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Update UMI test
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@pinin4fjords
pinin4fjords committed Dec 19, 2024
1 parent cd97229 commit bdcd760
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Showing 2 changed files with 97 additions and 27 deletions.
2 changes: 2 additions & 0 deletions tests/umi.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,9 @@ nextflow_pipeline {
skip_bbsplit = true
umi_dedup_tool = 'umicollapse'
aligner = 'hisat2'
publish_dir_mode = 'link'
outdir = "$outputDir"
save_umi_intermeds = true
}
}

Expand Down
122 changes: 95 additions & 27 deletions tests/umi.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -612,6 +612,10 @@
"star_salmon/RAP1_IAA_30M_REP1",
"star_salmon/RAP1_IAA_30M_REP1.umi_dedup.sorted.bam",
"star_salmon/RAP1_IAA_30M_REP1.umi_dedup.sorted.bam.bai",
"star_salmon/RAP1_IAA_30M_REP1.umi_dedup.transcriptome.bam",
"star_salmon/RAP1_IAA_30M_REP1.umi_dedup.transcriptome.filtered.bam",
"star_salmon/RAP1_IAA_30M_REP1.umi_dedup.transcriptome.sorted.bam",
"star_salmon/RAP1_IAA_30M_REP1.umi_dedup.transcriptome.sorted.bam.bai",
"star_salmon/RAP1_IAA_30M_REP1/aux_info",
"star_salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv",
"star_salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz",
Expand All @@ -629,6 +633,9 @@
"star_salmon/RAP1_UNINDUCED_REP1",
"star_salmon/RAP1_UNINDUCED_REP1.umi_dedup.sorted.bam",
"star_salmon/RAP1_UNINDUCED_REP1.umi_dedup.sorted.bam.bai",
"star_salmon/RAP1_UNINDUCED_REP1.umi_dedup.transcriptome.bam",
"star_salmon/RAP1_UNINDUCED_REP1.umi_dedup.transcriptome.sorted.bam",
"star_salmon/RAP1_UNINDUCED_REP1.umi_dedup.transcriptome.sorted.bam.bai",
"star_salmon/RAP1_UNINDUCED_REP1/aux_info",
"star_salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv",
"star_salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz",
Expand All @@ -646,6 +653,9 @@
"star_salmon/RAP1_UNINDUCED_REP2",
"star_salmon/RAP1_UNINDUCED_REP2.umi_dedup.sorted.bam",
"star_salmon/RAP1_UNINDUCED_REP2.umi_dedup.sorted.bam.bai",
"star_salmon/RAP1_UNINDUCED_REP2.umi_dedup.transcriptome.bam",
"star_salmon/RAP1_UNINDUCED_REP2.umi_dedup.transcriptome.sorted.bam",
"star_salmon/RAP1_UNINDUCED_REP2.umi_dedup.transcriptome.sorted.bam.bai",
"star_salmon/RAP1_UNINDUCED_REP2/aux_info",
"star_salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv",
"star_salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz",
Expand All @@ -663,6 +673,10 @@
"star_salmon/WT_REP1",
"star_salmon/WT_REP1.umi_dedup.sorted.bam",
"star_salmon/WT_REP1.umi_dedup.sorted.bam.bai",
"star_salmon/WT_REP1.umi_dedup.transcriptome.bam",
"star_salmon/WT_REP1.umi_dedup.transcriptome.filtered.bam",
"star_salmon/WT_REP1.umi_dedup.transcriptome.sorted.bam",
"star_salmon/WT_REP1.umi_dedup.transcriptome.sorted.bam.bai",
"star_salmon/WT_REP1/aux_info",
"star_salmon/WT_REP1/aux_info/ambig_info.tsv",
"star_salmon/WT_REP1/aux_info/expected_bias.gz",
Expand All @@ -680,6 +694,10 @@
"star_salmon/WT_REP2",
"star_salmon/WT_REP2.umi_dedup.sorted.bam",
"star_salmon/WT_REP2.umi_dedup.sorted.bam.bai",
"star_salmon/WT_REP2.umi_dedup.transcriptome.bam",
"star_salmon/WT_REP2.umi_dedup.transcriptome.filtered.bam",
"star_salmon/WT_REP2.umi_dedup.transcriptome.sorted.bam",
"star_salmon/WT_REP2.umi_dedup.transcriptome.sorted.bam.bai",
"star_salmon/WT_REP2/aux_info",
"star_salmon/WT_REP2/aux_info/ambig_info.tsv",
"star_salmon/WT_REP2/aux_info/expected_bias.gz",
Expand Down Expand Up @@ -1261,10 +1279,18 @@
"trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt",
"umitools",
"umitools/RAP1_IAA_30M_REP1.umi_extract.log",
"umitools/RAP1_IAA_30M_REP1.umi_extract_1.fastq.gz",
"umitools/RAP1_IAA_30M_REP1.umi_extract_2.fastq.gz",
"umitools/RAP1_UNINDUCED_REP1.umi_extract.fastq.gz",
"umitools/RAP1_UNINDUCED_REP1.umi_extract.log",
"umitools/RAP1_UNINDUCED_REP2.umi_extract.fastq.gz",
"umitools/RAP1_UNINDUCED_REP2.umi_extract.log",
"umitools/WT_REP1.umi_extract.log",
"umitools/WT_REP2.umi_extract.log"
"umitools/WT_REP1.umi_extract_1.fastq.gz",
"umitools/WT_REP1.umi_extract_2.fastq.gz",
"umitools/WT_REP2.umi_extract.log",
"umitools/WT_REP2.umi_extract_1.fastq.gz",
"umitools/WT_REP2.umi_extract_2.fastq.gz"
],
[
"genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055",
Expand Down Expand Up @@ -1467,14 +1493,22 @@
"WT_REP2.umi_dedup.sorted_per_umi_per_position.tsv:md5,6f5656947a7f0076df446e6f40430027",
"WT_REP2.umi_dedup.transcriptome.sorted_edit_distance.tsv:md5,3e3c6a7e8996e566350742e9911366d3",
"WT_REP2.umi_dedup.transcriptome.sorted_per_umi.tsv:md5,0c986c4cb7a77f650a19e2c454b9b179",
"WT_REP2.umi_dedup.transcriptome.sorted_per_umi_per_position.tsv:md5,af9028dbdab81de3854a32cd1d19ac8b"
"WT_REP2.umi_dedup.transcriptome.sorted_per_umi_per_position.tsv:md5,af9028dbdab81de3854a32cd1d19ac8b",
"RAP1_IAA_30M_REP1.umi_extract_1.fastq.gz:md5,e83d7f738fbbfaa541a2e71fe4663447",
"RAP1_IAA_30M_REP1.umi_extract_2.fastq.gz:md5,4f2873cbf584d6e84187238a4ae2b8fa",
"RAP1_UNINDUCED_REP1.umi_extract.fastq.gz:md5,9e42242fd68baac592140f63a8a716ce",
"RAP1_UNINDUCED_REP2.umi_extract.fastq.gz:md5,5a92b642927b8603c4765e5305e23e9c",
"WT_REP1.umi_extract_1.fastq.gz:md5,f312fac9c384a889ae4f959839263604",
"WT_REP1.umi_extract_2.fastq.gz:md5,ffca24924108fd54151620b7538b9e1a",
"WT_REP2.umi_extract_1.fastq.gz:md5,c3180451a24ce51fc35c1684521ae287",
"WT_REP2.umi_extract_2.fastq.gz:md5,067ff23f8d1307ad241cd70bc186b5c1"
]
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.10.2"
"nf-test": "0.9.2",
"nextflow": "24.10.3"
},
"timestamp": "2024-12-11T18:07:55.751564456"
"timestamp": "2024-12-19T21:54:27.627773754"
},
"Params: --aligner hisat2 --umi_dedup_tool 'umicollapse'": {
"content": [
Expand Down Expand Up @@ -2130,13 +2164,13 @@
"hisat2/stringtie/WT_REP2.coverage.gtf",
"hisat2/stringtie/WT_REP2.gene.abundance.txt",
"hisat2/stringtie/WT_REP2.transcripts.gtf",
"hisat2/umitools",
"hisat2/umitools/genomic_dedup_log",
"hisat2/umitools/genomic_dedup_log/RAP1_IAA_30M_REP1.umi_dedup.sorted_UMICollapse.log",
"hisat2/umitools/genomic_dedup_log/RAP1_UNINDUCED_REP1.umi_dedup.sorted_UMICollapse.log",
"hisat2/umitools/genomic_dedup_log/RAP1_UNINDUCED_REP2.umi_dedup.sorted_UMICollapse.log",
"hisat2/umitools/genomic_dedup_log/WT_REP1.umi_dedup.sorted_UMICollapse.log",
"hisat2/umitools/genomic_dedup_log/WT_REP2.umi_dedup.sorted_UMICollapse.log",
"hisat2/umicollapse",
"hisat2/umicollapse/genomic_dedup_log",
"hisat2/umicollapse/genomic_dedup_log/RAP1_IAA_30M_REP1.umi_dedup.sorted_UMICollapse.log",
"hisat2/umicollapse/genomic_dedup_log/RAP1_UNINDUCED_REP1.umi_dedup.sorted_UMICollapse.log",
"hisat2/umicollapse/genomic_dedup_log/RAP1_UNINDUCED_REP2.umi_dedup.sorted_UMICollapse.log",
"hisat2/umicollapse/genomic_dedup_log/WT_REP1.umi_dedup.sorted_UMICollapse.log",
"hisat2/umicollapse/genomic_dedup_log/WT_REP2.umi_dedup.sorted_UMICollapse.log",
"multiqc",
"multiqc/hisat2",
"multiqc/hisat2/multiqc_report.html",
Expand Down Expand Up @@ -2548,10 +2582,18 @@
"trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt",
"umitools",
"umitools/RAP1_IAA_30M_REP1.umi_extract.log",
"umitools/RAP1_IAA_30M_REP1.umi_extract_1.fastq.gz",
"umitools/RAP1_IAA_30M_REP1.umi_extract_2.fastq.gz",
"umitools/RAP1_UNINDUCED_REP1.umi_extract.fastq.gz",
"umitools/RAP1_UNINDUCED_REP1.umi_extract.log",
"umitools/RAP1_UNINDUCED_REP2.umi_extract.fastq.gz",
"umitools/RAP1_UNINDUCED_REP2.umi_extract.log",
"umitools/WT_REP1.umi_extract.log",
"umitools/WT_REP2.umi_extract.log"
"umitools/WT_REP1.umi_extract_1.fastq.gz",
"umitools/WT_REP1.umi_extract_2.fastq.gz",
"umitools/WT_REP2.umi_extract.log",
"umitools/WT_REP2.umi_extract_1.fastq.gz",
"umitools/WT_REP2.umi_extract_2.fastq.gz"
],
[
"genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055",
Expand Down Expand Up @@ -2621,6 +2663,11 @@
"e_data.ctab:md5,593daf0b84f008c0c64319990ef2fd42",
"i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b",
"i_data.ctab:md5,01c675638f918a70ea689f618a2610bc",
"RAP1_IAA_30M_REP1.umi_dedup.sorted_UMICollapse.log:md5,d6eaaabd7053bef88f3af2b6fc2df45b",
"RAP1_UNINDUCED_REP1.umi_dedup.sorted_UMICollapse.log:md5,441be871ac12aa94f871fab9e8b6b4bf",
"RAP1_UNINDUCED_REP2.umi_dedup.sorted_UMICollapse.log:md5,8a0025a58969badeb3dc35a7c1bdd68e",
"WT_REP1.umi_dedup.sorted_UMICollapse.log:md5,75e6da19996c3ea6fde5cdd4be2dcfda",
"WT_REP2.umi_dedup.sorted_UMICollapse.log:md5,87cdd1eadc3db19bd9f45bb941b1e1a7",
"cutadapt_filtered_reads_plot.txt:md5,3f122969fa288888e5abef061b7963f2",
"cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,5e8a821c9a4deb46c11bc65969b8864f",
"cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,bf8abefa7c5f2f1e1140749983279d9d",
Expand Down Expand Up @@ -2688,22 +2735,27 @@
"cmd_info.json:md5,809380ddce725a8fab75dd7741b64bf6",
"lib_format_counts.json:md5,d231ba7624b67eb654989f69530e2925",
"R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676",
"tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe"
"tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe",
"RAP1_IAA_30M_REP1.umi_extract_1.fastq.gz:md5,e83d7f738fbbfaa541a2e71fe4663447",
"RAP1_IAA_30M_REP1.umi_extract_2.fastq.gz:md5,4f2873cbf584d6e84187238a4ae2b8fa",
"RAP1_UNINDUCED_REP1.umi_extract.fastq.gz:md5,9e42242fd68baac592140f63a8a716ce",
"RAP1_UNINDUCED_REP2.umi_extract.fastq.gz:md5,5a92b642927b8603c4765e5305e23e9c",
"WT_REP1.umi_extract_1.fastq.gz:md5,f312fac9c384a889ae4f959839263604",
"WT_REP1.umi_extract_2.fastq.gz:md5,ffca24924108fd54151620b7538b9e1a",
"WT_REP2.umi_extract_1.fastq.gz:md5,c3180451a24ce51fc35c1684521ae287",
"WT_REP2.umi_extract_2.fastq.gz:md5,067ff23f8d1307ad241cd70bc186b5c1"
]
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.10.2"
"nf-test": "0.9.2",
"nextflow": "24.10.3"
},
"timestamp": "2024-12-11T18:01:45.228731692"
"timestamp": "2024-12-19T22:07:42.25625667"
},
"--umi_dedup_tool 'umitools - stub": {
"content": [
32,
31,
{
"BBMAP_BBSPLIT": {
"bbmap": 39.1
},
"CAT_FASTQ": {
"cat": 9.5
},
Expand Down Expand Up @@ -2793,20 +2845,36 @@
"trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt",
"umitools",
"umitools/RAP1_IAA_30M_REP1.umi_extract.log",
"umitools/RAP1_IAA_30M_REP1.umi_extract_1.fastq.gz",
"umitools/RAP1_IAA_30M_REP1.umi_extract_2.fastq.gz",
"umitools/RAP1_UNINDUCED_REP1.umi_extract.fastq.gz",
"umitools/RAP1_UNINDUCED_REP1.umi_extract.log",
"umitools/RAP1_UNINDUCED_REP2.umi_extract.fastq.gz",
"umitools/RAP1_UNINDUCED_REP2.umi_extract.log",
"umitools/WT_REP1.umi_extract.log",
"umitools/WT_REP2.umi_extract.log"
"umitools/WT_REP1.umi_extract_1.fastq.gz",
"umitools/WT_REP1.umi_extract_2.fastq.gz",
"umitools/WT_REP2.umi_extract.log",
"umitools/WT_REP2.umi_extract_1.fastq.gz",
"umitools/WT_REP2.umi_extract_2.fastq.gz"
],
[
"genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
"genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
"genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e",
"RAP1_IAA_30M_REP1.umi_extract_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
"RAP1_IAA_30M_REP1.umi_extract_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
"RAP1_UNINDUCED_REP1.umi_extract.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
"RAP1_UNINDUCED_REP2.umi_extract.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
"WT_REP1.umi_extract_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
"WT_REP1.umi_extract_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
"WT_REP2.umi_extract_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
"WT_REP2.umi_extract_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.10.2"
"nf-test": "0.9.2",
"nextflow": "24.10.3"
},
"timestamp": "2024-12-11T18:08:48.404716766"
"timestamp": "2024-12-19T21:55:24.38516136"
}
}
}

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