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Code Issues Releases Packages Activity

Small update on the output channels

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This commit is contained in:
Nicolas Vannieuwkerke 2022-05-10 12:34:52 +02:00
parent c18391aa49
commit b7134855e4
2 changed files with 54 additions and 52 deletions
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8
modules/rtgtools/vcfeval/main.nf
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@ -15,14 +15,14 @@ process RTGTOOLS_VCFEVAL {
path(sdf) path(sdf)
output: output:
tuple val(meta), path("**{done,progress,.log}") , emit: logs tuple val(meta), path("**results/{done,progress,*.log}") , emit: logs
tuple val(meta), path("**tp.vcf.gz"), path("**tp.vcf.gz.tbi") , emit: tp tuple val(meta), path("**tp.vcf.gz"), path("**tp.vcf.gz.tbi") , emit: tp
tuple val(meta), path("**fn.vcf.gz"), path("**fn.vcf.gz.tbi") , emit: fn tuple val(meta), path("**fn.vcf.gz"), path("**fn.vcf.gz.tbi") , emit: fn
tuple val(meta), path("**fp.vcf.gz"), path("**fp.vcf.gz.tbi") , emit: fp tuple val(meta), path("**fp.vcf.gz"), path("**fp.vcf.gz.tbi") , emit: fp
tuple val(meta), path("**baseline.vcf.gz"), path("**baseline.vcf.gz.tbi") , emit: baseline tuple val(meta), path("**baseline.vcf.gz"), path("**baseline.vcf.gz.tbi") , emit: baseline
tuple val(meta), path("**.tsv.gz") , emit: roc tuple val(meta), path("**.tsv.gz") , emit: roc
tuple val(meta), path("**summary.txt") , emit: summary tuple val(meta), path("**results/summary.txt") , emit: summary
tuple val(meta), path("**phasing.txt") , emit: phasing tuple val(meta), path("**results/phasing.txt") , emit: phasing
path "versions.yml" , emit: versions path "versions.yml" , emit: versions
when: when:
@ -46,7 +46,7 @@ process RTGTOOLS_VCFEVAL {
$bed_regions \\ $bed_regions \\
$eval_regions \\ $eval_regions \\
--calls=$query_vcf \\ --calls=$query_vcf \\
--output=$prefix \\ --output=${prefix}_results \\
--template=$sdf \\ --template=$sdf \\
--threads=$task.cpus \\ --threads=$task.cpus \\

98
tests/modules/rtgtools/vcfeval/test.yml
View file

@ -4,36 +4,37 @@
- rtgtools - rtgtools
- rtgtools/vcfeval - rtgtools/vcfeval
files: files:
- path: output/rtgtools/done - path: output/rtgtools/test_results/done
- path: output/rtgtools/fn.vcf.gz - path: output/rtgtools/test_results/fn.vcf.gz
md5sum: 4577a8c3226b9f8ed9e260c3bd4b1259 md5sum: be9c9106055bfad4c5985bc0d33efd56
- path: output/rtgtools/fn.vcf.gz.tbi - path: output/rtgtools/test_results/fn.vcf.gz.tbi
md5sum: 092a7a3162e7cff25d273525751eb284 md5sum: 092a7a3162e7cff25d273525751eb284
- path: output/rtgtools/fp.vcf.gz - path: output/rtgtools/test_results/fp.vcf.gz
md5sum: 1417bb8ac7a0e202df660291a74de0db md5sum: e0f0ff841dc63e9fb61fd3a5db137ced
- path: output/rtgtools/fp.vcf.gz.tbi - path: output/rtgtools/test_results/fp.vcf.gz.tbi
md5sum: 092a7a3162e7cff25d273525751eb284 md5sum: 092a7a3162e7cff25d273525751eb284
- path: output/rtgtools/non_snp_roc.tsv.gz - path: output/rtgtools/test_results/non_snp_roc.tsv.gz
md5sum: 8fd51a1e5084d15d43880cb1e31a0180 md5sum: ad5bad32c48f05aef232e2c0e708877a
- path: output/rtgtools/phasing.txt - path: output/rtgtools/test_results/phasing.txt
md5sum: 133677dbd8be657439ea2b03fdfb8795 md5sum: 133677dbd8be657439ea2b03fdfb8795
- path: output/rtgtools/progress - path: output/rtgtools/test_results/progress
- path: output/rtgtools/snp_roc.tsv.gz - path: output/rtgtools/test_results/snp_roc.tsv.gz
md5sum: ff2ece544adfcefaa06da054876a9ae3 md5sum: 6785b83d66486e7e6c75c5a5b1574c09
- path: output/rtgtools/summary.txt - path: output/rtgtools/test_results/summary.txt
md5sum: f4c8df93c8bdab603036bbc27b4a28c3 md5sum: f4c8df93c8bdab603036bbc27b4a28c3
- path: output/rtgtools/tp-baseline.vcf.gz - path: output/rtgtools/test_results/tp-baseline.vcf.gz
md5sum: 4577a8c3226b9f8ed9e260c3bd4b1259 md5sum: be9c9106055bfad4c5985bc0d33efd56
- path: output/rtgtools/tp-baseline.vcf.gz.tbi - path: output/rtgtools/test_results/tp-baseline.vcf.gz.tbi
md5sum: 092a7a3162e7cff25d273525751eb284 md5sum: 092a7a3162e7cff25d273525751eb284
- path: output/rtgtools/tp.vcf.gz - path: output/rtgtools/test_results/tp.vcf.gz
md5sum: 1417bb8ac7a0e202df660291a74de0db md5sum: e0f0ff841dc63e9fb61fd3a5db137ced
- path: output/rtgtools/tp.vcf.gz.tbi - path: output/rtgtools/test_results/tp.vcf.gz.tbi
md5sum: 092a7a3162e7cff25d273525751eb284 md5sum: 092a7a3162e7cff25d273525751eb284
- path: output/rtgtools/vcfeval.log - path: output/rtgtools/test_results/vcfeval.log
- path: output/rtgtools/test_results/weighted_roc.tsv.gz
md5sum: fa7c046ea0084172f1ef91f19de07b2b
- path: output/rtgtools/versions.yml - path: output/rtgtools/versions.yml
- path: output/rtgtools/weighted_roc.tsv.gz md5sum: 270ed7a5a8e347b251eb4aa2198f98e8
md5sum: 5209f1bdeb03704714ae92b183d08e0f
- name: rtgtools vcfeval test_rtgtools_vcfeval_no_optional_inputs - name: rtgtools vcfeval test_rtgtools_vcfeval_no_optional_inputs
command: nextflow run tests/modules/rtgtools/vcfeval -entry test_rtgtools_vcfeval_no_optional_inputs -c tests/config/nextflow.config command: nextflow run tests/modules/rtgtools/vcfeval -entry test_rtgtools_vcfeval_no_optional_inputs -c tests/config/nextflow.config
@ -41,33 +42,34 @@
- rtgtools - rtgtools
- rtgtools/vcfeval - rtgtools/vcfeval
files: files:
- path: output/rtgtools/done - path: output/rtgtools/test_results/done
- path: output/rtgtools/fn.vcf.gz - path: output/rtgtools/test_results/fn.vcf.gz
md5sum: e51420e4be520ae309a2384830bf4c15 md5sum: c11c889a4f42c8ea325748bd768ea34d
- path: output/rtgtools/fn.vcf.gz.tbi - path: output/rtgtools/test_results/fn.vcf.gz.tbi
md5sum: 092a7a3162e7cff25d273525751eb284 md5sum: 092a7a3162e7cff25d273525751eb284
- path: output/rtgtools/fp.vcf.gz - path: output/rtgtools/test_results/fp.vcf.gz
md5sum: 7d818cf526983de6cbb5cf517c44a8f7 md5sum: 138e85c1cd79f8fea9a33e81ce0c734c
- path: output/rtgtools/fp.vcf.gz.tbi - path: output/rtgtools/test_results/fp.vcf.gz.tbi
md5sum: 092a7a3162e7cff25d273525751eb284 md5sum: 092a7a3162e7cff25d273525751eb284
- path: output/rtgtools/non_snp_roc.tsv.gz - path: output/rtgtools/test_results/non_snp_roc.tsv.gz
md5sum: a535fb80081b43b19788347152b6b8b4 md5sum: 34fb78a008dfc0bef02807b8a7012b07
- path: output/rtgtools/phasing.txt - path: output/rtgtools/test_results/phasing.txt
md5sum: 133677dbd8be657439ea2b03fdfb8795 md5sum: 133677dbd8be657439ea2b03fdfb8795
- path: output/rtgtools/progress - path: output/rtgtools/test_results/progress
- path: output/rtgtools/snp_roc.tsv.gz - path: output/rtgtools/test_results/snp_roc.tsv.gz
md5sum: 6006656c4a534935c7873398287bc110 md5sum: a4c5761c2653e2d04fc84c1cea13b1f0
- path: output/rtgtools/summary.txt - path: output/rtgtools/test_results/summary.txt
md5sum: f33feb32f84958fb931063044fba369b md5sum: f33feb32f84958fb931063044fba369b
- path: output/rtgtools/tp-baseline.vcf.gz - path: output/rtgtools/test_results/tp-baseline.vcf.gz
md5sum: ed68ea567a26d3b864ada79e9253bc97 md5sum: d1c2d990899edf127ea5fcca8866fcb0
- path: output/rtgtools/tp-baseline.vcf.gz.tbi - path: output/rtgtools/test_results/tp-baseline.vcf.gz.tbi
md5sum: 3518deff814eed340b0f5386294b5879 md5sum: 3307008fea47adb75c46d395c5567bc0
- path: output/rtgtools/tp.vcf.gz - path: output/rtgtools/test_results/tp.vcf.gz
md5sum: 92fd51021d101c99da066324655d24c9 md5sum: e35b4dab82894eee9b77c81f9bc89cca
- path: output/rtgtools/tp.vcf.gz.tbi - path: output/rtgtools/test_results/tp.vcf.gz.tbi
md5sum: 169063c1f570f0055059f3cb3518a8b4 md5sum: 45d8f8793140944f129e728299918c88
- path: output/rtgtools/vcfeval.log - path: output/rtgtools/test_results/vcfeval.log
- path: output/rtgtools/test_results/weighted_roc.tsv.gz
md5sum: 5b8efc9e9381f604880412800f58e4e9
- path: output/rtgtools/versions.yml - path: output/rtgtools/versions.yml
- path: output/rtgtools/weighted_roc.tsv.gz md5sum: 55568e4bbe5ab7e634a1f392abb89cc4
md5sum: 0ba825084bd6b94accdf54fff23ea18c