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update snaps
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@alanmmobbs93
alanmmobbs93 committed Dec 31, 2024
1 parent 2f204c0 commit 4822d75
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Showing 4 changed files with 257 additions and 19 deletions.
2 changes: 1 addition & 1 deletion modules/local/dream/differential/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ process DREAM_DIFFERENTIAL {
tuple val(meta), path("*.MArrayMM.dream.rds") , emit: rdata
tuple val(meta), path("*.dream.model.txt") , emit: model
tuple val(meta), path('*.dream.contrasts_plot.png') , emit: contrasts_png
//tuple val(meta), path('*.dream.var_plot.png') , emit: var_png
tuple val(meta), path('*.dream.var_plot.png') , emit: var_png
tuple val(meta), path("*.R_sessionInfo.log") , emit: session_info
tuple val(meta), path("*.normalised_counts.tsv") , emit: normalised_counts, optional: true
path "versions.yml" , emit: versions
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5 changes: 2 additions & 3 deletions modules/local/dream/differential/resources/usr/bin/dream_de.R
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Original file line number Diff line number Diff line change
Expand Up @@ -172,10 +172,9 @@ opt[vector_opt] <- lapply(strsplit(unlist(opt[vector_opt]), ","), as.numeric)
# Save first version of RData, useful for debuging with all original parameters already set
cat("Exporting preliminary RData\n")

work_dir <- getwd() ## for dev purposes
#work_dir <- "/workspace/differentialabundance/.nf-test/tests/8e59e4416c387ccf4c4422737e6af6c5/work/e6/e26f7e844ae8d4da05284db2ab2130"
work_dir <- getwd() ## for dev purposes
save.image("dream_de.RData")
#setwd(work_dir); load("dream_de.RData")
#setwd(work_dir); load("dream_de.RData") ## for dev purposes

################################################
################################################
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112 changes: 99 additions & 13 deletions modules/local/dream/differential/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -59,7 +59,7 @@
"sample_number"
]
},
"treatment_mCherry_hND6.dream.model.txt:md5,d2113d82b76046c319e6602da2ad74d6"
"treatment_mCherry_hND6.dream.model.txt:md5,17788b137dd6c2b2a8ed887aa7404f8d"
]
],
"4": [
Expand Down Expand Up @@ -89,13 +89,28 @@
"sample_number"
]
},
"treatment_mCherry_hND6.R_sessionInfo.log:md5,e591353ef3f5d63a74889d57f7ce37c6"
"treatment_mCherry_hND6.dream.var_plot.png:md5,d2b36eb27f2437140e97e47cf9fa243c"
]
],
"6": [

[
{
"id": "test-bf",
"contrast_id": "treatment_mCherry_hND6",
"contrast_variable": "treatment",
"contrast_reference": "mCherry",
"contrast_target": "hND6",
"blocking_factors": [
"sample_number"
]
},
"treatment_mCherry_hND6.R_sessionInfo.log:md5,e591353ef3f5d63a74889d57f7ce37c6"
]
],
"7": [

],
"8": [
"versions.yml:md5,56f3e82916abb64aa39ae9d008d71978"
],
"contrasts_png": [
Expand Down Expand Up @@ -140,7 +155,7 @@
"sample_number"
]
},
"treatment_mCherry_hND6.dream.model.txt:md5,d2113d82b76046c319e6602da2ad74d6"
"treatment_mCherry_hND6.dream.model.txt:md5,17788b137dd6c2b2a8ed887aa7404f8d"
]
],
"normalised_counts": [
Expand Down Expand Up @@ -191,6 +206,21 @@
"treatment_mCherry_hND6.R_sessionInfo.log:md5,e591353ef3f5d63a74889d57f7ce37c6"
]
],
"var_png": [
[
{
"id": "test-bf",
"contrast_id": "treatment_mCherry_hND6",
"contrast_variable": "treatment",
"contrast_reference": "mCherry",
"contrast_target": "hND6",
"blocking_factors": [
"sample_number"
]
},
"treatment_mCherry_hND6.dream.var_plot.png:md5,d2b36eb27f2437140e97e47cf9fa243c"
]
],
"versions": [
"versions.yml:md5,56f3e82916abb64aa39ae9d008d71978"
]
Expand All @@ -200,7 +230,7 @@
"nf-test": "0.9.2",
"nextflow": "24.10.3"
},
"timestamp": "2024-12-31T15:13:43.961604981"
"timestamp": "2024-12-31T22:35:42.737618467"
},
"Mus musculus - expression table - contrasts + blocking factors stub": {
"content": [
Expand Down Expand Up @@ -292,13 +322,28 @@
"sample_number"
]
},
"treatment_mCherry_hND6.R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e"
"treatment_mCherry_hND6.dream.var_plot.png:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"6": [

[
{
"id": "test-stub",
"contrast_id": "treatment_mCherry_hND6",
"contrast_variable": "treatment",
"contrast_reference": "mCherry",
"contrast_target": "hND6",
"blocking_factors": [
"sample_number"
]
},
"treatment_mCherry_hND6.R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"7": [

],
"8": [
"versions.yml:md5,8338b523d0f508917db713c8a0cb7fdf"
],
"contrasts_png": [
Expand Down Expand Up @@ -394,6 +439,21 @@
"treatment_mCherry_hND6.R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"var_png": [
[
{
"id": "test-stub",
"contrast_id": "treatment_mCherry_hND6",
"contrast_variable": "treatment",
"contrast_reference": "mCherry",
"contrast_target": "hND6",
"blocking_factors": [
"sample_number"
]
},
"treatment_mCherry_hND6.dream.var_plot.png:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,8338b523d0f508917db713c8a0cb7fdf"
]
Expand All @@ -403,7 +463,7 @@
"nf-test": "0.9.2",
"nextflow": "24.10.3"
},
"timestamp": "2024-12-31T15:14:06.967877527"
"timestamp": "2024-12-31T22:35:59.811030788"
},
"Mus musculus - expression table - contrasts": {
"content": [
Expand Down Expand Up @@ -457,7 +517,7 @@
"contrast_target": "hND6",
"blocking_factors": null
},
"treatment_mCherry_hND6.dream.model.txt:md5,d2113d82b76046c319e6602da2ad74d6"
"treatment_mCherry_hND6.dream.model.txt:md5,17788b137dd6c2b2a8ed887aa7404f8d"
]
],
"4": [
Expand All @@ -483,13 +543,26 @@
"contrast_target": "hND6",
"blocking_factors": null
},
"treatment_mCherry_hND6.R_sessionInfo.log:md5,e591353ef3f5d63a74889d57f7ce37c6"
"treatment_mCherry_hND6.dream.var_plot.png:md5,d2b36eb27f2437140e97e47cf9fa243c"
]
],
"6": [

[
{
"id": "test",
"contrast_id": "treatment_mCherry_hND6",
"contrast_variable": "treatment",
"contrast_reference": "mCherry",
"contrast_target": "hND6",
"blocking_factors": null
},
"treatment_mCherry_hND6.R_sessionInfo.log:md5,e591353ef3f5d63a74889d57f7ce37c6"
]
],
"7": [

],
"8": [
"versions.yml:md5,56f3e82916abb64aa39ae9d008d71978"
],
"contrasts_png": [
Expand Down Expand Up @@ -528,7 +601,7 @@
"contrast_target": "hND6",
"blocking_factors": null
},
"treatment_mCherry_hND6.dream.model.txt:md5,d2113d82b76046c319e6602da2ad74d6"
"treatment_mCherry_hND6.dream.model.txt:md5,17788b137dd6c2b2a8ed887aa7404f8d"
]
],
"normalised_counts": [
Expand Down Expand Up @@ -573,6 +646,19 @@
"treatment_mCherry_hND6.R_sessionInfo.log:md5,e591353ef3f5d63a74889d57f7ce37c6"
]
],
"var_png": [
[
{
"id": "test",
"contrast_id": "treatment_mCherry_hND6",
"contrast_variable": "treatment",
"contrast_reference": "mCherry",
"contrast_target": "hND6",
"blocking_factors": null
},
"treatment_mCherry_hND6.dream.var_plot.png:md5,d2b36eb27f2437140e97e47cf9fa243c"
]
],
"versions": [
"versions.yml:md5,56f3e82916abb64aa39ae9d008d71978"
]
Expand All @@ -582,6 +668,6 @@
"nf-test": "0.9.2",
"nextflow": "24.10.3"
},
"timestamp": "2024-12-31T15:04:49.424578334"
"timestamp": "2024-12-31T22:35:16.708141029"
}
}
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