules (#420) * Fixes for PR 371 * Fix tags * Add md5sum * Add md5sums for stringtie * Fix tests for modules where subtool = build * Fix pytest_software name conflicts * Change _ to / in test.yml tags * Nope...that didnt work * Fix sequenzautils/bam2seqz tests --- tests/config/pytest_software.yml | 10 +------- tests/config/test_data.config | 5 +++- .../sarscov2/illumina/bedgraph/test.bedgraph | 4 +++ .../gcwiggle => illumina/wig}/test.wig.gz | Bin tests/software/bowtie/align/main.nf | 6 ++--- tests/software/bowtie/align/test.yml | 24 +++++++++--------- tests/software/bowtie/build_test/main.nf | 2 +- tests/software/bowtie/build_test/test.yml | 12 ++++----- .../callmolecularconsensusreads/test.yml | 2 +- tests/software/fgbio/sortbam/test.yml | 2 +- .../gatk4/createsequencedictionary/test.yml | 2 +- tests/software/gatk4/haplotypecaller/test.yml | 2 +- tests/software/gatk4/markduplicates/test.yml | 2 +- tests/software/hisat2/align/test.yml | 8 +++--- tests/software/hisat2/build_test/test.yml | 2 +- .../hisat2/extractsplicesites/test.yml | 2 +- tests/software/minimap2/align/main.nf | 4 +-- tests/software/msisensor/msi/test.yml | 2 +- tests/software/msisensor/scan/test.yml | 2 +- .../picard/collectmultiplemetrics/test.yml | 2 +- tests/software/sequenzautils/bam2seqz/main.nf | 8 +++--- .../software/sequenzautils/bam2seqz/test.yml | 3 ++- .../software/sequenzautils/gcwiggle/test.yml | 2 +- tests/software/stringtie/main.nf | 8 +++--- tests/software/stringtie/test.yml | 4 +-- tests/software/subread/featurecounts/test.yml | 6 ++--- tests/software/ucsc/bed12tobigbed/main.nf | 4 +-- tests/software/ucsc/bedgraphtobigwig/main.nf | 4 +-- tests/software/ucsc/bedgraphtobigwig/test.yml | 2 +- 29 files changed, 68 insertions(+), 68 deletions(-) create mode 100644 tests/data/genomics/sarscov2/illumina/bedgraph/test.bedgraph rename tests/data/genomics/sarscov2/{genome/gcwiggle => illumina/wig}/test.wig.gz (100%) diff --git a/tests/config/pytest_software.yml b/tests/config/pytest_software.yml index 330f0430..ede4f5a9 100644 --- a/tests/config/pytest_software.yml +++ b/tests/config/pytest_software.yml @@ -450,14 +450,6 @@ seqkit/split2: - software/seqkit/split2/** - tests/software/seqkit/split2/** -sequenza/bam2seqz: - - software/sequenza/bam2seqz/** - - tests/software/sequenza/bam2seqz/** - -sequenza/wiggle: - - software/sequenza/wiggle/** - - tests/software/sequenza/wiggle/** - sequenzautils/bam2seqz: - software/sequenzautils/bam2seqz/** - tests/software/sequenzautils/bam2seqz/** @@ -538,7 +530,7 @@ vcftools: - software/vcftools/** - tests/software/vcftools/** -yara: +yara/mapper: - software/yara/mapper/** - tests/software/yara/mapper/** diff --git a/tests/config/test_data.config b/tests/config/test_data.config index 0c2eebad..1163d53f 100644 --- a/tests/config/test_data.config +++ b/tests/config/test_data.config @@ -28,7 +28,7 @@ params { all_sites_fas = "${test_data_dir}/genomics/sarscov2/genome/alignment/all_sites.fas" informative_sites_fas = "${test_data_dir}/genomics/sarscov2/genome/alignment/informative_sites.fas" - + contigs_fasta = "${test_data_dir}/genomics/sarscov2/genome/contigs.fasta" } 'illumina' { @@ -50,6 +50,9 @@ params { test_methylated_1_fastq_gz = "${test_data_dir}/genomics/sarscov2/illumina/fastq/test_methylated_1.fastq.gz" test_methylated_2_fastq_gz = "${test_data_dir}/genomics/sarscov2/illumina/fastq/test_methylated_2.fastq.gz" + test_bedgraph = "${test_data_dir}/genomics/sarscov2/illumina/bedgraph/test.bedgraph" + test_wig_gz = "${test_data_dir}/genomics/sarscov2/illumina/wig/test.wig.gz" + test_baserecalibrator_table = "${test_data_dir}/genomics/sarscov2/illumina/gatk/test.baserecalibrator.table" test_vcf = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.vcf" diff --git a/tests/data/genomics/sarscov2/illumina/bedgraph/test.bedgraph b/tests/data/genomics/sarscov2/illumina/bedgraph/test.bedgraph new file mode 100644 index 00000000..572e592c --- /dev/null +++ b/tests/data/genomics/sarscov2/illumina/bedgraph/test.bedgraph @@ -0,0 +1,4 @@ +MT192765.1 1242 1264 1 +MT192765.1 1573 1595 0.3 +MT192765.1 1623 1651 1 +MT192765.1 1942 1964 0.2 diff --git a/tests/data/genomics/sarscov2/genome/gcwiggle/test.wig.gz b/tests/data/genomics/sarscov2/illumina/wig/test.wig.gz similarity index 100% rename from tests/data/genomics/sarscov2/genome/gcwiggle/test.wig.gz rename to tests/data/genomics/sarscov2/illumina/wig/test.wig.gz diff --git a/tests/software/bowtie/align/main.nf b/tests/software/bowtie/align/main.nf index 3a299862..a34de8b5 100644 --- a/tests/software/bowtie/align/main.nf +++ b/tests/software/bowtie/align/main.nf @@ -17,10 +17,10 @@ workflow test_bowtie_align_single_end { workflow test_bowtie_align_paired_end { input = [ [ id:'test', single_end:false ], // meta map - [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true), - file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ] + [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] ] - fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) + fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) BOWTIE_BUILD ( fasta ) BOWTIE_ALIGN ( input, BOWTIE_BUILD.out.index ) diff --git a/tests/software/bowtie/align/test.yml b/tests/software/bowtie/align/test.yml index 18bd9151..f6868b0f 100644 --- a/tests/software/bowtie/align/test.yml +++ b/tests/software/bowtie/align/test.yml @@ -8,17 +8,17 @@ - path: ./output/bowtie/test.bam - path: ./output/bowtie/test.out md5sum: 4b9140ceadb8a18ae9330885370f8a0b - - path: ./output/index/bowtie/test_genome.3.ebwt + - path: ./output/index/bowtie/genome.3.ebwt md5sum: 4ed93abba181d8dfab2e303e33114777 - - path: ./output/index/bowtie/test_genome.2.ebwt + - path: ./output/index/bowtie/genome.2.ebwt md5sum: 02b44af9f94c62ecd3c583048e25d4cf - - path: ./output/index/bowtie/test_genome.rev.2.ebwt + - path: ./output/index/bowtie/genome.rev.2.ebwt md5sum: 9e6b0c4c1ddb99ae71ff8a4fe5ec6459 - - path: ./output/index/bowtie/test_genome.4.ebwt + - path: ./output/index/bowtie/genome.4.ebwt md5sum: c25be5f8b0378abf7a58c8a880b87626 - - path: ./output/index/bowtie/test_genome.rev.1.ebwt + - path: ./output/index/bowtie/genome.rev.1.ebwt md5sum: b37aaf11853e65a3b13561f27a912b06 - - path: ./output/index/bowtie/test_genome.1.ebwt + - path: ./output/index/bowtie/genome.1.ebwt md5sum: d9b76ecf9fd0413240173273b38d8199 - name: bowtie align paired-end @@ -30,15 +30,15 @@ files: - path: ./output/bowtie/test.bam - path: ./output/bowtie/test.out - - path: ./output/index/bowtie/test_genome.3.ebwt + - path: ./output/index/bowtie/genome.3.ebwt md5sum: 4ed93abba181d8dfab2e303e33114777 - - path: ./output/index/bowtie/test_genome.2.ebwt + - path: ./output/index/bowtie/genome.2.ebwt md5sum: 02b44af9f94c62ecd3c583048e25d4cf - - path: ./output/index/bowtie/test_genome.rev.2.ebwt + - path: ./output/index/bowtie/genome.rev.2.ebwt md5sum: 9e6b0c4c1ddb99ae71ff8a4fe5ec6459 - - path: ./output/index/bowtie/test_genome.4.ebwt + - path: ./output/index/bowtie/genome.4.ebwt md5sum: c25be5f8b0378abf7a58c8a880b87626 - - path: ./output/index/bowtie/test_genome.rev.1.ebwt + - path: ./output/index/bowtie/genome.rev.1.ebwt md5sum: b37aaf11853e65a3b13561f27a912b06 - - path: ./output/index/bowtie/test_genome.1.ebwt + - path: ./output/index/bowtie/genome.1.ebwt md5sum: d9b76ecf9fd0413240173273b38d8199 diff --git a/tests/software/bowtie/build_test/main.nf b/tests/software/bowtie/build_test/main.nf index 0aec86a1..beff9e1f 100644 --- a/tests/software/bowtie/build_test/main.nf +++ b/tests/software/bowtie/build_test/main.nf @@ -5,7 +5,7 @@ nextflow.enable.dsl = 2 include { BOWTIE_BUILD } from '../../../../software/bowtie/build/main.nf' addParams( options: [:] ) workflow test_bowtie_build { - fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) + fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) BOWTIE_BUILD ( fasta ) } diff --git a/tests/software/bowtie/build_test/test.yml b/tests/software/bowtie/build_test/test.yml index cc5b3256..2bd73b13 100644 --- a/tests/software/bowtie/build_test/test.yml +++ b/tests/software/bowtie/build_test/test.yml @@ -4,15 +4,15 @@ - bowtie - bowtie/build files: - - path: ./output/index/bowtie/test_genome.3.ebwt + - path: ./output/index/bowtie/genome.3.ebwt md5sum: 4ed93abba181d8dfab2e303e33114777 - - path: ./output/index/bowtie/test_genome.2.ebwt + - path: ./output/index/bowtie/genome.2.ebwt md5sum: 02b44af9f94c62ecd3c583048e25d4cf - - path: ./output/index/bowtie/test_genome.rev.2.ebwt + - path: ./output/index/bowtie/genome.rev.2.ebwt md5sum: 9e6b0c4c1ddb99ae71ff8a4fe5ec6459 - - path: ./output/index/bowtie/test_genome.4.ebwt + - path: ./output/index/bowtie/genome.4.ebwt md5sum: c25be5f8b0378abf7a58c8a880b87626 - - path: ./output/index/bowtie/test_genome.rev.1.ebwt + - path: ./output/index/bowtie/genome.rev.1.ebwt md5sum: b37aaf11853e65a3b13561f27a912b06 - - path: ./output/index/bowtie/test_genome.1.ebwt + - path: ./output/index/bowtie/genome.1.ebwt md5sum: d9b76ecf9fd0413240173273b38d8199 diff --git a/tests/software/fgbio/callmolecularconsensusreads/test.yml b/tests/software/fgbio/callmolecularconsensusreads/test.yml index ed2f80eb..325ab7fb 100644 --- a/tests/software/fgbio/callmolecularconsensusreads/test.yml +++ b/tests/software/fgbio/callmolecularconsensusreads/test.yml @@ -1,8 +1,8 @@ - name: fgbio callmolecularconsensusreads command: nextflow run tests/software/fgbio/callmolecularconsensusreads -entry test_fgbio_callmolecularconsensusreads -c tests/config/nextflow.config tags: - - fgbio_callmolecularconsensusreads - fgbio + - fgbio/callmolecularconsensusreads files: - path: output/fgbio/test_molreads.bam md5sum: 7010bcdc037c36af13dbc370c06c76d3 diff --git a/tests/software/fgbio/sortbam/test.yml b/tests/software/fgbio/sortbam/test.yml index 7e70189f..9407f180 100644 --- a/tests/software/fgbio/sortbam/test.yml +++ b/tests/software/fgbio/sortbam/test.yml @@ -1,8 +1,8 @@ - name: fgbio sortbam command: nextflow run tests/software/fgbio/sortbam -entry test_fgbio_sortbam -c tests/config/nextflow.config tags: - - fgbio_sortbam - fgbio + - fgbio/sortbam files: - path: output/fgbio/test.bam md5sum: 56987f74214cdc72ae840e0007ff4935 diff --git a/tests/software/gatk4/createsequencedictionary/test.yml b/tests/software/gatk4/createsequencedictionary/test.yml index 4b849d5a..99e73e8e 100644 --- a/tests/software/gatk4/createsequencedictionary/test.yml +++ b/tests/software/gatk4/createsequencedictionary/test.yml @@ -2,7 +2,7 @@ command: nextflow run tests/software/gatk4/createsequencedictionary -entry test_gatk4_createsequencedictionary -c tests/config/nextflow.config tags: - gatk4 - - gatk4_createsequencedictionary + - gatk4/createsequencedictionary files: - path: output/gatk4/genome.dict md5sum: 7362679f176e0f52add03c08f457f646 diff --git a/tests/software/gatk4/haplotypecaller/test.yml b/tests/software/gatk4/haplotypecaller/test.yml index 42fd9e18..3418e360 100644 --- a/tests/software/gatk4/haplotypecaller/test.yml +++ b/tests/software/gatk4/haplotypecaller/test.yml @@ -1,8 +1,8 @@ - name: gatk4 haplotypecaller test_gatk4_haplotypecaller command: nextflow run tests/software/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller -c tests/config/nextflow.config tags: - - gatk4_haplotypecaller - gatk4 + - gatk4/haplotypecaller files: - path: output/gatk4/test.vcf.gz should_exist: true diff --git a/tests/software/gatk4/markduplicates/test.yml b/tests/software/gatk4/markduplicates/test.yml index 669598c5..816ab5ec 100644 --- a/tests/software/gatk4/markduplicates/test.yml +++ b/tests/software/gatk4/markduplicates/test.yml @@ -2,7 +2,7 @@ command: nextflow run tests/software/gatk4/markduplicates -entry test_gatk4_markduplicates -c tests/config/nextflow.config tags: - gatk4 - - gatk4_markduplicates + - gatk4/markduplicates files: - path: output/gatk4/test.bam md5sum: b58d47345e3ce5825c0641c9d6e6cb7a diff --git a/tests/software/hisat2/align/test.yml b/tests/software/hisat2/align/test.yml index 5017c628..ce303b23 100644 --- a/tests/software/hisat2/align/test.yml +++ b/tests/software/hisat2/align/test.yml @@ -1,9 +1,9 @@ - name: hisat2 align test_hisat2_align_single_end command: nextflow run tests/software/hisat2/align -entry test_hisat2_align_single_end -c tests/config/nextflow.config tags: - - hisat2_align_single_end - - hisat2_align - hisat2 + - hisat2/align + - hisat2_align_single_end files: - path: output/hisat2/test.hisat2.summary.log md5sum: 7b8a9e61b7646da1089b041333c41a87 @@ -30,9 +30,9 @@ - name: hisat2 align test_hisat2_align_paired_end command: nextflow run tests/software/hisat2/align -entry test_hisat2_align_paired_end -c tests/config/nextflow.config tags: - - hisat2_align_paired_end - - hisat2_align - hisat2 + - hisat2/align + - hisat2_align_paired_end files: - path: output/hisat2/test.hisat2.summary.log md5sum: 9839b31db795958cc4b70711a3414e9c diff --git a/tests/software/hisat2/build_test/test.yml b/tests/software/hisat2/build_test/test.yml index 8b805dd3..28223354 100644 --- a/tests/software/hisat2/build_test/test.yml +++ b/tests/software/hisat2/build_test/test.yml @@ -2,7 +2,7 @@ command: nextflow run tests/software/hisat2/build_test -entry test_hisat2_build -c tests/config/nextflow.config tags: - hisat2 - - hisat2_build + - hisat2/build files: - path: output/hisat2/genome.splice_sites.txt md5sum: d41d8cd98f00b204e9800998ecf8427e diff --git a/tests/software/hisat2/extractsplicesites/test.yml b/tests/software/hisat2/extractsplicesites/test.yml index 71375a96..8cb8157e 100644 --- a/tests/software/hisat2/extractsplicesites/test.yml +++ b/tests/software/hisat2/extractsplicesites/test.yml @@ -2,7 +2,7 @@ command: nextflow run tests/software/hisat2/extractsplicesites -entry test_hisat2_extractsplicesites -c tests/config/nextflow.config tags: - hisat2 - - hisat2_extractsplicesites + - hisat2/extractsplicesites files: - path: output/hisat2/genome.splice_sites.txt md5sum: d41d8cd98f00b204e9800998ecf8427e diff --git a/tests/software/minimap2/align/main.nf b/tests/software/minimap2/align/main.nf index 522431e1..349332ae 100644 --- a/tests/software/minimap2/align/main.nf +++ b/tests/software/minimap2/align/main.nf @@ -15,8 +15,8 @@ workflow test_minimap2_align_single_end { workflow test_minimap2_align_paired_end { input = [ [ id:'test', single_end:false ], // meta map - [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true), - file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ] + [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] ] fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true) diff --git a/tests/software/msisensor/msi/test.yml b/tests/software/msisensor/msi/test.yml index 152bf60a..e3cbefb9 100644 --- a/tests/software/msisensor/msi/test.yml +++ b/tests/software/msisensor/msi/test.yml @@ -2,7 +2,7 @@ command: nextflow run ./tests/software/msisensor/msi -entry test_msisensor_msi -c tests/config/nextflow.config tags: - msisensor - - msisensor_msi + - msisensor/msi files: - path: output/msisensor/test md5sum: a3290f7539dbbf83777e8590156c0e28 diff --git a/tests/software/msisensor/scan/test.yml b/tests/software/msisensor/scan/test.yml index 7d8f6e5c..aa567e37 100644 --- a/tests/software/msisensor/scan/test.yml +++ b/tests/software/msisensor/scan/test.yml @@ -2,7 +2,7 @@ command: nextflow run ./tests/software/msisensor/scan -entry test_msisensor_scan -c tests/config/nextflow.config tags: - msisensor - - msisensor_scan + - msisensor/scan files: - path: output/msisensor/test.msisensor_scan.tab md5sum: b7ae85acdcfc1a51e867ab3446d6fb59 diff --git a/tests/software/picard/collectmultiplemetrics/test.yml b/tests/software/picard/collectmultiplemetrics/test.yml index 20ca5da3..15eb4b57 100644 --- a/tests/software/picard/collectmultiplemetrics/test.yml +++ b/tests/software/picard/collectmultiplemetrics/test.yml @@ -2,7 +2,7 @@ command: nextflow run ./tests/software/picard/collectmultiplemetrics -entry test_picard_collectmultiplemetrics -c tests/config/nextflow.config tags: - picard - - picard_collectmultiplemetrics + - picard/collectmultiplemetrics files: # These can't be md5'd consistently - path: ./output/picard/test.CollectMultipleMetrics.alignment_summary_metrics diff --git a/tests/software/sequenzautils/bam2seqz/main.nf b/tests/software/sequenzautils/bam2seqz/main.nf index 898093a6..4268ca01 100755 --- a/tests/software/sequenzautils/bam2seqz/main.nf +++ b/tests/software/sequenzautils/bam2seqz/main.nf @@ -5,7 +5,7 @@ nextflow.enable.dsl = 2 include { SEQUENZAUTILS_BAM2SEQZ } from '../../../../software/sequenzautils/bam2seqz/main.nf' addParams( options: [:] ) workflow test_sequenzautils_bam2seqz { - + tumourbam = file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) normalbam = file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true) @@ -13,8 +13,8 @@ workflow test_sequenzautils_bam2seqz { tumourbam, normalbam ] - fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - wigfile = file(params.test_data['sarscov2']['genome']['test_wig_gz'], checkIfExists: true) + fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + wig = file(params.test_data['sarscov2']['illumina']['test_wig_gz'], checkIfExists: true) - SEQUENZAUTILS_BAM2SEQZ ( input, fasta, wigfile ) + SEQUENZAUTILS_BAM2SEQZ ( input, fasta, wig ) } diff --git a/tests/software/sequenzautils/bam2seqz/test.yml b/tests/software/sequenzautils/bam2seqz/test.yml index c3f0c058..2bd65d4c 100644 --- a/tests/software/sequenzautils/bam2seqz/test.yml +++ b/tests/software/sequenzautils/bam2seqz/test.yml @@ -2,6 +2,7 @@ command: nextflow run ./tests/software/sequenzautils/bam2seqz -entry test_sequenzautils_bam2seqz -c tests/config/nextflow.config tags: - sequenzautils - - sequenzautils_bam2seqz + - sequenzautils/bam2seqz files: - path: output/sequenzautils/test.seqz.gz + md5sum: 12b41979a498ac10c0aff162b12e6a6e diff --git a/tests/software/sequenzautils/gcwiggle/test.yml b/tests/software/sequenzautils/gcwiggle/test.yml index d8922f3e..db656799 100644 --- a/tests/software/sequenzautils/gcwiggle/test.yml +++ b/tests/software/sequenzautils/gcwiggle/test.yml @@ -4,6 +4,6 @@ command: nextflow run ./tests/software/sequenzautils/gcwiggle -entry test_sequenzautils_gcwiggle -c tests/config/nextflow.config tags: - sequenzautils - - sequenzautils_gcwiggle + - sequenzautils/gcwiggle files: - path: output/sequenzautils/test.wig.gz diff --git a/tests/software/stringtie/main.nf b/tests/software/stringtie/main.nf index 1c9aacc1..eff35c8a 100644 --- a/tests/software/stringtie/main.nf +++ b/tests/software/stringtie/main.nf @@ -10,8 +10,8 @@ include { STRINGTIE as STRINGTIE_REVERSE } from '../../../software/stringtie/mai */ workflow test_stringtie_forward { input = [ [ id:'test', strandedness:'forward' ], // meta map - [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true) ] ] - gtf = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.gtf", checkIfExists: true) + [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ] ] + gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) STRINGTIE_FORWARD ( input, gtf ) } @@ -21,9 +21,9 @@ workflow test_stringtie_forward { */ workflow test_stringtie_reverse { input = [ [ id:'test', strandedness:'reverse' ], // meta map - [ file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true) ] + [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ] ] - gtf = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.gtf", checkIfExists: true) + gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) STRINGTIE_REVERSE ( input, gtf ) } diff --git a/tests/software/stringtie/test.yml b/tests/software/stringtie/test.yml index e690268c..0e3a2ed7 100644 --- a/tests/software/stringtie/test.yml +++ b/tests/software/stringtie/test.yml @@ -4,7 +4,7 @@ - stringtie files: - path: ./output/test_stringtie_forward/test.transcripts.gtf - md5sum: cbce87f06598eb756e7670ba3217a42f + md5sum: 8abb6a87581bd7a61af74085b5a6daec - path: ./output/test_stringtie_forward/test.gene.abundance.txt md5sum: 7d8bce7f2a922e367cedccae7267c22e - path: ./output/test_stringtie_forward/test.coverage.gtf @@ -26,7 +26,7 @@ - stringtie files: - path: ./output/test_stringtie_reverse/test.transcripts.gtf - md5sum: bb992085e42bad19877c847dae496c80 + md5sum: 8bdcda06f39183fa4312644bd0e41bb5 - path: ./output/test_stringtie_reverse/test.gene.abundance.txt md5sum: 7385b870b955dae2c2ab78a70cf05cce - path: ./output/test_stringtie_reverse/test.coverage.gtf diff --git a/tests/software/subread/featurecounts/test.yml b/tests/software/subread/featurecounts/test.yml index 8609aa5d..443ae2a6 100644 --- a/tests/software/subread/featurecounts/test.yml +++ b/tests/software/subread/featurecounts/test.yml @@ -2,8 +2,8 @@ command: nextflow run tests/software/subread/featurecounts -entry test_subread_featurecounts_forward -c tests/config/nextflow.config tags: - subread + - subread/featurecounts - subread_featurecounts_forward - - subread_featurecounts files: - path: output/subread/test.featureCounts.txt.summary md5sum: d78617192451a57f6ef249ddcaf13720 @@ -14,7 +14,7 @@ command: nextflow run tests/software/subread/featurecounts -entry test_subread_featurecounts_reverse -c tests/config/nextflow.config tags: - subread - - subread_featurecounts + - subread/featurecounts - subread_featurecounts_reverse files: - path: output/subread/test.featureCounts.txt.summary @@ -26,7 +26,7 @@ command: nextflow run tests/software/subread/featurecounts -entry test_subread_featurecounts_unstranded -c tests/config/nextflow.config tags: - subread - - subread_featurecounts + - subread/featurecounts - subread_featurecounts_unstranded files: - path: output/subread/test.featureCounts.txt.summary diff --git a/tests/software/ucsc/bed12tobigbed/main.nf b/tests/software/ucsc/bed12tobigbed/main.nf index 60118346..3adc25bf 100644 --- a/tests/software/ucsc/bed12tobigbed/main.nf +++ b/tests/software/ucsc/bed12tobigbed/main.nf @@ -6,9 +6,9 @@ include { UCSC_BED12TOBIGBED } from '../../../../software/ucsc/bed12tobigbed/mai workflow test_ucsc_bed12tobigbed { input = [ [ id: 'test' ], // meta map - [ file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed12", checkIfExists: true ) ] + [ file(params.test_data['sarscov2']['genome']['test_bed12'], checkIfExists: true ) ] ] - sizes = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.sizes", checkIfExists: true) + sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true) UCSC_BED12TOBIGBED ( input, sizes ) } diff --git a/tests/software/ucsc/bedgraphtobigwig/main.nf b/tests/software/ucsc/bedgraphtobigwig/main.nf index b533c4b7..099a9ea6 100644 --- a/tests/software/ucsc/bedgraphtobigwig/main.nf +++ b/tests/software/ucsc/bedgraphtobigwig/main.nf @@ -6,9 +6,9 @@ include { UCSC_BEDGRAPHTOBIGWIG } from '../../../../software/ucsc/bedgraphtobig workflow test_ucsc_bedgraphtobigwig { input = [ [ id:'test' ], // meta map - [ file('https://raw.githubusercontent.com/igvteam/igv.js/master/test/data/wig/bedgraph-example-uscs.bedgraph', checkIfExists: true) ] + [ file(params.test_data['sarscov2']['illumina']['test_bedgraph'], checkIfExists: true) ] ] - sizes = file('https://raw.githubusercontent.com/igvteam/igv.js/master/test/data/wig/chrom.sizes', checkIfExists: true) + sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true) UCSC_BEDGRAPHTOBIGWIG ( input, sizes ) } diff --git a/tests/software/ucsc/bedgraphtobigwig/test.yml b/tests/software/ucsc/bedgraphtobigwig/test.yml index c2476623..a83b3039 100644 --- a/tests/software/ucsc/bedgraphtobigwig/test.yml +++ b/tests/software/ucsc/bedgraphtobigwig/test.yml @@ -4,4 +4,4 @@ - ucsc/bedgraphtobigwig files: - path: output/ucsc/test.bigWig - md5sum: 5346de25b01ecbff91b63178b3bfbeec + md5sum: 910ecc7f57e3bbd5fac5a8edba4f615d