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Add missing bam and flagstat files
1 parent 07e700b commit 2da70df

2 files changed

Lines changed: 58 additions & 128 deletions

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‎tests/test.nf.test‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -60,8 +60,8 @@ nextflow_pipeline {
6060
def stable_name_authentication = getAllFilesFromDir("$outputDir/authentication" , includeDir: false , ignore: null , ignoreFile: null , include: unstable_patterns_auth)
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6262
// Deduplication - TODO -> snapshot both lists are empty!?
63-
def stable_content_deduplication = getAllFilesFromDir("$outputDir/deduplication" , includeDir: false , ignore: null , ignoreFile: null , include: ['*.flagstat'] )
64-
def stable_name_deduplication = getAllFilesFromDir("$outputDir/deduplication" , includeDir: false , ignore: null , ignoreFile: null , include: ['*.{bam,bai}'] )
63+
def stable_content_deduplication = getAllFilesFromDir("$outputDir/deduplication" , includeDir: false , ignore: null , ignoreFile: null , include: ['**/*.flagstat'] )
64+
def stable_name_deduplication = getAllFilesFromDir("$outputDir/deduplication" , includeDir: false , ignore: null , ignoreFile: null , include: ['**/*.{bam,bai}'] )
6565
// def bams_deduplication = getAllFilesFromDir("$outputDir/deduplication" , includeDir: false , ignore: null , ignoreFile: null , include: ['*.bam'] )
6666

6767
// Final_bams
@@ -80,8 +80,8 @@ nextflow_pipeline {
8080
def stable_name_preprocessing = getAllFilesFromDir("$outputDir/preprocessing" , includeDir: false , ignore: null , ignoreFile: null , include: ['**/*.{zip,log,html}'] )
8181

8282
// Read filtering - TODO -> snapshot both lists are empty!?
83-
def stable_content_readfiltering = getAllFilesFromDir("$outputDir/read_filtering" , includeDir: false , ignore: null , ignoreFile: null , include: ['*.flagstat'] )
84-
def stable_name_readfiltering = getAllFilesFromDir("$outputDir/read_filtering" , includeDir: false , ignore: null , ignoreFile: null , include: ['*.{bam,bai}'] )
83+
def stable_content_readfiltering = getAllFilesFromDir("$outputDir/read_filtering" , includeDir: false , ignore: null , ignoreFile: null , include: ['**/*.flagstat'] )
84+
def stable_name_readfiltering = getAllFilesFromDir("$outputDir/read_filtering" , includeDir: false , ignore: null , ignoreFile: null , include: ['**/*.{bam,bai}'] )
8585

8686
// MQC
8787
// preprocessing

‎tests/test.nf.test.snap‎

Lines changed: 54 additions & 124 deletions
Original file line numberDiff line numberDiff line change
@@ -70,6 +70,28 @@
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"JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause.command.log",
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"JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause.c_curve.txt",
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"JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause.command.log",
73+
"JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause_dedupped.bam",
74+
"JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause_dedupped.bam.bai",
75+
"JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_dedupped.bam",
76+
"JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_dedupped.bam.bai",
77+
"JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_dedupped.bam",
78+
"JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_dedupped.bam.bai",
79+
"JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause_dedupped.flagstat",
80+
"JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_dedupped.flagstat",
81+
"JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_dedupped.flagstat",
82+
"JK2782_Mammoth_MT_Krause.bam",
83+
"JK2782_Mammoth_MT_Krause.bam.bai",
84+
"JK2802_Mammoth_MT_Krause.bam",
85+
"JK2802_Mammoth_MT_Krause.bam.bai",
86+
"JK2782_Mammoth_MT_Krause.flagstat",
87+
"JK2802_Mammoth_MT_Krause.flagstat",
88+
"JK2782_JK2782_TGGCCGATCAACGA_BAM_8_Mammoth_MT_Krause.flagstat",
89+
"JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_sorted.bam",
90+
"JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_sorted.bam.bai",
91+
"JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_sorted.bam",
92+
"JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_sorted.bam.bai",
93+
"JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_sorted.flagstat",
94+
"JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_sorted.flagstat",
7395
"agogo.css",
7496
"ajax-loader.gif",
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"basic.css",
@@ -160,28 +182,6 @@
160182
"mapped_reads_nucleotide_content.txt",
161183
"mapping_quality_across_reference.txt",
162184
"mapping_quality_histogram.txt",
163-
"JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause_dedupped.bam",
164-
"JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause_dedupped.bam.bai",
165-
"JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_dedupped.bam",
166-
"JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_dedupped.bam.bai",
167-
"JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_dedupped.bam",
168-
"JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_dedupped.bam.bai",
169-
"JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause_dedupped.flagstat",
170-
"JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_dedupped.flagstat",
171-
"JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_dedupped.flagstat",
172-
"JK2782_Mammoth_MT_Krause.bam",
173-
"JK2782_Mammoth_MT_Krause.bam.bai",
174-
"JK2802_Mammoth_MT_Krause.bam",
175-
"JK2802_Mammoth_MT_Krause.bam.bai",
176-
"JK2782_Mammoth_MT_Krause.flagstat",
177-
"JK2802_Mammoth_MT_Krause.flagstat",
178-
"JK2782_JK2782_TGGCCGATCAACGA_BAM_8_Mammoth_MT_Krause.flagstat",
179-
"JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_sorted.bam",
180-
"JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_sorted.bam.bai",
181-
"JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_sorted.bam",
182-
"JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_sorted.bam.bai",
183-
"JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_sorted.flagstat",
184-
"JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_sorted.flagstat",
185185
"fastp-insert-size-plot.txt",
186186
"fastp-seq-content-gc-plot_Merged_and_filtered.txt",
187187
"fastp-seq-content-gc-plot_Read_1_After_filtering.txt",
@@ -397,22 +397,35 @@
397397
"nf-test": "0.9.2",
398398
"nextflow": "24.10.5"
399399
},
400-
"timestamp": "2025-03-21T12:31:58.383130372"
400+
"timestamp": "2025-03-25T15:20:25.261875508"
401401
},
402402
"read_filtering": {
403403
"content": [
404404
[
405-
405+
"JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause_filtered.flagstat:md5,39fd430cc77fc71f71d75a221c1b7880",
406+
"JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_filtered.flagstat:md5,a9fbd8c9a6f8bb02b191f4140f91d04a",
407+
"JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_filtered.flagstat:md5,f6c739b729c06e17ca205c64478ad823"
406408
],
407409
[
408-
410+
"JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause_filtered.bam",
411+
"JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause_filtered.bam.bai",
412+
"JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause_lengthonly.filtered.bam",
413+
"JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause_lengthonly.filtered.bam.bai",
414+
"JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_filtered.bam",
415+
"JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_filtered.bam.bai",
416+
"JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_lengthonly.filtered.bam",
417+
"JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_lengthonly.filtered.bam.bai",
418+
"JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_filtered.bam",
419+
"JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_filtered.bam.bai",
420+
"JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_lengthonly.filtered.bam",
421+
"JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_lengthonly.filtered.bam.bai"
409422
]
410423
],
411424
"meta": {
412425
"nf-test": "0.9.2",
413-
"nextflow": "24.10.4"
426+
"nextflow": "24.10.5"
414427
},
415-
"timestamp": "2025-03-07T11:16:19.687384"
428+
"timestamp": "2025-03-25T15:20:25.630620821"
416429
},
417430
"preprocessing": {
418431
"content": [
@@ -465,17 +478,24 @@
465478
"deduplication": {
466479
"content": [
467480
[
468-
481+
"JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause_dedupped.flagstat:md5,715d840d3bab5a05934825cd9b799ef3",
482+
"JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_dedupped.flagstat:md5,dde5f59b006afdae2ff5fab85bc8ea92",
483+
"JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_dedupped.flagstat:md5,fb4d234136f242c20db27979caa604cf"
469484
],
470485
[
471-
486+
"JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause_dedupped.bam",
487+
"JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause_dedupped.bam.bai",
488+
"JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_dedupped.bam",
489+
"JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_dedupped.bam.bai",
490+
"JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_dedupped.bam",
491+
"JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_dedupped.bam.bai"
472492
]
473493
],
474494
"meta": {
475495
"nf-test": "0.9.2",
476-
"nextflow": "24.10.4"
496+
"nextflow": "24.10.5"
477497
},
478-
"timestamp": "2025-03-07T11:16:17.952993"
498+
"timestamp": "2025-03-25T15:20:25.486895792"
479499
},
480500
"multiqc": {
481501
"content": [
@@ -729,91 +749,7 @@
729749
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730750
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731751
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732-
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733-
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765-
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812-
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752+
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817753
],
818754
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819755
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@@ -842,19 +778,13 @@
842778
"Length_plot_combined_data.svg",
843779
"Length_plot_forward_reverse_separated.svg",
844780
"edit_distance.pdf",
845-
"edit_distance.svg",
846-
"genome_gc_content_per_window.png",
847-
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"qualimapReport.html",
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"mapped_reads_gc-content_distribution.txt"
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}

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