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Sofia Stamouli
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Adress comments for md5 for kmcp, samtools
1 parent 13eddcb commit 12c9d2b

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2 files changed

+52
-52
lines changed

2 files changed

+52
-52
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‎tests/default.nf.test‎

Lines changed: 7 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -21,9 +21,11 @@ nextflow_pipeline {
2121
//BBDuk
2222
def stable_content_bbduk = getAllFilesFromDir("$outputDir/bbduk", relative: true, includeDir: false, ignore: null, ignoreFile: 'tests/.nftignore', include: ['*','**/*'])
2323

24-
//bowtie2
25-
def stable_content_bowtie2 = getAllFilesFromDir("$outputDir/bowtie2/align", relative: true, includeDir: false, ignore: null, ignoreFile: 'tests/.nftignore', include: ['*','**/*'])
24+
//bracken
25+
def stable_content_bracken = getAllFilesFromDir("$outputDir/bracken", relative: false, includeDir: false, ignore: null, ignoreFile: 'tests/.nftignore', include: ['*','**/*'])
2626

27+
//bowtie2
28+
def stable_content_bowtie2 = getAllFilesFromDir("$outputDir/bowtie2/align", relative: false, includeDir: false, ignore: null, ignoreFile: 'tests/.nftignore', include: ['*','**/*'])
2729

2830
//centrifuge
2931
def stable_content_centrifuge = getAllFilesFromDir("$outputDir/centrifuge", relative: true, includeDir: false, ignore: null, ignoreFile: 'tests/.nftignore', include: ['*','**/*'])
@@ -41,7 +43,7 @@ nextflow_pipeline {
4143
def stable_content_kraken2 = getAllFilesFromDir("$outputDir/kraken2", relative: true, includeDir: false, ignore: null, ignoreFile: 'tests/.nftignore', include: ['*','**/*'])
4244

4345
//kmcp
44-
def stable_content_kmcp = getAllFilesFromDir("$outputDir/kmcp", relative: true, includeDir: false, ignore: null, ignoreFile: 'tests/.nftignore', include: ['*','**/*'])
46+
def stable_content_kmcp = getAllFilesFromDir("$outputDir/kmcp", relative: false, includeDir: false, ignore: null, ignoreFile: 'tests/.nftignore', include: ['*','**/*'])
4547

4648
//krona
4749
def stable_content_krona = getAllFilesFromDir("$outputDir/krona", relative: true, includeDir: false, ignore: null, ignoreFile: 'tests/.nftignore', include: ['*','**/*'])
@@ -60,7 +62,7 @@ nextflow_pipeline {
6062
def stable_content_porechopabi = getAllFilesFromDir("$outputDir/porechop_abi", relative: true, includeDir: false, ignore: null, ignoreFile: 'tests/.nftignore', include: ['*','**/*'])
6163

6264
//samtools
63-
def stable_content_samtools = getAllFilesFromDir("$outputDir/samtools", relative: true, includeDir: false, ignore: null, ignoreFile: 'tests/.nftignore', include: ['*','**/*'])
65+
def stable_content_samtools = getAllFilesFromDir("$outputDir/samtools", relative: false, includeDir: false, ignore: null, ignoreFile: 'tests/.nftignore', include: ['*','**/*'])
6466

6567

6668
//taxpasta
@@ -82,7 +84,7 @@ nextflow_pipeline {
8284
{ assert snapshot( getAllFilesFromDir("$outputDir/bbduk", include: ['*.bbduk.log']).collect{file -> file.getName() + ' contains string:' + file.text.contains("Reads Processed:") },
8385
stable_content_bbduk).match("bbduk")},
8486
{ assert snapshot (stable_content_bowtie2).match("bowtie2")},
85-
{ assert snapshot (path("$outputDir/bracken")).match("bracken")},
87+
{ assert snapshot (stable_content_bracken).match("bracken")},
8688
{ assert snapshot( getAllFilesFromDir("$outputDir/centrifuge", include: ['*.txt', '**/*.txt']).collect{file -> file.getName() + ' contains string:' + (file.text.contains("Homo sapiens") || file.text.contains("unclassified")) },
8789
path("$outputDir/centrifuge/db3/2612_db3.centrifuge.mapped.fastq.gz").linesGzip.findAll { l -> l.contains('@ERR5766176.5733') },
8890
path("$outputDir/centrifuge/db3/2612_db3.centrifuge.unmapped.fastq.gz").linesGzip.findAll { l -> l.contains('@ERR5766176.191984') },

‎tests/default.nf.test.snap‎

Lines changed: 45 additions & 47 deletions
Original file line numberDiff line numberDiff line change
@@ -375,7 +375,7 @@
375375
"nf-test": "0.9.3",
376376
"nextflow": "25.04.8"
377377
},
378-
"timestamp": "2026-01-16T13:31:58.783880001"
378+
"timestamp": "2026-01-16T14:45:24.140320686"
379379
},
380380
"krona": {
381381
"content": [
@@ -400,22 +400,22 @@
400400
"nf-test": "0.9.3",
401401
"nextflow": "25.04.8"
402402
},
403-
"timestamp": "2026-01-16T13:32:08.03866791"
403+
"timestamp": "2026-01-16T14:45:33.564494384"
404404
},
405405
"bowtie2": {
406406
"content": [
407407
[
408-
"2612_ERR5766176.bowtie2.log",
409-
"2612_ERR5766176_B.bowtie2.log",
410-
"2612_ERR5766180.bowtie2.log",
411-
"2613_ERR5766181.bowtie2.log"
408+
"2612_ERR5766176.bowtie2.log:md5,9ecf931cf545c9f4777dd4586dd883d2",
409+
"2612_ERR5766176_B.bowtie2.log:md5,9ecf931cf545c9f4777dd4586dd883d2",
410+
"2612_ERR5766180.bowtie2.log:md5,a7487ce9c549a7f8fb5694fd0889f929",
411+
"2613_ERR5766181.bowtie2.log:md5,6cb148fdf3840de7a8a1f5315847817b"
412412
]
413413
],
414414
"meta": {
415415
"nf-test": "0.9.3",
416416
"nextflow": "25.04.8"
417417
},
418-
"timestamp": "2026-01-16T13:31:58.850186628"
418+
"timestamp": "2026-01-16T14:45:24.205535958"
419419
},
420420
"nanoq": {
421421
"content": [
@@ -427,23 +427,23 @@
427427
"nf-test": "0.9.3",
428428
"nextflow": "25.04.8"
429429
},
430-
"timestamp": "2026-01-16T13:32:08.113344691"
430+
"timestamp": "2026-01-16T14:45:33.652170167"
431431
},
432432
"samtools": {
433433
"content": [
434434
[
435-
"stats/2612_ERR5766176.stats",
436-
"stats/2612_ERR5766176_B.stats",
437-
"stats/2612_ERR5766180.stats",
438-
"stats/2613_ERR5766181.stats",
439-
"stats/ERR3201952_ERR3201952.stats"
435+
"2612_ERR5766176.stats:md5,14ac2eb1b383e7f9be7514ebd1a39b0f",
436+
"2612_ERR5766176_B.stats:md5,f1ab2d05e62dcafe2ac865318b6ef6bf",
437+
"2612_ERR5766180.stats:md5,73eb6b8421a3c094a3bbb6667035bf10",
438+
"2613_ERR5766181.stats:md5,d082f298244d082f095c1febb4c51ce4",
439+
"ERR3201952_ERR3201952.stats:md5,4b27072b8c9224f1eefece14d3977d27"
440440
]
441441
],
442442
"meta": {
443443
"nf-test": "0.9.3",
444444
"nextflow": "25.04.8"
445445
},
446-
"timestamp": "2026-01-16T13:32:08.215193328"
446+
"timestamp": "2026-01-16T14:45:33.754957743"
447447
},
448448
"taxpasta": {
449449
"content": [
@@ -482,7 +482,7 @@
482482
"nf-test": "0.9.3",
483483
"nextflow": "25.04.8"
484484
},
485-
"timestamp": "2026-01-16T13:32:08.275369772"
485+
"timestamp": "2026-01-16T14:45:33.817820158"
486486
},
487487
"bbduk": {
488488
"content": [
@@ -503,7 +503,7 @@
503503
"nf-test": "0.9.3",
504504
"nextflow": "25.04.8"
505505
},
506-
"timestamp": "2026-01-16T13:31:58.830127369"
506+
"timestamp": "2026-01-16T14:45:24.184668816"
507507
},
508508
"ganon": {
509509
"content": [
@@ -546,7 +546,7 @@
546546
"nf-test": "0.9.3",
547547
"nextflow": "25.04.8"
548548
},
549-
"timestamp": "2026-01-16T13:32:03.53221881"
549+
"timestamp": "2026-01-16T14:45:28.796149607"
550550
},
551551
"kaiju": {
552552
"content": [
@@ -578,27 +578,25 @@
578578
"nf-test": "0.9.3",
579579
"nextflow": "25.04.8"
580580
},
581-
"timestamp": "2026-01-16T13:32:03.924401964"
581+
"timestamp": "2026-01-16T14:45:29.195589155"
582582
},
583583
"bracken": {
584584
"content": [
585585
[
586586
"bracken_db1_combined_reports.txt:md5,b2ed57d8f683210cc0e306abdef12c3d",
587-
[
588-
"2611_db1.bracken.kraken2.report_bracken.txt:md5,2d098b8c7767c2211984028877ebf977",
589-
"2611_db1.bracken.tsv:md5,74af1e5c159628b9d746fc53be5409bf",
590-
"2612_db1.bracken.kraken2.report_bracken.txt:md5,7087bcab68e936a8a9c67caafcbd6183",
591-
"2612_db1.bracken.tsv:md5,330c1d6f98cbc6d44dec3e83d9eeccd7",
592-
"2613_db1.bracken.kraken2.report_bracken.txt:md5,56647e7054f565a9affaabd5b18b4bd8",
593-
"2613_db1.bracken.tsv:md5,751961958ba36955dc0867e314d9da8b"
594-
]
587+
"2611_db1.bracken.kraken2.report_bracken.txt:md5,2d098b8c7767c2211984028877ebf977",
588+
"2611_db1.bracken.tsv:md5,74af1e5c159628b9d746fc53be5409bf",
589+
"2612_db1.bracken.kraken2.report_bracken.txt:md5,7087bcab68e936a8a9c67caafcbd6183",
590+
"2612_db1.bracken.tsv:md5,330c1d6f98cbc6d44dec3e83d9eeccd7",
591+
"2613_db1.bracken.kraken2.report_bracken.txt:md5,56647e7054f565a9affaabd5b18b4bd8",
592+
"2613_db1.bracken.tsv:md5,751961958ba36955dc0867e314d9da8b"
595593
]
596594
],
597595
"meta": {
598596
"nf-test": "0.9.3",
599597
"nextflow": "25.04.8"
600598
},
601-
"timestamp": "2026-01-16T13:31:58.879946602"
599+
"timestamp": "2026-01-16T14:45:24.230182237"
602600
},
603601
"diamond": {
604602
"content": [
@@ -651,7 +649,7 @@
651649
"nf-test": "0.9.3",
652650
"nextflow": "25.04.8"
653651
},
654-
"timestamp": "2026-01-16T13:32:03.463774328"
652+
"timestamp": "2026-01-16T14:45:28.723437381"
655653
},
656654
"metaphlan": {
657655
"content": [
@@ -672,12 +670,12 @@
672670
"2613_metaphlan4.metaphlan.bowtie2out.txt contains string:true"
673671
],
674672
[
675-
"2611_metaphlan3.metaphlan.biom contains string:false",
676-
"2612_metaphlan3.metaphlan.biom contains string:false",
677-
"2613_metaphlan3.metaphlan.biom contains string:false",
678-
"2611_metaphlan4.metaphlan.biom contains string:false",
679-
"2612_metaphlan4.metaphlan.biom contains string:false",
680-
"2613_metaphlan4.metaphlan.biom contains string:false"
673+
"2611_metaphlan3.metaphlan_profile.txt contains string:true",
674+
"2612_metaphlan3.metaphlan_profile.txt contains string:true",
675+
"2613_metaphlan3.metaphlan_profile.txt contains string:true",
676+
"2611_metaphlan4.metaphlan_profile.txt contains string:true",
677+
"2612_metaphlan4.metaphlan_profile.txt contains string:true",
678+
"2613_metaphlan4.metaphlan_profile.txt contains string:true"
681679
],
682680
true,
683681
true,
@@ -686,8 +684,8 @@
686684
"2612_metaphlan3.metaphlan.sam:md5,1d9a386aa3f52b1013a22180bcccc9d7",
687685
"2613_metaphlan3.metaphlan.sam:md5,1d9a386aa3f52b1013a22180bcccc9d7",
688686
"2611_metaphlan4.metaphlan.sam:md5,79ac6b8433a0ce02df4895e346d9cdc8",
689-
"2612_metaphlan4.metaphlan.sam:md5,c635deb37eb51c60f69b14c017a3f7bb",
690-
"2613_metaphlan4.metaphlan.sam:md5,b811f4d9c7a1c0f5cab2d7f56f4a2d70"
687+
"2612_metaphlan4.metaphlan.sam:md5,d5ec66207c97d0906ccbc6c345ae259b",
688+
"2613_metaphlan4.metaphlan.sam:md5,8fa82d89807c6f7c8bdaa9bcb09cd3ad"
691689
],
692690
[
693691
"metaphlan3/2611_metaphlan3.metaphlan.biom",
@@ -722,7 +720,7 @@
722720
"nf-test": "0.9.3",
723721
"nextflow": "25.04.8"
724722
},
725-
"timestamp": "2026-01-16T13:32:08.08787394"
723+
"timestamp": "2026-01-16T14:45:33.624581614"
726724
},
727725
"porechop_abi": {
728726
"content": [
@@ -735,7 +733,7 @@
735733
"nf-test": "0.9.3",
736734
"nextflow": "25.04.8"
737735
},
738-
"timestamp": "2026-01-16T13:32:08.194362006"
736+
"timestamp": "2026-01-16T14:45:33.733742966"
739737
},
740738
"kraken2": {
741739
"content": [
@@ -780,7 +778,7 @@
780778
"nf-test": "0.9.3",
781779
"nextflow": "25.04.8"
782780
},
783-
"timestamp": "2026-01-16T13:32:08.014296885"
781+
"timestamp": "2026-01-16T14:45:33.537703097"
784782
},
785783
"-profile test": {
786784
"content": [
@@ -927,7 +925,7 @@
927925
"nf-test": "0.9.3",
928926
"nextflow": "25.04.8"
929927
},
930-
"timestamp": "2026-01-16T13:31:58.745973599"
928+
"timestamp": "2026-01-16T14:45:24.103777513"
931929
},
932930
"centrifuge": {
933931
"content": [
@@ -972,7 +970,7 @@
972970
"nf-test": "0.9.3",
973971
"nextflow": "25.04.8"
974972
},
975-
"timestamp": "2026-01-16T13:32:03.409857475"
973+
"timestamp": "2026-01-16T14:45:28.664173672"
976974
},
977975
"nonpareil": {
978976
"content": [
@@ -1039,21 +1037,21 @@
10391037
"nf-test": "0.9.3",
10401038
"nextflow": "25.04.8"
10411039
},
1042-
"timestamp": "2026-01-16T13:32:08.164499366"
1040+
"timestamp": "2026-01-16T14:45:33.703952743"
10431041
},
10441042
"kmcp": {
10451043
"content": [
10461044
[
1047-
"db1/2611_db1.kmcp.profile",
1048-
"db1/2612_db1.kmcp.profile",
1049-
"db1/2613_db1.kmcp.profile"
1045+
"2611_db1.kmcp.profile:md5,8b50fa20b6e60078b4e82ee56ad9a687",
1046+
"2612_db1.kmcp.profile:md5,59d06b55c1df0739e92ab6d8ce23cd83",
1047+
"2613_db1.kmcp.profile:md5,3d8c1e51679639d6011e3cb9b679485b"
10501048
]
10511049
],
10521050
"meta": {
10531051
"nf-test": "0.9.3",
10541052
"nextflow": "25.04.8"
10551053
},
1056-
"timestamp": "2026-01-16T13:32:03.946347961"
1054+
"timestamp": "2026-01-16T14:45:29.220529059"
10571055
},
10581056
"fastp": {
10591057
"content": [
@@ -1088,6 +1086,6 @@
10881086
"nf-test": "0.9.3",
10891087
"nextflow": "25.04.8"
10901088
},
1091-
"timestamp": "2026-01-16T13:32:03.496214094"
1089+
"timestamp": "2026-01-16T14:45:28.758199749"
10921090
}
10931091
}

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