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update wcx predict (#100)
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* update wcx predict

* fix snap

* fix another snap

* update all pipeline snaps
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@nvnieuwk
nvnieuwk committed Sep 24, 2024
1 parent d0186f5 commit 8d99100
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Showing 9 changed files with 97 additions and 84 deletions.
2 changes: 1 addition & 1 deletion modules.json
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Expand Up @@ -163,7 +163,7 @@
},
"wisecondorx/predict": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "c3a2705bff298ffd2972bdb1b925b362491e2ee3",
"installed_by": ["modules"]
}
}
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4 changes: 2 additions & 2 deletions modules/nf-core/wisecondorx/predict/main.nf
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49 changes: 31 additions & 18 deletions modules/nf-core/wisecondorx/predict/meta.yml
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4 changes: 2 additions & 2 deletions modules/nf-core/wisecondorx/predict/tests/main.nf.test.snap
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42 changes: 21 additions & 21 deletions tests/pipeline/all_types/all.nf.test.snap
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Expand Up @@ -17,8 +17,8 @@
"PosCon1/PosCon1.sv.vcf.gz.tbi",
"PosCon1/PosCon1.wisecondorx_aberrations.bed",
"PosCon1/PosCon1.wisecondorx_bins.bed",
"PosCon1/PosCon1.wisecondorx_chr_statistics.txt",
"PosCon1/PosCon1.wisecondorx_segments.bed",
"PosCon1/PosCon1.wisecondorx_statistics.txt",
"PosCon1/chr1.png",
"PosCon1/chr22.png",
"PosCon1/genome_wide.png",
Expand All @@ -35,8 +35,8 @@
"PosCon2/PosCon2.sv.vcf.gz.tbi",
"PosCon2/PosCon2.wisecondorx_aberrations.bed",
"PosCon2/PosCon2.wisecondorx_bins.bed",
"PosCon2/PosCon2.wisecondorx_chr_statistics.txt",
"PosCon2/PosCon2.wisecondorx_segments.bed",
"PosCon2/PosCon2.wisecondorx_statistics.txt",
"PosCon2/chr1.png",
"PosCon2/chr22.png",
"PosCon2/genome_wide.png",
Expand All @@ -53,8 +53,8 @@
"PosCon3/PosCon3.sv.vcf.gz.tbi",
"PosCon3/PosCon3.wisecondorx_aberrations.bed",
"PosCon3/PosCon3.wisecondorx_bins.bed",
"PosCon3/PosCon3.wisecondorx_chr_statistics.txt",
"PosCon3/PosCon3.wisecondorx_segments.bed",
"PosCon3/PosCon3.wisecondorx_statistics.txt",
"PosCon3/chr1.png",
"PosCon3/chr22.png",
"PosCon3/genome_wide.png",
Expand All @@ -71,8 +71,8 @@
"PosCon4/PosCon4.sv.vcf.gz.tbi",
"PosCon4/PosCon4.wisecondorx_aberrations.bed",
"PosCon4/PosCon4.wisecondorx_bins.bed",
"PosCon4/PosCon4.wisecondorx_chr_statistics.txt",
"PosCon4/PosCon4.wisecondorx_segments.bed",
"PosCon4/PosCon4.wisecondorx_statistics.txt",
"PosCon4/chr1.png",
"PosCon4/chr22.png",
"PosCon4/genome_wide.png",
Expand All @@ -82,10 +82,10 @@
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.02.0"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-04-29T11:31:57.107814635"
"timestamp": "2024-09-24T16:41:59.329131636"
},
"concat": {
"content": [
Expand All @@ -101,8 +101,8 @@
"PosCon1/PosCon1.vcf.gz.tbi",
"PosCon1/PosCon1.wisecondorx_aberrations.bed",
"PosCon1/PosCon1.wisecondorx_bins.bed",
"PosCon1/PosCon1.wisecondorx_chr_statistics.txt",
"PosCon1/PosCon1.wisecondorx_segments.bed",
"PosCon1/PosCon1.wisecondorx_statistics.txt",
"PosCon1/chr1.png",
"PosCon1/chr22.png",
"PosCon1/genome_wide.png",
Expand All @@ -115,8 +115,8 @@
"PosCon2/PosCon2.vcf.gz.tbi",
"PosCon2/PosCon2.wisecondorx_aberrations.bed",
"PosCon2/PosCon2.wisecondorx_bins.bed",
"PosCon2/PosCon2.wisecondorx_chr_statistics.txt",
"PosCon2/PosCon2.wisecondorx_segments.bed",
"PosCon2/PosCon2.wisecondorx_statistics.txt",
"PosCon2/chr1.png",
"PosCon2/chr22.png",
"PosCon2/genome_wide.png",
Expand All @@ -129,8 +129,8 @@
"PosCon3/PosCon3.vcf.gz.tbi",
"PosCon3/PosCon3.wisecondorx_aberrations.bed",
"PosCon3/PosCon3.wisecondorx_bins.bed",
"PosCon3/PosCon3.wisecondorx_chr_statistics.txt",
"PosCon3/PosCon3.wisecondorx_segments.bed",
"PosCon3/PosCon3.wisecondorx_statistics.txt",
"PosCon3/chr1.png",
"PosCon3/chr22.png",
"PosCon3/genome_wide.png",
Expand All @@ -143,8 +143,8 @@
"PosCon4/PosCon4.vcf.gz.tbi",
"PosCon4/PosCon4.wisecondorx_aberrations.bed",
"PosCon4/PosCon4.wisecondorx_bins.bed",
"PosCon4/PosCon4.wisecondorx_chr_statistics.txt",
"PosCon4/PosCon4.wisecondorx_segments.bed",
"PosCon4/PosCon4.wisecondorx_statistics.txt",
"PosCon4/chr1.png",
"PosCon4/chr22.png",
"PosCon4/genome_wide.png",
Expand All @@ -154,10 +154,10 @@
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.02.0"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-04-29T11:33:35.756593527"
"timestamp": "2024-09-24T16:43:30.360357399"
},
"output callers": {
"content": [
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"PosCon1/wisecondorx/PosCon1.wisecondorx.vcf.gz.tbi",
"PosCon1/wisecondorx/PosCon1.wisecondorx_aberrations.bed",
"PosCon1/wisecondorx/PosCon1.wisecondorx_bins.bed",
"PosCon1/wisecondorx/PosCon1.wisecondorx_chr_statistics.txt",
"PosCon1/wisecondorx/PosCon1.wisecondorx_segments.bed",
"PosCon1/wisecondorx/PosCon1.wisecondorx_statistics.txt",
"PosCon1/wisecondorx/chr1.png",
"PosCon1/wisecondorx/chr22.png",
"PosCon1/wisecondorx/genome_wide.png",
Expand Down Expand Up @@ -222,8 +222,8 @@
"PosCon2/wisecondorx/PosCon2.wisecondorx.vcf.gz.tbi",
"PosCon2/wisecondorx/PosCon2.wisecondorx_aberrations.bed",
"PosCon2/wisecondorx/PosCon2.wisecondorx_bins.bed",
"PosCon2/wisecondorx/PosCon2.wisecondorx_chr_statistics.txt",
"PosCon2/wisecondorx/PosCon2.wisecondorx_segments.bed",
"PosCon2/wisecondorx/PosCon2.wisecondorx_statistics.txt",
"PosCon2/wisecondorx/chr1.png",
"PosCon2/wisecondorx/chr22.png",
"PosCon2/wisecondorx/genome_wide.png",
Expand Down Expand Up @@ -253,8 +253,8 @@
"PosCon3/wisecondorx/PosCon3.wisecondorx.vcf.gz.tbi",
"PosCon3/wisecondorx/PosCon3.wisecondorx_aberrations.bed",
"PosCon3/wisecondorx/PosCon3.wisecondorx_bins.bed",
"PosCon3/wisecondorx/PosCon3.wisecondorx_chr_statistics.txt",
"PosCon3/wisecondorx/PosCon3.wisecondorx_segments.bed",
"PosCon3/wisecondorx/PosCon3.wisecondorx_statistics.txt",
"PosCon3/wisecondorx/chr1.png",
"PosCon3/wisecondorx/chr22.png",
"PosCon3/wisecondorx/genome_wide.png",
Expand Down Expand Up @@ -284,8 +284,8 @@
"PosCon4/wisecondorx/PosCon4.wisecondorx.vcf.gz.tbi",
"PosCon4/wisecondorx/PosCon4.wisecondorx_aberrations.bed",
"PosCon4/wisecondorx/PosCon4.wisecondorx_bins.bed",
"PosCon4/wisecondorx/PosCon4.wisecondorx_chr_statistics.txt",
"PosCon4/wisecondorx/PosCon4.wisecondorx_segments.bed",
"PosCon4/wisecondorx/PosCon4.wisecondorx_statistics.txt",
"PosCon4/wisecondorx/chr1.png",
"PosCon4/wisecondorx/chr22.png",
"PosCon4/wisecondorx/genome_wide.png",
Expand All @@ -294,9 +294,9 @@
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.02.0"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-04-29T11:47:12.295054901"
"timestamp": "2024-09-24T16:45:01.53178248"
}
}
14 changes: 7 additions & 7 deletions tests/pipeline/cnv/cnv.nf.test.snap
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Expand Up @@ -14,8 +14,8 @@
"PosCon1.qdnaseq_segments.txt",
"PosCon1.wisecondorx_aberrations.bed",
"PosCon1.wisecondorx_bins.bed",
"PosCon1.wisecondorx_chr_statistics.txt",
"PosCon1.wisecondorx_segments.bed",
"PosCon1.wisecondorx_statistics.txt",
"chr1.png",
"chr22.png",
"genome_wide.png",
Expand All @@ -30,8 +30,8 @@
"PosCon2.qdnaseq_segments.txt",
"PosCon2.wisecondorx_aberrations.bed",
"PosCon2.wisecondorx_bins.bed",
"PosCon2.wisecondorx_chr_statistics.txt",
"PosCon2.wisecondorx_segments.bed",
"PosCon2.wisecondorx_statistics.txt",
"chr1.png",
"chr22.png",
"genome_wide.png",
Expand All @@ -46,8 +46,8 @@
"PosCon3.qdnaseq_segments.txt",
"PosCon3.wisecondorx_aberrations.bed",
"PosCon3.wisecondorx_bins.bed",
"PosCon3.wisecondorx_chr_statistics.txt",
"PosCon3.wisecondorx_segments.bed",
"PosCon3.wisecondorx_statistics.txt",
"chr1.png",
"chr22.png",
"genome_wide.png",
Expand All @@ -62,8 +62,8 @@
"PosCon4.qdnaseq_segments.txt",
"PosCon4.wisecondorx_aberrations.bed",
"PosCon4.wisecondorx_bins.bed",
"PosCon4.wisecondorx_chr_statistics.txt",
"PosCon4.wisecondorx_segments.bed",
"PosCon4.wisecondorx_statistics.txt",
"chr1.png",
"chr22.png",
"genome_wide.png",
Expand All @@ -85,10 +85,10 @@
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.02.0"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-03-13T11:31:18.794715638"
"timestamp": "2024-09-24T15:39:21.55695905"
},
"qdnaseq": {
"content": [
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10 changes: 5 additions & 5 deletions tests/pipeline/duplicates/duplicates.nf.test.snap
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Expand Up @@ -14,8 +14,8 @@
"PosCon1.sv.vcf.gz.tbi",
"PosCon1.wisecondorx_aberrations.bed",
"PosCon1.wisecondorx_bins.bed",
"PosCon1.wisecondorx_chr_statistics.txt",
"PosCon1.wisecondorx_segments.bed",
"PosCon1.wisecondorx_statistics.txt",
"chr1.png",
"chr22.png",
"genome_wide.png"
Expand All @@ -29,8 +29,8 @@
"PosCon3.sv.vcf.gz.tbi",
"PosCon3.wisecondorx_aberrations.bed",
"PosCon3.wisecondorx_bins.bed",
"PosCon3.wisecondorx_chr_statistics.txt",
"PosCon3.wisecondorx_segments.bed",
"PosCon3.wisecondorx_statistics.txt",
"chr1.png",
"chr22.png",
"genome_wide.png"
Expand All @@ -49,9 +49,9 @@
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.02.0"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-03-29T10:27:33.692986213"
"timestamp": "2024-09-24T16:47:37.185956628"
}
}
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