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test: Update the rest of the tests for new output
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@edmundmiller
edmundmiller committed Aug 11, 2024
1 parent 5f0c3b1 commit 6fb83a5
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Showing 12 changed files with 521 additions and 162 deletions.
39 changes: 19 additions & 20 deletions workflows/tests/aligner/bowtie2.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -20,26 +20,25 @@ nextflow_pipeline {
{ assert snapshot(UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml")).match("software_versions") },
{ assert snapshot(
workflow.trace.tasks().size(),
path("$outputDir/bbmap").list(),
// BUG https://github.com/nf-core/nascent/issues/102
// path("$outputDir/bedtools").list(),
// FIXME gtf2bed isn't deterministic
// path("$outputDir/bwa/featurecounts/gene").list(),
// FIXME cd4 isn't deterministic
// path("$outputDir/bwa/featurecounts/predicted").list(),
// path("$outputDir/deeptools").list(),
// path("$outputDir/fastp/*.json").list(),
// FIXME gtf2bed isn't deterministic
// path("$outputDir/gtf2bed").list(),
path("$outputDir/homer/cd4.bed"),
path("$outputDir/homer/jurkat.bed"),
// FIXME https://github.com/nf-core/nascent/issues/148
// path("$outputDir/preseq").list(),
// path("$outputDir/rseqc").list(),
// FIXME Bowtie2 isn't deterministic
bam("$outputDir/samtools/cd4_REP1.sorted.bam").getHeaderMD5(),
bam("$outputDir/samtools/cd4_REP2.sorted.bam").getHeaderMD5(),
bam("$outputDir/samtools/jurkat.sorted.bam").getHeaderMD5(),
UTILS.getAllFilesFromDir("$outputDir/preprocessing/fastp/", ".json"),
// NOTE Not deterministic
path("$outputDir/bowtie2/cd4_REP1.sorted.bam").exists(),
path("$outputDir/bowtie2/cd4_REP2.sorted.bam").exists(),
path("$outputDir/bowtie2/jurkat.sorted.bam").exists(),
path("$outputDir/bowtie2/log").list(),
path("$outputDir/bowtie2/samtools_stats").list(),
path("$outputDir/quality_control/bbsplit").list(),
UTILS.getAllFilesFromDir("$outputDir/quality_control/preseq", ".txt"),
path("$outputDir/quality_control/rseqc/read_duplication/xls").list(),
path("$outputDir/quality_control/rseqc/read_duplication/rscript").list(),
path("$outputDir/quality_control/rseqc/infer_experiment").list(),
path("$outputDir/quality_control/rseqc/read_distribution").list(),
path("$outputDir/coverage_graphs/").list(),
path("$outputDir/transcript_identification/homer/cd4.bed"),
path("$outputDir/transcript_identification/homer/jurkat.bed"),
path("$outputDir/transcript_identification/intersect/").list(),
path("$outputDir/transcript_identification/filtered/").list(),
path("$outputDir/multiqc/multiqc_report.html").exists(),
).match("output_files")
}
)
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88 changes: 83 additions & 5 deletions workflows/tests/aligner/bowtie2.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,30 @@
"output_files": {
"content": [
75,
[
"cd4_REP1.trimmed.fastp.json:md5,bd9a3344c1591d6be4d524451f9dca53",
"cd4_REP2.trimmed.fastp.json:md5,bc6e3f9ff7835f220535cc393b8eb25f",
"jurkat.trimmed.fastp.json:md5,65f7247a87479c7157c7357d575336e2"
],
true,
true,
true,
[
"cd4_REP1.bowtie2.log:md5,024c3b6bca27f3836cdd86c0287d2971",
"cd4_REP2.bowtie2.log:md5,089af358aad637ec94c10172eb024773",
"jurkat.bowtie2.log:md5,24031e901f4ce11cfb227c7d30d1373a"
],
[
"cd4_REP1.sorted.bam.flagstat:md5,14e684e73cb41155ab1168a0a99a97e6",
"cd4_REP1.sorted.bam.idxstats:md5,e32ac3215ba948bb7dd1559dab6c3c36",
"cd4_REP1.sorted.bam.stats:md5,490f84b5520b83daa95653671ce43921",
"cd4_REP2.sorted.bam.flagstat:md5,e00d036bcbea6f944d45fb5cb7c34516",
"cd4_REP2.sorted.bam.idxstats:md5,0803f2dce4b972ccc14943e22145c3e8",
"cd4_REP2.sorted.bam.stats:md5,f8872ba7ef4b4e66b16a4ca3d63c1a65",
"jurkat.sorted.bam.flagstat:md5,1b24ceabc8cecf34d745d06cf9d43cd0",
"jurkat.sorted.bam.idxstats:md5,15e67d4d9d71c6cc6c37d5ce5414ede0",
"jurkat.sorted.bam.stats:md5,ff1a4b8f6456a539943a14c8daeb75d3"
],
[
"cd4_REP1.coverage.hist.txt:md5,ffd8c0a94869dd782779fc871a9b781a",
"cd4_REP1.coverage.stats.txt:md5,bebdef1adcce4296878f8699a0f5cb32",
Expand All @@ -10,17 +34,71 @@
"jurkat.coverage.hist.txt:md5,656e30e8c4bd12e45a036c62c18730c1",
"jurkat.coverage.stats.txt:md5,627f0ec96ea9bdbd7f41b09b64c389d6"
],
[
"cd4_REP1.c_curve.txt:md5,cf4743abdd355595d6ec1fb3f38e66e5",
"cd4_REP1.lc_extrap.txt:md5,cbacd5a2e62bccbb73a5d0f5d0791304",
"cd4_REP2.c_curve.txt:md5,cf4743abdd355595d6ec1fb3f38e66e5",
"cd4_REP2.lc_extrap.txt:md5,cd3d0f6bc45ff35f6729fb7d66ffaf09",
"jurkat.c_curve.txt:md5,cf4743abdd355595d6ec1fb3f38e66e5",
"jurkat.lc_extrap.txt:md5,85206c3788cd2d1cede39fbd6bab5a5c"
],
[
"cd4_REP1.pos.DupRate.xls:md5,8d377e230fc1df98fd10045ed686ba2b",
"cd4_REP1.seq.DupRate.xls:md5,9d01f20cefc5a5d76c42c64715933705",
"cd4_REP2.pos.DupRate.xls:md5,6939c35f32445351210b07b17a9e424d",
"cd4_REP2.seq.DupRate.xls:md5,ef56fed7d960a88eca66d5514faed7fb",
"jurkat.pos.DupRate.xls:md5,17f5622123e0d0b97f200e53fe7e165d",
"jurkat.seq.DupRate.xls:md5,566934dad135bc0168c36a8f8d297065"
],
[
"cd4_REP1.DupRate_plot.r:md5,6b19f80622d25eab51fa5962deac7882",
"cd4_REP2.DupRate_plot.r:md5,94d0e7599e7a83a5ea2f251cb8f2b879",
"jurkat.DupRate_plot.r:md5,d081ee3f5ef5f85ff8fccd013fe04f71"
],
[
"cd4_REP1.infer_experiment.txt:md5,a17e22cdbaa5db454d3dfa0624c8acdf",
"cd4_REP2.infer_experiment.txt:md5,d705d9b2c2d8fab525df84b4c943c34a",
"jurkat.infer_experiment.txt:md5,0b4fb80f4ec8466778fa224e4f274e4e"
],
[
"cd4_REP1.read_distribution.txt:md5,1df0ae48c81e68ea1d5602897a865f2b",
"cd4_REP2.read_distribution.txt:md5,ff1b593276f36df0cbf7bbc1361e6aad",
"jurkat.read_distribution.txt:md5,a67baffde38aa7a85223148532a18ba4"
],
[
"cd4_REP1.dreg.bedGraph:md5,f48ab66b1ddaf0d1b4867183aedb670a",
"cd4_REP1.minus.bedGraph:md5,6930097f008d44b850d8bb5c681e0d1d",
"cd4_REP1.minus.bigWig:md5,a28d277b360522476ceead81b28adc7f",
"cd4_REP1.plus.bedGraph:md5,c9f9c25c6af4285d7535907e37d62793",
"cd4_REP1.plus.bigWig:md5,fb555dbbb1458d56f167660ebfa0f4f0",
"cd4_REP2.dreg.bedGraph:md5,754cbac7c960a8d3424a11f14f78ff71",
"cd4_REP2.minus.bedGraph:md5,843cdcf18dcd791a7d2030c37eb8d62f",
"cd4_REP2.minus.bigWig:md5,782c83b97ea4794f191a6ac7f9231151",
"cd4_REP2.plus.bedGraph:md5,12892778f9451ed5d3578955f14dda7e",
"cd4_REP2.plus.bigWig:md5,ef622d439b5b90bf6d0232ed2faa9ab6",
"jurkat.dreg.bedGraph:md5,01bab031eee63726446d9260f6ebd3eb",
"jurkat.minus.bedGraph:md5,529ad9cfc3f050366f54a2d99085b94b",
"jurkat.minus.bigWig:md5,f211b5371583f0e373c508ad6ab311ee",
"jurkat.plus.bedGraph:md5,2475bada8a001c763caffa12c5c0e98e",
"jurkat.plus.bigWig:md5,c30a99c3f603b268442f8b6081f6f2c9"
],
"cd4.bed:md5,c311e32ebdca7f3e978a271407de7241",
"jurkat.bed:md5,5e170e72c4e2b27a7bb0a6de7b735c1c",
"7945f971cd63ad99ff2d9cc81e19ea39",
"43982cec9077e7030428267841cf04ef",
"8813c6dd42cabd94042f4f9e4aee3560"
[
"cd4_intersect.bed:md5,d41d8cd98f00b204e9800998ecf8427e",
"jurkat_intersect.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
],
[
"cd4_filtered.bed:md5,c8bb282144d8078c0e4c809fe0878a12",
"jurkat_filtered.bed:md5,1341da464eab0ef94e921de514f46495"
],
true
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-08-03T22:17:27.92555495"
"timestamp": "2024-08-11T13:47:28.150239282"
},
"software_versions": {
"content": [
Expand All @@ -30,6 +108,6 @@
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-08-04T21:59:33.78683953"
"timestamp": "2024-08-11T13:47:28.018231429"
}
}
9 changes: 6 additions & 3 deletions workflows/tests/aligner/bwa.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,6 @@ nextflow_pipeline {
bam("$outputDir/bwa/cd4_REP4.sorted.bam").getSamLinesMD5(),
bam("$outputDir/bwa/jurkat_REP1.sorted.bam").getSamLinesMD5(),
bam("$outputDir/bwa/jurkat_REP2.sorted.bam").getSamLinesMD5(),
path("$outputDir/bwa/log").list(),
path("$outputDir/bwa/samtools_stats").list(),
path("$outputDir/quality_control/bbsplit").list(),
UTILS.getAllFilesFromDir("$outputDir/quality_control/preseq", ".txt"),
Expand All @@ -39,10 +38,14 @@ nextflow_pipeline {
path("$outputDir/coverage_graphs/").list(),
path("$outputDir/transcript_identification/homer/cd4.bed"),
path("$outputDir/transcript_identification/homer/jurkat.bed"),
// FIXME UTILS.getAllFilesFromDir("$outputDir/transcript_identification/pints/", ".bed"),
// FIXME Not determinstic because of the order of files
// Add to the other tests when fixed
// UTILS.getAllFilesFromDir("$outputDir/transcript_identification/pints/", ".bed"),
path("$outputDir/transcript_identification/intersect/").list(),
path("$outputDir/transcript_identification/filtered/").list(),
// FIXME path("$outputDir/quantification/").list(),
// FIXME Not determinstic because of the order of files
// Add to the other tests when fixed
// path("$outputDir/quantification/").list(),
path("$outputDir/multiqc/multiqc_report.html").exists(),
).match("output_files")
}
Expand Down
23 changes: 13 additions & 10 deletions workflows/tests/aligner/bwa.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -10,28 +10,31 @@
"jurkat_REP1.trimmed.fastp.json:md5,329fd8e56421a196fc2ebd37ab3bc22d",
"jurkat_REP2.trimmed.fastp.json:md5,8bad5b02a27e5386255b998a6a69db15"
],
[

],
"c529a16c839e85e119b98354f109352d",
"9e63b682af88fa902cf92b5c485845b1",
"2aa200bbbce374ec7dedb9b46ce4aae1",
"122274730dd5386e1b26c174df886a8b",
"c2adf5327ff6d4edda2fdad00c7cb9bf",
"63fea3b1e2e08e5f6fdf3f7ba0aa7818",
[
"cd4_REP1.sorted.bam.flagstat:md5,863e2d506d5cc4239af98a5f31bbc906",
"cd4_REP1.sorted.bam.idxstats:md5,b1dd8bcbd23c53c21f0e11082d9315f2",
"cd4_REP1.sorted.bam.stats:md5,ba177ae2d9a5ab5a972bc056df28acc1",
"cd4_REP1.sorted.bam.stats:md5,1536c80bae78b2062508e1de210f6387",
"cd4_REP2.sorted.bam.flagstat:md5,0fd86dbf8f799fad49ba471702979bdc",
"cd4_REP2.sorted.bam.idxstats:md5,53204e4c6a9f68664087e4a8123be46a",
"cd4_REP2.sorted.bam.stats:md5,8c8fc51169528132b1cca54d3689e3c0",
"cd4_REP2.sorted.bam.stats:md5,561610e53fb676ac83252712dcac30d4",
"cd4_REP3.sorted.bam.flagstat:md5,793c9cadbf80e35dbae3774e9b5bd93f",
"cd4_REP3.sorted.bam.idxstats:md5,42de227ff397013cf288759871b0e938",
"cd4_REP3.sorted.bam.stats:md5,fe5be813bf2d55fd0e4877c650a0b266",
"cd4_REP3.sorted.bam.stats:md5,9c8a44ba139ce9a24449779f5d3c9228",
"cd4_REP4.sorted.bam.flagstat:md5,ed6c609505097f3cc9d9902d69e016f8",
"cd4_REP4.sorted.bam.idxstats:md5,959dc185ae59de4cebe374026711a55e",
"cd4_REP4.sorted.bam.stats:md5,46bf6f2b140d369986027bc2f588b440",
"cd4_REP4.sorted.bam.stats:md5,edc57478278aa35b7376cee9afd634a7",
"jurkat_REP1.sorted.bam.flagstat:md5,fd5f02b0f02a407447b804b1d80f5421",
"jurkat_REP1.sorted.bam.idxstats:md5,c61af0847c1ad76c06a8de2815975b32",
"jurkat_REP1.sorted.bam.stats:md5,3f1b0a4214daa368a307f856f7a809dc",
"jurkat_REP1.sorted.bam.stats:md5,ce9ff516908d86fb6db6ce44d5a3904b",
"jurkat_REP2.sorted.bam.flagstat:md5,86ed47bd41a745ab59de473082c7742d",
"jurkat_REP2.sorted.bam.idxstats:md5,3db8f88c1f836eb5d10f37ca1df81ae9",
"jurkat_REP2.sorted.bam.stats:md5,48732cff30d5a9a272f68fc850b0eb84"
"jurkat_REP2.sorted.bam.stats:md5,026c558e8c36136ef19bfbef6b12ce2b"
],
[
"cd4_REP1.coverage.hist.txt:md5,7cbb473be8d3b32ff2e52fdf4e5d10d2",
Expand Down Expand Up @@ -147,7 +150,7 @@
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-08-10T12:48:55.984269469"
"timestamp": "2024-08-11T14:09:09.905409258"
},
"Should work with gzipped references": {
"content": [
Expand Down
36 changes: 17 additions & 19 deletions workflows/tests/aligner/bwamem2.nf.test
View file
Original file line number Diff line number Diff line change
Expand Up @@ -18,25 +18,23 @@ nextflow_pipeline {
{ assert snapshot(UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml")).match("software_versions") },
{ assert snapshot(
workflow.trace.tasks().size(),
path("$outputDir/bbmap").list(),
// BUG https://github.com/nf-core/nascent/issues/102
// path("$outputDir/bedtools").list(),
// FIXME gtf2bed isn't deterministic
// path("$outputDir/bwa/featurecounts/gene").list(),
// FIXME cd4 isn't deterministic
// path("$outputDir/bwa/featurecounts/predicted").list(),
// path("$outputDir/deeptools").list(),
// path("$outputDir/fastp/*.json").list(),
// FIXME gtf2bed isn't deterministic
// path("$outputDir/gtf2bed").list(),
path("$outputDir/homer/cd4.bed"),
path("$outputDir/homer/jurkat.bed"),
// FIXME https://github.com/nf-core/nascent/issues/148
// path("$outputDir/preseq").list(),
// path("$outputDir/rseqc").list(),
bam("$outputDir/samtools/cd4_REP1.sorted.bam").getSamLinesMD5(),
bam("$outputDir/samtools/cd4_REP2.sorted.bam").getSamLinesMD5(),
bam("$outputDir/samtools/jurkat.sorted.bam").getSamLinesMD5(),
UTILS.getAllFilesFromDir("$outputDir/preprocessing/fastp/", ".json"),
bam("$outputDir/bwamem2/cd4_REP1.sorted.bam").getSamLinesMD5(),
bam("$outputDir/bwamem2/cd4_REP2.sorted.bam").getSamLinesMD5(),
bam("$outputDir/bwamem2/jurkat.sorted.bam").getSamLinesMD5(),
path("$outputDir/bwamem2/samtools_stats").list(),
path("$outputDir/quality_control/bbsplit").list(),
UTILS.getAllFilesFromDir("$outputDir/quality_control/preseq", ".txt"),
path("$outputDir/quality_control/rseqc/read_duplication/xls").list(),
path("$outputDir/quality_control/rseqc/read_duplication/rscript").list(),
path("$outputDir/quality_control/rseqc/infer_experiment").list(),
path("$outputDir/quality_control/rseqc/read_distribution").list(),
path("$outputDir/coverage_graphs/").list(),
path("$outputDir/transcript_identification/homer/cd4.bed"),
path("$outputDir/transcript_identification/homer/jurkat.bed"),
path("$outputDir/transcript_identification/intersect/").list(),
path("$outputDir/transcript_identification/filtered/").list(),
path("$outputDir/multiqc/multiqc_report.html").exists(),
).match("output_files")
}
)
Expand Down
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