fix(tests): remove md5sum for all mosdepth tests + update dependency for these tests

CHANGELOG.md

@@ -26,6 +26,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#1488](https://github.com/nf-core/sarek/pull/1488) - Fixing call to `GATK4_HAPLOTYPECALLER` and thereby also the test-profile `test_full_germline`
 - [#1494](https://github.com/nf-core/sarek/pull/1494) - Fix Cloud Storage objects are immutable on GCP [#1491](https://github.com/nf-core/sarek/issues/1491)
 - [#1496](https://github.com/nf-core/sarek/pull/1496) - Fix multiple DOI handling in manifest
+- [#1499](https://github.com/nf-core/sarek/pull/1499) - Remove all md5sum for mosdepth tests
+- [#1499](https://github.com/nf-core/sarek/pull/1499) - Add mosdepth dependency to all tests runnning it
 
 ### Removed
 

tests/config/pytesttags.yml

@@ -76,6 +76,7 @@ validation_checks:
 alignment_to_fastq:
   - conf/modules/alignment_to_fastq.config
   - modules/nf-core/cat/fastq/**
+  - modules/nf-core/mosdepth/**
   - modules/nf-core/samtools/collatefastq/**
   - modules/nf-core/samtools/merge/**
   - modules/nf-core/samtools/view/**
@@ -92,6 +93,7 @@ umi:
   - modules/nf-core/fgbio/callmolecularconsensusreads/**
   - modules/nf-core/fgbio/fastqtobam/**
   - modules/nf-core/fgbio/groupreadsbyumi/**
+  - modules/nf-core/mosdepth/**
   - modules/nf-core/samblaster/**
   - modules/nf-core/samtools/bam2fq/**
   - subworkflows/local/fastq_align_bwamem_mem2_dragmap/**
@@ -103,6 +105,7 @@ umi:
 fastp:
   - conf/modules/trimming.config
   - modules/nf-core/fastp/**
+  - modules/nf-core/mosdepth/**
   - tests/csv/3.0/fastq_single.csv
   - tests/test_fastp.yml
 
@@ -112,6 +115,7 @@ fastp:
 bwamem:
   - conf/modules/aligner.config
   - modules/nf-core/bwa/mem/**
+  - modules/nf-core/mosdepth/**
   - subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/**
   - tests/csv/3.0/fastq_single.csv
   - tests/test_aligner_bwamem.yml
@@ -120,6 +124,7 @@ bwamem:
 bwamem2:
   - conf/modules/aligner.config
   - modules/nf-core/bwamem2/mem/**
+  - modules/nf-core/mosdepth/**
   - subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/**
   - tests/csv/3.0/fastq_single.csv
   - tests/test_aligner_bwamem2.yml
@@ -128,6 +133,7 @@ bwamem2:
 dragmap:
   - conf/modules/aligner.config
   - modules/nf-core/dragmap/align/**
+  - modules/nf-core/mosdepth/**
   - subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/**
   - tests/csv/3.0/fastq_single.csv
   - tests/test_aligner_dragmap.yml
@@ -174,6 +180,7 @@ prepare_recalibration:
   - conf/modules/prepare_recalibration.config
   - modules/nf-core/gatk4/baserecalibrator/**
   - modules/nf-core/gatk4/gatherbqsrreports/**
+  - modules/nf-core/mosdepth/**
   - modules/nf-core/samtools/convert/**
   - subworkflows/local/bam_baserecalibrator/**
   - tests/csv/3.0/mapped_single_bam.csv
@@ -188,6 +195,7 @@ recalibrate:
   - modules/nf-core/samtools/convert/**
   - modules/nf-core/samtools/index/**
   - modules/nf-core/samtools/merge/**
+  - modules/nf-core/mosdepth/**
   - subworkflows/local/bam_applybqsr/**
   - subworkflows/local/cram_merge_index_samtools/**
   - tests/csv/3.0/prepare_recalibration_single_bam.csv
@@ -201,6 +209,7 @@ intervals:
   - modules/local/build_intervals/**
   - modules/local/create_intervals_bed/**
   - modules/nf-core/gatk4/intervallisttobed/**
+  - modules/nf-core/mosdepth/**
   - modules/nf-core/tabix/bgziptabix/**
   - subworkflows/local/prepare_intervals/**
   - tests/csv/3.0/fastq_single.csv
@@ -215,6 +224,7 @@ gatk4spark:
   - modules/nf-core/gatk4spark/baserecalibrator/**
   - modules/nf-core/gatk4/estimatelibrarycomplexity/**
   - modules/nf-core/gatk4spark/markduplicates/**
+  - modules/nf-core/mosdepth/**
   - subworkflows/local/bam_applybqsr_spark/**
   - subworkflows/local/bam_baserecalibrator_spark/**
   - subworkflows/local/bam_markduplicates_spark/**
@@ -229,6 +239,7 @@ cnvkit:
   - modules/nf-core/cnvkit/antitarget/**
   - modules/nf-core/cnvkit/batch/**
   - modules/nf-core/cnvkit/reference/**
+  - modules/nf-core/mosdepth/**
   - subworkflows/local/bam_variant_calling_cnvkit/**
   - subworkflows/local/bam_variant_calling_germline_all/**
   - subworkflows/local/bam_variant_calling_somatic_all/**
@@ -249,6 +260,7 @@ controlfreec:
   - modules/nf-core/controlfreec/freec2bed/**
   - modules/nf-core/controlfreec/freec2circos/**
   - modules/nf-core/controlfreec/makegraph2/**
+  - modules/nf-core/mosdepth/**
   - modules/nf-core/samtools/mpileup/**
   - subworkflows/local/bam_variant_calling_mpileup/**
   - subworkflows/local/bam_variant_calling_somatic_all/**
@@ -264,6 +276,7 @@ deepvariant:
   - conf/modules/deepvariant.config
   - modules/nf-core/deepvariant/**
   - modules/nf-core/gatk4/mergevcfs/**
+  - modules/nf-core/mosdepth/**
   - modules/nf-core/tabix/tabix/**
   - subworkflows/local/bam_variant_calling_deepvariant/**
   - subworkflows/local/bam_variant_calling_germline_all/**
@@ -276,6 +289,7 @@ freebayes:
   - modules/nf-core/bcftools/sort/**
   - modules/nf-core/freebayes/**
   - modules/nf-core/gatk4/mergevcfs/**
+  - modules/nf-core/mosdepth/**
   - modules/nf-core/tabix/tabix/**
   - subworkflows/local/bam_variant_calling_freebayes/**
   - subworkflows/local/bam_variant_calling_germline_all/**
@@ -293,6 +307,7 @@ haplotypecaller:
   - modules/nf-core/gatk4/filtervarianttranches/**
   - modules/nf-core/gatk4/haplotypecaller/**
   - modules/nf-core/gatk4/mergevcfs/**
+  - modules/nf-core/mosdepth/**
   - modules/nf-core/samtools/index/**
   - modules/nf-core/samtools/merge/**
   - subworkflows/local/bam_merge_index_samtools/**
@@ -379,6 +394,7 @@ joint_germline:
   - modules/nf-core/gatk4/haplotypecaller/**
   - modules/nf-core/gatk4/mergevcfs/**
   - modules/nf-core/gatk4/variantrecalibrator/**
+  - modules/nf-core/mosdepth/**
   - modules/nf-core/samtools/index/**
   - modules/nf-core/samtools/merge/**
   - subworkflows/local/bam_joint_calling_germline_gatk/**
@@ -418,6 +434,7 @@ manta:
   - modules/nf-core/manta/germline/**
   - modules/nf-core/manta/somatic/**
   - modules/nf-core/manta/tumoronly/**
+  - modules/nf-core/mosdepth/**
   - subworkflows/local/bam_variant_calling_germline_all/**
   - subworkflows/local/bam_variant_calling_germline_manta/**
   - subworkflows/local/bam_variant_calling_somatic_all/**
@@ -433,6 +450,7 @@ manta:
 mpileup:
   - conf/modules/mpileup.config
   - modules/nf-core/cat/cat/**
+  - modules/nf-core/mosdepth/**
   - modules/nf-core/samtools/mpileup/**
   - subworkflows/local/bam_variant_calling_germline_all/**
   - subworkflows/local/bam_variant_calling_mpileup/**
@@ -447,6 +465,7 @@ msisensorpro:
   - conf/modules/msisensorpro.config
   - modules/nf-core/msisensorpro/msi_somatic/**
   - modules/nf-core/msisensorpro/scan/**
+  - modules/nf-core/mosdepth/**
   - subworkflows/local/bam_variant_calling_somatic_all/**
   - tests/csv/3.0/recalibrated_somatic.csv
   - tests/test_msisensorpro.yml
@@ -462,6 +481,7 @@ mutect2:
   - modules/nf-core/gatk4/mergemutectstats/**
   - modules/nf-core/gatk4/mergevcfs/**
   - modules/nf-core/gatk4/mutect2/**
+  - modules/nf-core/mosdepth/**
   - subworkflows/local/bam_variant_calling_somatic_all/**
   - subworkflows/local/bam_variant_calling_somatic_mutect2/**
   - subworkflows/local/bam_variant_calling_tumor_only_all/**
@@ -473,6 +493,7 @@ mutect2:
 strelka:
   - conf/modules/strelka.config
   - modules/nf-core/gatk4/mergevcfs/**
+  - modules/nf-core/mosdepth/**
   - modules/nf-core/strelka/germline/**
   - modules/nf-core/strelka/somatic/**
   - subworkflows/local/bam_variant_calling_germline_all/**
@@ -492,6 +513,7 @@ strelka_bp:
   - conf/modules/strelka.config
   - modules/nf-core/gatk4/mergevcfs/**
   - modules/nf-core/manta/somatic/**
+  - modules/nf-core/mosdepth/**
   - modules/nf-core/strelka/somatic/**
   - subworkflows/local/bam_variant_calling_germline_all/**
   - subworkflows/local/bam_variant_calling_somatic_all/**
@@ -505,6 +527,7 @@ strelka_bp:
 tiddit:
   - conf/modules/tiddit.config
   - modules/nf-core/svdb/merge/**.nf
+  - modules/nf-core/mosdepth/**
   - modules/nf-core/tabix/bgziptabix/**
   - modules/nf-core/tiddit/sv/**
   - subworkflows/local/bam_variant_calling_germline_all/**

tests/test_aligner_bwamem.yml

@@ -42,25 +42,15 @@
     - path: results/reports/markduplicates/test/test.md.cram.metrics
       contains: ["test	17094	1534	168	1046782	12429	197	0	0.635998", "1.0	0.999991	1171"]
     - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
-      md5sum: b61e1acee11a6ddf7ce3232a5948a6a0
     - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
-      md5sum: 1a382f98d488d2ae3df83a0d87caafc1
     - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
-      md5sum: 839108358878ada89e1eaddf6e0541ba
     - path: results/reports/mosdepth/test/test.md.regions.bed.gz
-      md5sum: 0aaee6da65050bedcd40b9fbf0622873
     - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
-      md5sum: 544e02fcca548749a0af758d0a2df352
     - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
-      md5sum: b61e1acee11a6ddf7ce3232a5948a6a0
     - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
-      md5sum: 1a382f98d488d2ae3df83a0d87caafc1
     - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
-      md5sum: 839108358878ada89e1eaddf6e0541ba
     - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
-      md5sum: 0aaee6da65050bedcd40b9fbf0622873
     - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
-      md5sum: 544e02fcca548749a0af758d0a2df352
     - path: results/reports/samtools/test/test.md.cram.stats
     # conda changes md5sums for test
     - path: results/reports/samtools/test/test.recal.cram.stats

tests/test_aligner_bwamem2.yml

@@ -42,25 +42,15 @@
     - path: results/reports/markduplicates/test/test.md.cram.metrics
       contains: ["test	17094	1534	168	1046782	12429	197	0	0.635998", "1.0	0.999991	1171"]
     - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
-      md5sum: b61e1acee11a6ddf7ce3232a5948a6a0
     - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
-      md5sum: 1a382f98d488d2ae3df83a0d87caafc1
     - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
-      md5sum: 839108358878ada89e1eaddf6e0541ba
     - path: results/reports/mosdepth/test/test.md.regions.bed.gz
-      md5sum: 0aaee6da65050bedcd40b9fbf0622873
     - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
-      md5sum: 544e02fcca548749a0af758d0a2df352
     - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
-      md5sum: b61e1acee11a6ddf7ce3232a5948a6a0
     - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
-      md5sum: 1a382f98d488d2ae3df83a0d87caafc1
     - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
-      md5sum: 839108358878ada89e1eaddf6e0541ba
     - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
-      md5sum: 0aaee6da65050bedcd40b9fbf0622873
     - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
-      md5sum: 544e02fcca548749a0af758d0a2df352
     - path: results/reports/samtools/test/test.md.cram.stats
     # conda changes md5sums for test
     - path: results/reports/samtools/test/test.recal.cram.stats

tests/test_aligner_dragmap.yml

@@ -55,25 +55,15 @@
     - path: results/reports/markduplicates/test/test.md.cram.metrics
       contains: ["LB0	27214	1086	322	1037558	20017	100	0	0.687981"]
     - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
-      md5sum: b0d7d5de1e00132bb5b47e1b3d90d944
     - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
-      md5sum: 02b88d7ec0ca8ff23ba688c35939fa05
     - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
-      md5sum: 1792d98676f597f755749f4286c5102d
     - path: results/reports/mosdepth/test/test.md.regions.bed.gz
-      md5sum: 590119568d091ce3a88f7fe4f43f24ff
     - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
-      md5sum: 2e7fe057ead0622e6a2a6b0ed1832315
     - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
-      md5sum: b0d7d5de1e00132bb5b47e1b3d90d944
     - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
-      md5sum: 02b88d7ec0ca8ff23ba688c35939fa05
     - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
-      md5sum: 1792d98676f597f755749f4286c5102d
     - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
-      md5sum: 590119568d091ce3a88f7fe4f43f24ff
     - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
-      md5sum: 2e7fe057ead0622e6a2a6b0ed1832315
     - path: results/reports/samtools/test/test.md.cram.stats
     # conda changes md5sums for test
     - path: results/reports/samtools/test/test.recal.cram.stats

tests/test_alignment_to_fastq.yml

@@ -25,25 +25,15 @@
     - path: results/reports/markduplicates/test/test.md.cram.metrics
       contains: ["test	0	2820	2	2	0	828	0	0.293617	3807", "1.0	0.999986	1178	1178", "2.0	1.47674	800	800", "100.0	1.911145	0	0"]
     - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
-      md5sum: 9cb9b181119256ed17a77dcf44d58285
     - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
-      md5sum: 75e1ce7e55af51f4985fa91654a5ea2d
     - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
-      md5sum: dbe376360e437c89190139ef0ae6769a
     - path: results/reports/mosdepth/test/test.md.regions.bed.gz
-      md5sum: d9b53915d473710ff0260a0ff694fd32
     - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
-      md5sum: d0713716f63ac573f4a3385733e9a537
     - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
-      md5sum: 9cb9b181119256ed17a77dcf44d58285
     - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
-      md5sum: 75e1ce7e55af51f4985fa91654a5ea2d
     - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
-      md5sum: dbe376360e437c89190139ef0ae6769a
     - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
-      md5sum: d9b53915d473710ff0260a0ff694fd32
     - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
-      md5sum: d0713716f63ac573f4a3385733e9a537
     - path: results/reports/samtools/test/test.md.cram.stats
     # conda changes md5sums for test
     - path: results/reports/samtools/test/test.recal.cram.stats

tests/test_cnvkit.yml

@@ -58,27 +58,17 @@
     - path: results/cnvkit
       should_exist: false
     - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt
-      md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
     - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt
-      md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
     - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt
-      md5sum: 103098d0bf76ed82d2b87d5f242b099a
     - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz
-      md5sum: b5888cf7395c57d39879a5faa6159eb3
     - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi
-      md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
     - path: results/reports/samtools/sample3/sample3.recal.cram.stats
     # conda changes md5sums for test
     - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt
-      md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
     - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt
-      md5sum: 39005ffaac22871ffaaf19656fe69c5b
     - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt
-      md5sum: 68d4b98f17361fddf73052ead34fa370
     - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz
-      md5sum: 2819e995eafded35f53328c4ec19ba58
     - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi
-      md5sum: 393c2749068304d8545b501b9d4658e4
     - path: results/reports/samtools/sample4/sample4.recal.cram.stats
     # conda changes md5sums for test
 - name: Run variant calling on tumor_only sample with cnvkit
@@ -113,15 +103,10 @@
     - path: results/cnvkit
       should_exist: false
     - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt
-      md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
     - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.region.dist.txt
-      md5sum: 39005ffaac22871ffaaf19656fe69c5b
     - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt
-      md5sum: 68d4b98f17361fddf73052ead34fa370
     - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz
-      md5sum: 2819e995eafded35f53328c4ec19ba58
     - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi
-      md5sum: 393c2749068304d8545b501b9d4658e4
     - path: results/reports/samtools/sample2/sample2.recal.cram.stats
 - name: Run variant calling on germline sample with cnvkit
   command: nextflow run main.nf -profile test,tools_germline --tools cnvkit --outdir results
@@ -157,15 +142,10 @@
     - path: results/cnvkit
       should_exist: false
     - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt
-      md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
     - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.region.dist.txt
-      md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
     - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt
-      md5sum: 103098d0bf76ed82d2b87d5f242b099a
     - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz
-      md5sum: b5888cf7395c57d39879a5faa6159eb3
     - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz.csi
-      md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
     - path: results/reports/samtools/sample1/sample1.recal.cram.stats
 - name: Run variant calling on somatic samples with cnvkit and skip variant calling on matched normal
   command: nextflow run main.nf -profile test,tools_somatic --tools cnvkit --only_paired_variant_calling --outdir results
@@ -203,26 +183,16 @@
     - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
       md5sum: b4a49faf170e436ec32dcc21ccc3ce8f
     - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt
-      md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
     - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt
-      md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
     - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt
-      md5sum: 103098d0bf76ed82d2b87d5f242b099a
     - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz
-      md5sum: b5888cf7395c57d39879a5faa6159eb3
     - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi
-      md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
     - path: results/reports/samtools/sample3/sample3.recal.cram.stats
     # conda changes md5sums for test
     - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt
-      md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
     - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt
-      md5sum: 39005ffaac22871ffaaf19656fe69c5b
     - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt
-      md5sum: 68d4b98f17361fddf73052ead34fa370
     - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz
-      md5sum: 2819e995eafded35f53328c4ec19ba58
     - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi
-      md5sum: 393c2749068304d8545b501b9d4658e4
     - path: results/reports/samtools/sample4/sample4.recal.cram.stats
     # conda changes md5sums for test