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Fix argNorm/DeepARG overwriting output #409

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merged 6 commits into from
Jul 27, 2024
Merged

Fix argNorm/DeepARG overwriting output #409

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d398116
Update modules.config + update deeparg version string
jasmezz Jul 26, 2024
21e868b
Update argnorm nf-tests
jasmezz Jul 26, 2024
30de9e7
Update changelog
jasmezz Jul 26, 2024
5fecc6a
Update changelog
jasmezz Jul 26, 2024
b8a7a49
Update argnorm nf-tests
jasmezz Jul 27, 2024
fae8879
Update md5sums (preannotated)
jasmezz Jul 27, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -38,6 +38,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#402](https://github.com/nf-core/funcscan/pull/402) Fixed BGC length calculation for antiSMASH hits by comBGC. (by @jasmezz)
- [#406](https://github.com/nf-core/funcscan/pull/406) Fixed prediction tools not being executed if annotation workflow skipped. (by @jasmezz)
- [#407](https://github.com/nf-core/funcscan/pull/407) Fixed comBGC bug when parsing multiple antiSMASH files. (by @jasmezz)
- [#409](https://github.com/nf-core/funcscan/pull/409) Fixed argNorm overwriting its output for DeepARG. (by @jasmezz, @jfy133)

### `Dependencies`

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2 changes: 1 addition & 1 deletion conf/modules.config
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Expand Up @@ -655,7 +655,7 @@ process {
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
ext.prefix = { "${meta.id}.normalized.tsv" }
ext.prefix = { input_tsv.toString().endsWith(".potential.ARG.deeparg.tsv") ? "${meta.id}.potential.ARG.normalized.tsv" : "${meta.id}.ARG.normalized.tsv" }
ext.args = "--hamronized"
}

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2 changes: 1 addition & 1 deletion subworkflows/local/arg.nf
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Expand Up @@ -151,7 +151,7 @@ workflow ARG {
// Note: currently hardcoding versions as unreported by DeepARG
// Make sure to update on version bump.
ch_input_to_hamronization_deeparg = DEEPARG_PREDICT.out.arg.mix( DEEPARG_PREDICT.out.potential_arg )
HAMRONIZATION_DEEPARG ( ch_input_to_hamronization_deeparg, 'tsv', '1.0.2', params.arg_deeparg_db_version )
HAMRONIZATION_DEEPARG ( ch_input_to_hamronization_deeparg, 'tsv', '1.0.4', params.arg_deeparg_db_version )
ch_versions = ch_versions.mix( HAMRONIZATION_DEEPARG.out.versions )
ch_input_to_hamronization_summarize = ch_input_to_hamronization_summarize.mix( HAMRONIZATION_DEEPARG.out.tsv )

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35 changes: 21 additions & 14 deletions tests/test_preannotated.nf.test
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Expand Up @@ -121,22 +121,29 @@ nextflow_pipeline {
{ assert path("$outputDir/arg/fargene/sample_3/fargene_analysis.log").text.contains("fARGene is done.") },

// hAMRonization
{ assert path("$outputDir/reports/hamronization_summarize/hamronization_combined_report.tsv").text.contains("NODE_5471_length_1861_cov_6.744186") },
{ assert snapshot(path("$outputDir/reports/hamronization_summarize/hamronization_combined_report.tsv")).match("hamronization") },

// argNorm
{ assert path("$outputDir/arg/argnorm/amrfinderplus/sample_1.normalized.tsv").text.contains("ARO:0000016") },
{ assert path("$outputDir/arg/argnorm/amrfinderplus/sample_2.normalized.tsv").text.contains("ARO:0000016") },
{ assert path("$outputDir/arg/argnorm/amrfinderplus/sample_3.normalized.tsv").text.contains("ARO:0000016") },

{ assert path("$outputDir/arg/argnorm/deeparg/sample_1.normalized.tsv").text.contains("ARO:3004054") },
{ assert path("$outputDir/arg/argnorm/deeparg/sample_2.normalized.tsv").text.contains("ARO") },
{ assert path("$outputDir/arg/argnorm/deeparg/sample_2.normalized.tsv").text.contains("confers_resistance_to") },
{ assert path("$outputDir/arg/argnorm/deeparg/sample_2.normalized.tsv").text.contains("resistance_to_drug_classes") },
{ assert path("$outputDir/arg/argnorm/deeparg/sample_3.normalized.tsv").text.contains("ARO:3000157") },

{ assert path("$outputDir/arg/argnorm/abricate/sample_1.normalized.tsv").text.contains("ARO:3000282") },
{ assert path("$outputDir/arg/argnorm/abricate/sample_2.normalized.tsv").text.contains("ARO:3000282") },
{ assert path("$outputDir/arg/argnorm/abricate/sample_3.normalized.tsv").text.contains("ARO:3000282") }
{ assert snapshot(
path("$outputDir/arg/argnorm/amrfinderplus/sample_1.normalized.tsv"),
path("$outputDir/arg/argnorm/amrfinderplus/sample_2.normalized.tsv"),
path("$outputDir/arg/argnorm/amrfinderplus/sample_3.normalized.tsv")
).match("argnorm_amrfinderplus") },

{ assert snapshot(
path("$outputDir/arg/argnorm/deeparg/sample_1.ARG.normalized.tsv"),
path("$outputDir/arg/argnorm/deeparg/sample_1.potential.ARG.normalized.tsv"),
path("$outputDir/arg/argnorm/deeparg/sample_2.ARG.normalized.tsv"),
path("$outputDir/arg/argnorm/deeparg/sample_2.potential.ARG.normalized.tsv"),
path("$outputDir/arg/argnorm/deeparg/sample_3.ARG.normalized.tsv"),
path("$outputDir/arg/argnorm/deeparg/sample_3.potential.ARG.normalized.tsv")
).match("argnorm_deeparg") },

{ assert snapshot(
path("$outputDir/arg/argnorm/abricate/sample_1.normalized.tsv"),
path("$outputDir/arg/argnorm/abricate/sample_2.normalized.tsv"),
path("$outputDir/arg/argnorm/abricate/sample_3.normalized.tsv")
).match("argnorm_abricate") }
)
}
}
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151 changes: 100 additions & 51 deletions tests/test_preannotated.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,43 +1,4 @@
{
"abricate": {
"content": [
"sample_1.txt:md5,427cec26e354ac6b0ab6047ec6621202",
"sample_2.txt:md5,4c140c932a48a22bcd8ae911bda8f4c7",
"sample_3.txt:md5,d6534efe3d03173749d003bf9e624e68"
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.3"
},
"timestamp": "2024-07-24T12:16:20.743136"
},
"fargene": {
"content": [
"results_summary.txt:md5,2c8a073d2a7938e8aedcc097e6df2aa5",
"results_summary.txt:md5,3b86a5513e89e22a4c8b9279678ce0c0",
"results_summary.txt:md5,2c8a073d2a7938e8aedcc097e6df2aa5",
"results_summary.txt:md5,59f2e69c670d72f0c0a401e0dc90cbeb",
"results_summary.txt:md5,59f2e69c670d72f0c0a401e0dc90cbeb",
"results_summary.txt:md5,59f2e69c670d72f0c0a401e0dc90cbeb"
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.3"
},
"timestamp": "2024-07-24T12:16:20.849995"
},
"rgi": {
"content": [
"sample_1.txt:md5,dde77ae2dc240ee4717d8d33a92dfb66",
"sample_2.txt:md5,0e652d35ef6e9272aa194b55db609e75",
"sample_3.txt:md5,dde77ae2dc240ee4717d8d33a92dfb66"
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.3"
},
"timestamp": "2024-07-24T12:16:20.809033"
},
"deeparg": {
"content": [
"sample_1.align.daa.tsv:md5,0e71c37318bdc6cba792196d0455293d",
Expand All @@ -51,7 +12,7 @@
"nf-test": "0.9.0",
"nextflow": "24.04.3"
},
"timestamp": "2024-07-24T12:16:20.699516"
"timestamp": "2024-07-27T08:11:24.751995878"
},
"ampir": {
"content": [
Expand All @@ -66,20 +27,31 @@
"nf-test": "0.9.0",
"nextflow": "24.04.3"
},
"timestamp": "2024-07-24T12:16:20.560802"
"timestamp": "2024-07-27T08:11:24.436374797"
},
"ampcombi": {
"argnorm_amrfinderplus": {
"content": [
"Ampcombi_cluster.log:md5,4c78f5f134edf566f39e04e3ab7d8558",
"Ampcombi_complete.log:md5,3dabfea4303bf94bd4f5d78c5b8c83c1",
true,
true
"sample_1.normalized.tsv:md5,0a7f76ceb606ac46730a51dd57290768",
"sample_2.normalized.tsv:md5,602afce3ee0ee179855c848bd87208fe",
"sample_3.normalized.tsv:md5,d4fb8fbd890217eb4d667d7a4dd80c9b"
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.3"
},
"timestamp": "2024-07-27T08:11:25.55764618"
},
"argnorm_abricate": {
"content": [
"sample_1.normalized.tsv:md5,ddd8d454672c57b798f477ca32504a42",
"sample_2.normalized.tsv:md5,0323fc890a8f698ac4b0ac25f5e65964",
"sample_3.normalized.tsv:md5,f71490c27790071bd5974ecc5502cf73"
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.3"
},
"timestamp": "2024-07-24T12:16:20.663035"
"timestamp": "2024-07-27T08:23:32.486921338"
},
"amplify": {
"content": [
Expand All @@ -91,7 +63,22 @@
"nf-test": "0.9.0",
"nextflow": "24.04.3"
},
"timestamp": "2024-07-24T12:16:20.593242"
"timestamp": "2024-07-27T08:11:24.483855968"
},
"argnorm_deeparg": {
"content": [
"sample_1.ARG.normalized.tsv:md5,26aa409bfd0fc9096f2ac404760cc492",
"sample_1.potential.ARG.normalized.tsv:md5,d6732b4b9765bfa47e27ba673e24b6a4",
"sample_2.ARG.normalized.tsv:md5,1a19b894a7315aaae5f799e4539e6619",
"sample_2.potential.ARG.normalized.tsv:md5,b241e22f9116d8f518ba8526d52ac4dc",
"sample_3.ARG.normalized.tsv:md5,d40d387176649ce80827420fef6a0169",
"sample_3.potential.ARG.normalized.tsv:md5,f331efd21ea143c180a15ae56a5210d3"
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.3"
},
"timestamp": "2024-07-27T08:23:32.446555281"
},
"macrel": {
"content": [
Expand All @@ -112,10 +99,72 @@
"sample_3.macrel_log.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"meta": {
"nf-test": "0.8.4",
"nf-test": "0.9.0",
"nextflow": "24.04.3"
},
"timestamp": "2024-07-27T08:11:24.514344973"
},
"hamronization": {
"content": [
"hamronization_combined_report.tsv:md5,bded2a60a7c2cb28ec35aa5cdcb85de5"
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.3"
},
"timestamp": "2024-07-27T08:11:25.408635625"
},
"abricate": {
"content": [
"sample_1.txt:md5,427cec26e354ac6b0ab6047ec6621202",
"sample_2.txt:md5,4c140c932a48a22bcd8ae911bda8f4c7",
"sample_3.txt:md5,d6534efe3d03173749d003bf9e624e68"
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.3"
},
"timestamp": "2024-07-27T08:11:24.87794287"
},
"fargene": {
"content": [
"results_summary.txt:md5,2c8a073d2a7938e8aedcc097e6df2aa5",
"results_summary.txt:md5,3b86a5513e89e22a4c8b9279678ce0c0",
"results_summary.txt:md5,2c8a073d2a7938e8aedcc097e6df2aa5",
"results_summary.txt:md5,59f2e69c670d72f0c0a401e0dc90cbeb",
"results_summary.txt:md5,59f2e69c670d72f0c0a401e0dc90cbeb",
"results_summary.txt:md5,59f2e69c670d72f0c0a401e0dc90cbeb"
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.3"
},
"timestamp": "2024-07-27T08:11:25.248986515"
},
"rgi": {
"content": [
"sample_1.txt:md5,dde77ae2dc240ee4717d8d33a92dfb66",
"sample_2.txt:md5,0e652d35ef6e9272aa194b55db609e75",
"sample_3.txt:md5,dde77ae2dc240ee4717d8d33a92dfb66"
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.3"
},
"timestamp": "2024-07-27T08:11:25.117843821"
},
"ampcombi": {
"content": [
"Ampcombi_cluster.log:md5,4c78f5f134edf566f39e04e3ab7d8558",
"Ampcombi_complete.log:md5,3dabfea4303bf94bd4f5d78c5b8c83c1",
true,
true
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.3"
},
"timestamp": "2024-07-24T20:37:52.576447033"
"timestamp": "2024-07-27T08:11:24.639509225"
},
"amrfinderplus": {
"content": [
Expand All @@ -127,6 +176,6 @@
"nf-test": "0.9.0",
"nextflow": "24.04.3"
},
"timestamp": "2024-07-24T12:16:20.777384"
"timestamp": "2024-07-27T08:11:24.994284774"
}
}
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