Skip to content

Commit bdcd760

Browse files
pinin4fjordspinin4fjords
committed
Update UMI test
1 parent cd97229 commit bdcd760

File tree

2 files changed

+97
-27
lines changed

2 files changed

+97
-27
lines changed

‎tests/umi.nf.test‎

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -14,7 +14,9 @@ nextflow_pipeline {
1414
skip_bbsplit = true
1515
umi_dedup_tool = 'umicollapse'
1616
aligner = 'hisat2'
17+
publish_dir_mode = 'link'
1718
outdir = "$outputDir"
19+
save_umi_intermeds = true
1820
}
1921
}
2022

‎tests/umi.nf.test.snap‎

Lines changed: 95 additions & 27 deletions
Original file line numberDiff line numberDiff line change
@@ -612,6 +612,10 @@
612612
"star_salmon/RAP1_IAA_30M_REP1",
613613
"star_salmon/RAP1_IAA_30M_REP1.umi_dedup.sorted.bam",
614614
"star_salmon/RAP1_IAA_30M_REP1.umi_dedup.sorted.bam.bai",
615+
"star_salmon/RAP1_IAA_30M_REP1.umi_dedup.transcriptome.bam",
616+
"star_salmon/RAP1_IAA_30M_REP1.umi_dedup.transcriptome.filtered.bam",
617+
"star_salmon/RAP1_IAA_30M_REP1.umi_dedup.transcriptome.sorted.bam",
618+
"star_salmon/RAP1_IAA_30M_REP1.umi_dedup.transcriptome.sorted.bam.bai",
615619
"star_salmon/RAP1_IAA_30M_REP1/aux_info",
616620
"star_salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv",
617621
"star_salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz",
@@ -629,6 +633,9 @@
629633
"star_salmon/RAP1_UNINDUCED_REP1",
630634
"star_salmon/RAP1_UNINDUCED_REP1.umi_dedup.sorted.bam",
631635
"star_salmon/RAP1_UNINDUCED_REP1.umi_dedup.sorted.bam.bai",
636+
"star_salmon/RAP1_UNINDUCED_REP1.umi_dedup.transcriptome.bam",
637+
"star_salmon/RAP1_UNINDUCED_REP1.umi_dedup.transcriptome.sorted.bam",
638+
"star_salmon/RAP1_UNINDUCED_REP1.umi_dedup.transcriptome.sorted.bam.bai",
632639
"star_salmon/RAP1_UNINDUCED_REP1/aux_info",
633640
"star_salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv",
634641
"star_salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz",
@@ -646,6 +653,9 @@
646653
"star_salmon/RAP1_UNINDUCED_REP2",
647654
"star_salmon/RAP1_UNINDUCED_REP2.umi_dedup.sorted.bam",
648655
"star_salmon/RAP1_UNINDUCED_REP2.umi_dedup.sorted.bam.bai",
656+
"star_salmon/RAP1_UNINDUCED_REP2.umi_dedup.transcriptome.bam",
657+
"star_salmon/RAP1_UNINDUCED_REP2.umi_dedup.transcriptome.sorted.bam",
658+
"star_salmon/RAP1_UNINDUCED_REP2.umi_dedup.transcriptome.sorted.bam.bai",
649659
"star_salmon/RAP1_UNINDUCED_REP2/aux_info",
650660
"star_salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv",
651661
"star_salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz",
@@ -663,6 +673,10 @@
663673
"star_salmon/WT_REP1",
664674
"star_salmon/WT_REP1.umi_dedup.sorted.bam",
665675
"star_salmon/WT_REP1.umi_dedup.sorted.bam.bai",
676+
"star_salmon/WT_REP1.umi_dedup.transcriptome.bam",
677+
"star_salmon/WT_REP1.umi_dedup.transcriptome.filtered.bam",
678+
"star_salmon/WT_REP1.umi_dedup.transcriptome.sorted.bam",
679+
"star_salmon/WT_REP1.umi_dedup.transcriptome.sorted.bam.bai",
666680
"star_salmon/WT_REP1/aux_info",
667681
"star_salmon/WT_REP1/aux_info/ambig_info.tsv",
668682
"star_salmon/WT_REP1/aux_info/expected_bias.gz",
@@ -680,6 +694,10 @@
680694
"star_salmon/WT_REP2",
681695
"star_salmon/WT_REP2.umi_dedup.sorted.bam",
682696
"star_salmon/WT_REP2.umi_dedup.sorted.bam.bai",
697+
"star_salmon/WT_REP2.umi_dedup.transcriptome.bam",
698+
"star_salmon/WT_REP2.umi_dedup.transcriptome.filtered.bam",
699+
"star_salmon/WT_REP2.umi_dedup.transcriptome.sorted.bam",
700+
"star_salmon/WT_REP2.umi_dedup.transcriptome.sorted.bam.bai",
683701
"star_salmon/WT_REP2/aux_info",
684702
"star_salmon/WT_REP2/aux_info/ambig_info.tsv",
685703
"star_salmon/WT_REP2/aux_info/expected_bias.gz",
@@ -1261,10 +1279,18 @@
12611279
"trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt",
12621280
"umitools",
12631281
"umitools/RAP1_IAA_30M_REP1.umi_extract.log",
1282+
"umitools/RAP1_IAA_30M_REP1.umi_extract_1.fastq.gz",
1283+
"umitools/RAP1_IAA_30M_REP1.umi_extract_2.fastq.gz",
1284+
"umitools/RAP1_UNINDUCED_REP1.umi_extract.fastq.gz",
12641285
"umitools/RAP1_UNINDUCED_REP1.umi_extract.log",
1286+
"umitools/RAP1_UNINDUCED_REP2.umi_extract.fastq.gz",
12651287
"umitools/RAP1_UNINDUCED_REP2.umi_extract.log",
12661288
"umitools/WT_REP1.umi_extract.log",
1267-
"umitools/WT_REP2.umi_extract.log"
1289+
"umitools/WT_REP1.umi_extract_1.fastq.gz",
1290+
"umitools/WT_REP1.umi_extract_2.fastq.gz",
1291+
"umitools/WT_REP2.umi_extract.log",
1292+
"umitools/WT_REP2.umi_extract_1.fastq.gz",
1293+
"umitools/WT_REP2.umi_extract_2.fastq.gz"
12681294
],
12691295
[
12701296
"genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055",
@@ -1467,14 +1493,22 @@
14671493
"WT_REP2.umi_dedup.sorted_per_umi_per_position.tsv:md5,6f5656947a7f0076df446e6f40430027",
14681494
"WT_REP2.umi_dedup.transcriptome.sorted_edit_distance.tsv:md5,3e3c6a7e8996e566350742e9911366d3",
14691495
"WT_REP2.umi_dedup.transcriptome.sorted_per_umi.tsv:md5,0c986c4cb7a77f650a19e2c454b9b179",
1470-
"WT_REP2.umi_dedup.transcriptome.sorted_per_umi_per_position.tsv:md5,af9028dbdab81de3854a32cd1d19ac8b"
1496+
"WT_REP2.umi_dedup.transcriptome.sorted_per_umi_per_position.tsv:md5,af9028dbdab81de3854a32cd1d19ac8b",
1497+
"RAP1_IAA_30M_REP1.umi_extract_1.fastq.gz:md5,e83d7f738fbbfaa541a2e71fe4663447",
1498+
"RAP1_IAA_30M_REP1.umi_extract_2.fastq.gz:md5,4f2873cbf584d6e84187238a4ae2b8fa",
1499+
"RAP1_UNINDUCED_REP1.umi_extract.fastq.gz:md5,9e42242fd68baac592140f63a8a716ce",
1500+
"RAP1_UNINDUCED_REP2.umi_extract.fastq.gz:md5,5a92b642927b8603c4765e5305e23e9c",
1501+
"WT_REP1.umi_extract_1.fastq.gz:md5,f312fac9c384a889ae4f959839263604",
1502+
"WT_REP1.umi_extract_2.fastq.gz:md5,ffca24924108fd54151620b7538b9e1a",
1503+
"WT_REP2.umi_extract_1.fastq.gz:md5,c3180451a24ce51fc35c1684521ae287",
1504+
"WT_REP2.umi_extract_2.fastq.gz:md5,067ff23f8d1307ad241cd70bc186b5c1"
14711505
]
14721506
],
14731507
"meta": {
1474-
"nf-test": "0.9.0",
1475-
"nextflow": "24.10.2"
1508+
"nf-test": "0.9.2",
1509+
"nextflow": "24.10.3"
14761510
},
1477-
"timestamp": "2024-12-11T18:07:55.751564456"
1511+
"timestamp": "2024-12-19T21:54:27.627773754"
14781512
},
14791513
"Params: --aligner hisat2 --umi_dedup_tool 'umicollapse'": {
14801514
"content": [
@@ -2130,13 +2164,13 @@
21302164
"hisat2/stringtie/WT_REP2.coverage.gtf",
21312165
"hisat2/stringtie/WT_REP2.gene.abundance.txt",
21322166
"hisat2/stringtie/WT_REP2.transcripts.gtf",
2133-
"hisat2/umitools",
2134-
"hisat2/umitools/genomic_dedup_log",
2135-
"hisat2/umitools/genomic_dedup_log/RAP1_IAA_30M_REP1.umi_dedup.sorted_UMICollapse.log",
2136-
"hisat2/umitools/genomic_dedup_log/RAP1_UNINDUCED_REP1.umi_dedup.sorted_UMICollapse.log",
2137-
"hisat2/umitools/genomic_dedup_log/RAP1_UNINDUCED_REP2.umi_dedup.sorted_UMICollapse.log",
2138-
"hisat2/umitools/genomic_dedup_log/WT_REP1.umi_dedup.sorted_UMICollapse.log",
2139-
"hisat2/umitools/genomic_dedup_log/WT_REP2.umi_dedup.sorted_UMICollapse.log",
2167+
"hisat2/umicollapse",
2168+
"hisat2/umicollapse/genomic_dedup_log",
2169+
"hisat2/umicollapse/genomic_dedup_log/RAP1_IAA_30M_REP1.umi_dedup.sorted_UMICollapse.log",
2170+
"hisat2/umicollapse/genomic_dedup_log/RAP1_UNINDUCED_REP1.umi_dedup.sorted_UMICollapse.log",
2171+
"hisat2/umicollapse/genomic_dedup_log/RAP1_UNINDUCED_REP2.umi_dedup.sorted_UMICollapse.log",
2172+
"hisat2/umicollapse/genomic_dedup_log/WT_REP1.umi_dedup.sorted_UMICollapse.log",
2173+
"hisat2/umicollapse/genomic_dedup_log/WT_REP2.umi_dedup.sorted_UMICollapse.log",
21402174
"multiqc",
21412175
"multiqc/hisat2",
21422176
"multiqc/hisat2/multiqc_report.html",
@@ -2548,10 +2582,18 @@
25482582
"trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt",
25492583
"umitools",
25502584
"umitools/RAP1_IAA_30M_REP1.umi_extract.log",
2585+
"umitools/RAP1_IAA_30M_REP1.umi_extract_1.fastq.gz",
2586+
"umitools/RAP1_IAA_30M_REP1.umi_extract_2.fastq.gz",
2587+
"umitools/RAP1_UNINDUCED_REP1.umi_extract.fastq.gz",
25512588
"umitools/RAP1_UNINDUCED_REP1.umi_extract.log",
2589+
"umitools/RAP1_UNINDUCED_REP2.umi_extract.fastq.gz",
25522590
"umitools/RAP1_UNINDUCED_REP2.umi_extract.log",
25532591
"umitools/WT_REP1.umi_extract.log",
2554-
"umitools/WT_REP2.umi_extract.log"
2592+
"umitools/WT_REP1.umi_extract_1.fastq.gz",
2593+
"umitools/WT_REP1.umi_extract_2.fastq.gz",
2594+
"umitools/WT_REP2.umi_extract.log",
2595+
"umitools/WT_REP2.umi_extract_1.fastq.gz",
2596+
"umitools/WT_REP2.umi_extract_2.fastq.gz"
25552597
],
25562598
[
25572599
"genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055",
@@ -2621,6 +2663,11 @@
26212663
"e_data.ctab:md5,593daf0b84f008c0c64319990ef2fd42",
26222664
"i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b",
26232665
"i_data.ctab:md5,01c675638f918a70ea689f618a2610bc",
2666+
"RAP1_IAA_30M_REP1.umi_dedup.sorted_UMICollapse.log:md5,d6eaaabd7053bef88f3af2b6fc2df45b",
2667+
"RAP1_UNINDUCED_REP1.umi_dedup.sorted_UMICollapse.log:md5,441be871ac12aa94f871fab9e8b6b4bf",
2668+
"RAP1_UNINDUCED_REP2.umi_dedup.sorted_UMICollapse.log:md5,8a0025a58969badeb3dc35a7c1bdd68e",
2669+
"WT_REP1.umi_dedup.sorted_UMICollapse.log:md5,75e6da19996c3ea6fde5cdd4be2dcfda",
2670+
"WT_REP2.umi_dedup.sorted_UMICollapse.log:md5,87cdd1eadc3db19bd9f45bb941b1e1a7",
26242671
"cutadapt_filtered_reads_plot.txt:md5,3f122969fa288888e5abef061b7963f2",
26252672
"cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,5e8a821c9a4deb46c11bc65969b8864f",
26262673
"cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,bf8abefa7c5f2f1e1140749983279d9d",
@@ -2688,22 +2735,27 @@
26882735
"cmd_info.json:md5,809380ddce725a8fab75dd7741b64bf6",
26892736
"lib_format_counts.json:md5,d231ba7624b67eb654989f69530e2925",
26902737
"R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676",
2691-
"tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe"
2738+
"tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe",
2739+
"RAP1_IAA_30M_REP1.umi_extract_1.fastq.gz:md5,e83d7f738fbbfaa541a2e71fe4663447",
2740+
"RAP1_IAA_30M_REP1.umi_extract_2.fastq.gz:md5,4f2873cbf584d6e84187238a4ae2b8fa",
2741+
"RAP1_UNINDUCED_REP1.umi_extract.fastq.gz:md5,9e42242fd68baac592140f63a8a716ce",
2742+
"RAP1_UNINDUCED_REP2.umi_extract.fastq.gz:md5,5a92b642927b8603c4765e5305e23e9c",
2743+
"WT_REP1.umi_extract_1.fastq.gz:md5,f312fac9c384a889ae4f959839263604",
2744+
"WT_REP1.umi_extract_2.fastq.gz:md5,ffca24924108fd54151620b7538b9e1a",
2745+
"WT_REP2.umi_extract_1.fastq.gz:md5,c3180451a24ce51fc35c1684521ae287",
2746+
"WT_REP2.umi_extract_2.fastq.gz:md5,067ff23f8d1307ad241cd70bc186b5c1"
26922747
]
26932748
],
26942749
"meta": {
2695-
"nf-test": "0.9.0",
2696-
"nextflow": "24.10.2"
2750+
"nf-test": "0.9.2",
2751+
"nextflow": "24.10.3"
26972752
},
2698-
"timestamp": "2024-12-11T18:01:45.228731692"
2753+
"timestamp": "2024-12-19T22:07:42.25625667"
26992754
},
27002755
"--umi_dedup_tool 'umitools - stub": {
27012756
"content": [
2702-
32,
2757+
31,
27032758
{
2704-
"BBMAP_BBSPLIT": {
2705-
"bbmap": 39.1
2706-
},
27072759
"CAT_FASTQ": {
27082760
"cat": 9.5
27092761
},
@@ -2793,20 +2845,36 @@
27932845
"trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt",
27942846
"umitools",
27952847
"umitools/RAP1_IAA_30M_REP1.umi_extract.log",
2848+
"umitools/RAP1_IAA_30M_REP1.umi_extract_1.fastq.gz",
2849+
"umitools/RAP1_IAA_30M_REP1.umi_extract_2.fastq.gz",
2850+
"umitools/RAP1_UNINDUCED_REP1.umi_extract.fastq.gz",
27962851
"umitools/RAP1_UNINDUCED_REP1.umi_extract.log",
2852+
"umitools/RAP1_UNINDUCED_REP2.umi_extract.fastq.gz",
27972853
"umitools/RAP1_UNINDUCED_REP2.umi_extract.log",
27982854
"umitools/WT_REP1.umi_extract.log",
2799-
"umitools/WT_REP2.umi_extract.log"
2855+
"umitools/WT_REP1.umi_extract_1.fastq.gz",
2856+
"umitools/WT_REP1.umi_extract_2.fastq.gz",
2857+
"umitools/WT_REP2.umi_extract.log",
2858+
"umitools/WT_REP2.umi_extract_1.fastq.gz",
2859+
"umitools/WT_REP2.umi_extract_2.fastq.gz"
28002860
],
28012861
[
28022862
"genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
2803-
"genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
2863+
"genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e",
2864+
"RAP1_IAA_30M_REP1.umi_extract_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
2865+
"RAP1_IAA_30M_REP1.umi_extract_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
2866+
"RAP1_UNINDUCED_REP1.umi_extract.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
2867+
"RAP1_UNINDUCED_REP2.umi_extract.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
2868+
"WT_REP1.umi_extract_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
2869+
"WT_REP1.umi_extract_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
2870+
"WT_REP2.umi_extract_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
2871+
"WT_REP2.umi_extract_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
28042872
]
28052873
],
28062874
"meta": {
2807-
"nf-test": "0.9.0",
2808-
"nextflow": "24.10.2"
2875+
"nf-test": "0.9.2",
2876+
"nextflow": "24.10.3"
28092877
},
2810-
"timestamp": "2024-12-11T18:08:48.404716766"
2878+
"timestamp": "2024-12-19T21:55:24.38516136"
28112879
}
2812-
}
2880+
}

0 commit comments

Comments
 (0)