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Fix: Convert bcf_annotations.tbi from empty() to value channel to prevent stalling #1624

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merged 5 commits into from
Nov 17, 2024
Merged

Fix: Convert bcf_annotations.tbi from empty() to value channel to prevent stalling #1624

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514c81a
Fixes bug
bounlu Aug 16, 2024
1542401
Change to value channel
bounlu Aug 16, 2024
b7077d0
Merge remote-tracking branch 'origin/dev' into bounlu-patch-2
FriederikeHanssen Nov 15, 2024
2a04239
fix changelog
FriederikeHanssen Nov 15, 2024
15809f7
remove variable checksums from snapshots
FriederikeHanssen Nov 15, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -33,6 +33,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### Fixed

- [1624](https://github.com/nf-core/sarek/pull/1624) - Fix channel stalling for bcftools index
- [1657](https://github.com/nf-core/sarek/pull/1657) - Update all actions used in the GHA CI
- [1661](https://github.com/nf-core/sarek/pull/1661) - nf-test pipeline level tests
- [1673](https://github.com/nf-core/sarek/pull/1673) - Print warning message instead of silent error with Nextflow versions prior to 24.08.0edge
Expand Down
2 changes: 1 addition & 1 deletion main.nf
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Expand Up @@ -176,7 +176,7 @@ workflow NFCORE_SAREK {
rt_file = PREPARE_GENOME.out.rt_file

// Tabix indexed vcf files
bcftools_annotations_tbi = params.bcftools_annotations ? params.bcftools_annotations_tbi ? Channel.fromPath(params.bcftools_annotations_tbi).collect() : PREPARE_GENOME.out.bcftools_annotations_tbi : Channel.empty([])
bcftools_annotations_tbi = params.bcftools_annotations ? params.bcftools_annotations_tbi ? Channel.fromPath(params.bcftools_annotations_tbi).collect() : PREPARE_GENOME.out.bcftools_annotations_tbi : Channel.value([])
dbsnp_tbi = params.dbsnp ? params.dbsnp_tbi ? Channel.fromPath(params.dbsnp_tbi).collect() : PREPARE_GENOME.out.dbsnp_tbi : Channel.value([])
germline_resource_tbi = params.germline_resource ? params.germline_resource_tbi ? Channel.fromPath(params.germline_resource_tbi).collect() : PREPARE_GENOME.out.germline_resource_tbi : [] //do not change to Channel.value([]), the check for its existence then fails for Getpileupsumamries
known_indels_tbi = params.known_indels ? params.known_indels_tbi ? Channel.fromPath(params.known_indels_tbi).collect() : PREPARE_GENOME.out.known_indels_tbi : Channel.value([])
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58 changes: 21 additions & 37 deletions tests/variant_calling_strelka.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -160,7 +160,6 @@
"multiqc_bcftools_stats.txt:md5,b2bbb90ef05598e1a70cf36be416c3e2",
"multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86",
"vcftools_tstv_by_count.txt:md5,d4fdc9722fec46722bda2d04be6801d0",
"vcftools_tstv_by_qual.txt:md5,03c5d703ba275136e3b5e2c98488dacc",
"sample1.strelka.variants.bcftools_stats.txt:md5,2936f10f99295fb772d8c35f246e223d",
"sample4_vs_sample3.strelka.somatic_indels.bcftools_stats.txt:md5,1c57e5cd6424157536276002ef1a58d6",
"sample4_vs_sample3.strelka.somatic_snvs.bcftools_stats.txt:md5,8cf6d0b3f41436cd2f2aa09c9831764d",
Expand Down Expand Up @@ -190,23 +189,20 @@
"sample4.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
"sample1.strelka.variants.FILTER.summary:md5,fef8aeadd3b0f3b8c040c0da03bf1cbd",
"sample1.strelka.variants.TsTv.count:md5,c5b7a8eda2526d899098439ae4c06a49",
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"sample4_vs_sample3.strelka.somatic_indels.TsTv.count:md5,8dcfdbcaac118df1d5ad407dd2af699f",
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"sample4_vs_sample3.strelka.somatic_snvs.TsTv.count:md5,fc7af1f534890c4ad3025588b3af62ae",
"sample4_vs_sample3.strelka.somatic_snvs.TsTv.qual:md5,75af7d1b1e5a2f1bdfe5b530e37a6cbb"
"sample4_vs_sample3.strelka.somatic_snvs.TsTv.count:md5,fc7af1f534890c4ad3025588b3af62ae"
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"timestamp": "2024-11-15T22:22:40.803241819"
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"Run with profile test | --tools strelka --no_intervals | somatic": {
"content": [
Expand Down Expand Up @@ -356,7 +352,6 @@
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"multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86",
"vcftools_tstv_by_count.txt:md5,4244903e90d55bc6cd0cb9f6efcd8a80",
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"sample3.strelka.variants.bcftools_stats.txt:md5,c75a458b1aa0e1bae3b667d48684e13c",
"sample4_vs_sample3.strelka.somatic_indels.bcftools_stats.txt:md5,1c57e5cd6424157536276002ef1a58d6",
"sample4_vs_sample3.strelka.somatic_snvs.bcftools_stats.txt:md5,110810e5702ef11bc002bd0948dbdfff",
Expand All @@ -374,23 +369,20 @@
"sample4.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
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"timestamp": "2024-11-15T22:29:05.475529758"
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"Run with profile test | --tools strelka | somatic": {
"content": [
Expand Down Expand Up @@ -537,7 +529,6 @@
"multiqc_bcftools_stats.txt:md5,c2674bda60d8fa805601c436afe16f18",
"multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86",
"vcftools_tstv_by_count.txt:md5,3888b9a69fdeaf6667dcc600ff776413",
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"sample3.strelka.variants.bcftools_stats.txt:md5,d505d381e8c3906788e4135bb975ff84",
"sample4_vs_sample3.strelka.somatic_indels.bcftools_stats.txt:md5,1c57e5cd6424157536276002ef1a58d6",
"sample4_vs_sample3.strelka.somatic_snvs.bcftools_stats.txt:md5,8cf6d0b3f41436cd2f2aa09c9831764d",
Expand All @@ -555,23 +546,20 @@
"sample4.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
"sample3.strelka.variants.FILTER.summary:md5,fef8aeadd3b0f3b8c040c0da03bf1cbd",
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"timestamp": "2024-10-29T14:29:18.353277"
"timestamp": "2024-11-15T22:27:18.76415046"
},
"Run with profile test | --tools strelka | germline": {
"content": [
Expand Down Expand Up @@ -687,7 +675,6 @@
"multiqc_bcftools_stats.txt:md5,cde557db5eb46f8325c06e9bb32e7a94",
"multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86",
"vcftools_tstv_by_count.txt:md5,69cbd9060c01c1102ddf5839ee7b404a",
"vcftools_tstv_by_qual.txt:md5,6973bf3d8488aa52d64933412f0556df",
"sample1.strelka.variants.bcftools_stats.txt:md5,2936f10f99295fb772d8c35f246e223d",
"sample1.recal.mosdepth.global.dist.txt:md5,d9a4dd6429560b2b647da346050766c5",
"sample1.recal.mosdepth.region.dist.txt:md5,1f3dab381958e08eb00f7c5e1135f677",
Expand All @@ -696,18 +683,17 @@
"sample1.recal.regions.bed.gz.csi:md5,f17cc9d960aa4a1e96548d570585cc8a",
"sample1.recal.cram.stats:md5,bcc229318527e414e69aaa5cd092ad9b",
"sample1.strelka.variants.FILTER.summary:md5,fef8aeadd3b0f3b8c040c0da03bf1cbd",
"sample1.strelka.variants.TsTv.count:md5,c5b7a8eda2526d899098439ae4c06a49",
"sample1.strelka.variants.TsTv.qual:md5,f01534408c3a87893b523de5f39deb0b"
"sample1.strelka.variants.TsTv.count:md5,c5b7a8eda2526d899098439ae4c06a49"
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"nf-test": "0.9.0",
"nextflow": "24.10.0"
},
"timestamp": "2024-10-29T14:25:18.773706"
"timestamp": "2024-11-15T22:24:13.636617483"
},
"Run with profile test | --tools strelka --no_intervals | germline": {
"content": [
Expand Down Expand Up @@ -826,7 +812,6 @@
"multiqc_bcftools_stats.txt:md5,23c19e033f3086bec87c5e2022795e79",
"multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86",
"vcftools_tstv_by_count.txt:md5,ea99842f730543b5fd1a08d0e1d68278",
"vcftools_tstv_by_qual.txt:md5,a603c008a52ffd0297aa420743fbdc8d",
"sample1.strelka.variants.bcftools_stats.txt:md5,0e829f5d31d768a8e99786786282c9ef",
"sample1.recal.mosdepth.global.dist.txt:md5,d9a4dd6429560b2b647da346050766c5",
"sample1.recal.mosdepth.region.dist.txt:md5,1f3dab381958e08eb00f7c5e1135f677",
Expand All @@ -835,17 +820,16 @@
"sample1.recal.regions.bed.gz.csi:md5,f17cc9d960aa4a1e96548d570585cc8a",
"sample1.recal.cram.stats:md5,bcc229318527e414e69aaa5cd092ad9b",
"sample1.strelka.variants.FILTER.summary:md5,8697a0a983314e98b99b5f6038af65f6",
"sample1.strelka.variants.TsTv.count:md5,1481854d2a765f5641856ecf95ca4097",
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"timestamp": "2024-10-29T14:27:06.859001"
"timestamp": "2024-11-15T22:25:42.940353635"
}
}
}
32 changes: 9 additions & 23 deletions tests/variant_calling_strelka_bp.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -180,7 +180,6 @@
"multiqc_bcftools_stats.txt:md5,5c9c75a7ba51eec6d7ed539a5d0a2397",
"multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86",
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"sample3.manta.diploid_sv.bcftools_stats.txt:md5,8adad91e1c8dc8db63cf9b3607bee3a0",
"sample4_vs_sample3.manta.diploid_sv.bcftools_stats.txt:md5,17dc847445b98885bc18622f862f44d9",
"sample4_vs_sample3.manta.somatic_sv.bcftools_stats.txt:md5,a8660b352950f0b32768fcbbd6b48896",
Expand All @@ -201,32 +200,26 @@
"sample4.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
"sample3.manta.diploid_sv.FILTER.summary:md5,1ce42d34e4ae919afb519efc99146423",
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"timestamp": "2024-11-15T22:39:15.50268779"
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"Run with profile test | --tools manta,strelka | somatic": {
"content": [
Expand Down Expand Up @@ -406,7 +399,6 @@
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Expand All @@ -427,31 +419,25 @@
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},
"timestamp": "2024-10-29T14:36:40.89285"
"timestamp": "2024-11-15T22:37:23.231917992"
}
}
}
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