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update tests for new assets/samplesheet
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@sateeshperi
sateeshperi committed Dec 20, 2023
1 parent 17bea74 commit aaa2282
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Showing 4 changed files with 93 additions and 93 deletions.
30 changes: 15 additions & 15 deletions tests/pipeline/bismark_hisat/main.nf.test
View file
Original file line number Diff line number Diff line change
Expand Up @@ -28,33 +28,33 @@ nextflow_pipeline {

assertAll(
{ assert workflow.success },
{ assert snapshot(path("$outputDir/bismark_hisat/deduplicated/Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.bam"),
{ assert snapshot(path("$outputDir/bismark_hisat/deduplicated/Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.bam"),
path("$outputDir/bismark_hisat/deduplicated/SRR389222_trimmed_bismark_hisat2.deduplicated.bam"),
path("$outputDir/bismark_hisat/methylation_calls/bedGraph/Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.bedGraph.gz"),
path("$outputDir/bismark_hisat/methylation_calls/bedGraph/Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.bedGraph.gz"),
path("$outputDir/bismark_hisat/methylation_calls/bedGraph/SRR389222_trimmed_bismark_hisat2.deduplicated.bedGraph.gz"),
path("$outputDir/bismark_hisat/methylation_calls/mbias/Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.M-bias.txt"),
path("$outputDir/bismark_hisat/methylation_calls/mbias/Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.M-bias.txt"),
path("$outputDir/bismark_hisat/methylation_calls/mbias/SRR389222_trimmed_bismark_hisat2.deduplicated.M-bias.txt"),
path("$outputDir/bismark_hisat/methylation_calls/methylation_calls/").list(),
path("$outputDir/bismark_hisat/methylation_calls/methylation_coverage/Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.bismark.cov.gz"),
path("$outputDir/bismark_hisat/methylation_calls/methylation_coverage/Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.bismark.cov.gz"),
path("$outputDir/bismark_hisat/methylation_calls/methylation_coverage/SRR389222_trimmed_bismark_hisat2.deduplicated.bismark.cov.gz"),
path("$outputDir/bismark_hisat/methylation_calls/splitting_report/Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated_splitting_report.txt"),
path("$outputDir/bismark_hisat/methylation_calls/splitting_report/Ecoli_1_val_1_bismark_hisat2_pe.deduplicated_splitting_report.txt"),
path("$outputDir/bismark_hisat/methylation_calls/splitting_report/SRR389222_trimmed_bismark_hisat2.deduplicated_splitting_report.txt"),
path("$outputDir/cat/SRR389222.merged.fastq.gz"),
path("$outputDir/qualimap/Ecoli_10K/genome_results.txt"),
path("$outputDir/qualimap/Ecoli/genome_results.txt"),
path("$outputDir/qualimap/SRR389222/genome_results.txt")).match("single_end") },
{ assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_software_versions") },
{ assert new File("$outputDir/bismark_hisat/alignments/logs/Ecoli_10K_1_val_1_bismark_hisat2_PE_report.txt").exists() },
{ assert new File("$outputDir/bismark_hisat/alignments/logs/Ecoli_1_val_1_bismark_hisat2_PE_report.txt").exists() },
{ assert new File("$outputDir/bismark_hisat/alignments/logs/SRR389222_trimmed_bismark_hisat2_SE_report.txt").exists() },
{ assert new File("$outputDir/bismark_hisat/reports/Ecoli_10K_1_val_1_bismark_hisat2_PE_report.html").exists() },
{ assert new File("$outputDir/bismark_hisat/reports/Ecoli_1_val_1_bismark_hisat2_PE_report.html").exists() },
{ assert new File("$outputDir/bismark_hisat/reports/SRR389222_trimmed_bismark_hisat2_SE_report.html").exists() },
{ assert new File("$outputDir/bismark_hisat/summary/bismark_summary_report.html").exists() },
{ assert new File("$outputDir/bismark_hisat/summary/bismark_summary_report.txt").exists() },
{ assert new File("$outputDir/fastqc/Ecoli_10K_1_fastqc.html").exists() },
{ assert new File("$outputDir/fastqc/Ecoli_10K_2_fastqc.html").exists() },
{ assert new File("$outputDir/fastqc/Ecoli_1_fastqc.html").exists() },
{ assert new File("$outputDir/fastqc/Ecoli_2_fastqc.html").exists() },
{ assert new File("$outputDir/fastqc/SRR389222_fastqc.html").exists() },
{ assert new File("$outputDir/multiqc/bismark_hisat/multiqc_report.html").exists() },
{ assert new File("$outputDir/trimgalore/logs/Ecoli_10K_1.fastq.gz_trimming_report.txt").exists() },
{ assert new File("$outputDir/trimgalore/logs/Ecoli_10K_2.fastq.gz_trimming_report.txt").exists() },
{ assert new File("$outputDir/trimgalore/logs/Ecoli_1.fastq.gz_trimming_report.txt").exists() },
{ assert new File("$outputDir/trimgalore/logs/Ecoli_2.fastq.gz_trimming_report.txt").exists() },
{ assert new File("$outputDir/trimgalore/logs/SRR389222.fastq.gz_trimming_report.txt").exists() }
)
}
Expand Down Expand Up @@ -102,7 +102,7 @@ nextflow_pipeline {
path("$outputDir/bismark_hisat/methylation_calls/splitting_report/Ecoli_10K_methylated_R1_bismark_hisat2_pe_splitting_report.txt"),
path("$outputDir/bismark_hisat/methylation_calls/splitting_report/SRR389222.merged_bismark_hisat2_splitting_report.txt"),
path("$outputDir/cat/SRR389222.merged.fastq.gz"),
path("$outputDir/qualimap/Ecoli_10K/genome_results.txt"),
path("$outputDir/qualimap/Ecoli/genome_results.txt"),
path("$outputDir/qualimap/SRR389222/genome_results.txt")).match("single_end_rrbs") },
{ assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_rrbs_software_versions") },
{ assert new File("$outputDir/bismark_hisat/alignments/logs/Ecoli_10K_methylated_R1_bismark_hisat2_PE_report.txt").exists() },
Expand All @@ -111,8 +111,8 @@ nextflow_pipeline {
{ assert new File("$outputDir/bismark_hisat/reports/SRR389222.merged_bismark_hisat2_SE_report.html").exists() },
{ assert new File("$outputDir/bismark_hisat/summary/bismark_summary_report.html").exists() },
{ assert new File("$outputDir/bismark_hisat/summary/bismark_summary_report.txt").exists() },
{ assert new File("$outputDir/fastqc/Ecoli_10K_1_fastqc.html").exists() },
{ assert new File("$outputDir/fastqc/Ecoli_10K_2_fastqc.html").exists() },
{ assert new File("$outputDir/fastqc/Ecoli_1_fastqc.html").exists() },
{ assert new File("$outputDir/fastqc/Ecoli_2_fastqc.html").exists() },
{ assert new File("$outputDir/fastqc/SRR389222_fastqc.html").exists() },
{ assert new File("$outputDir/multiqc/bismark_hisat/multiqc_report.html").exists() }
)
Expand Down
84 changes: 42 additions & 42 deletions tests/pipeline/bismark_hisat/main.nf.test.snap
View file
Original file line number Diff line number Diff line change
Expand Up @@ -13,66 +13,66 @@
},
"single_end": {
"content": [
"Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.bam:md5,9e9b4adfeeb716e24ecba0bfad39c2e3",
"Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.bam:md5,ddfc84eb92f641020362f69e9e28a52d",
"SRR389222_trimmed_bismark_hisat2.deduplicated.bam:md5,aa60cf9dcf302c185b12ced6f302a06e",
"Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.bedGraph.gz:md5,539b06719ca6dcccaf2b86d8be571ace",
"SRR389222_trimmed_bismark_hisat2.deduplicated.bedGraph.gz:md5,dba86d0f60ad88aaeef1970ceef8376b",
"Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.M-bias.txt:md5,5fd8655f4b9dba2249a52b769fe50faf",
"Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.bedGraph.gz:md5,357196071c54757566cdd0bb7ab79fa8",
"SRR389222_trimmed_bismark_hisat2.deduplicated.bedGraph.gz:md5,b20f17236ff64db1114343ff333a6d5b",
"Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.M-bias.txt:md5,5fd8655f4b9dba2249a52b769fe50faf",
"SRR389222_trimmed_bismark_hisat2.deduplicated.M-bias.txt:md5,b19356395d4ae1ad83bd3ec38276e580",
[
"CHG_OB_Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,c2144bcfb7850b8c10bb8296dd2e09c1",
"CHG_OB_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,b0f6e9284b65d1bf3c813008c08656cc",
"CHG_OT_Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,7f49ecab1843458c28c3d6fe6a85149e",
"CHG_OT_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,5813137cea214c7759598ca442f29d47",
"CHH_OB_Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,4e8f5b27fbb933c572f269688004be38",
"CHH_OB_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,aca84c4d6fffb7bf72f4dcd4371dc89b",
"CHH_OT_Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,d173808471dbb7c50ef43eb1f5f29faa",
"CHH_OT_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,1018c276fa14900e7b1edad0e23fc7ff",
"CpG_OB_Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,3f58d13a3b47d639696dbb4478a39488",
"CpG_OB_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,0039a8c3f8971a5a99bc58bc1511fa0d",
"CpG_OT_Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,6dfc57a2892d7cd3bebb7cbc0878196b",
"CpG_OT_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,801c0dba9ca584d9c804a4254d7c4ea6"
"CHG_OB_Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,6d2ca2e6548640e3885c94a3ca6beae0",
"CHG_OB_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,9d8098ce1a27c23961e20b6a95f237d1",
"CHG_OT_Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,5e5aefaa3f63e73f30342ad843eb210b",
"CHG_OT_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,1180631ef093aade3a5195ce7ddfb3f6",
"CHH_OB_Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,abd48ddf1c9e844d8164de5150850d10",
"CHH_OB_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,6834286d8d07a1b3a4399f71b5b3c3f8",
"CHH_OT_Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,978ad87fef01e39283a620253320ee45",
"CHH_OT_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,c311a70c0c8b6a93c2055fcbec03a833",
"CpG_OB_Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,51f8b079b9fd91e23e495d9e0e289530",
"CpG_OB_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,4dae933bcdc8c7d1de2f5e7239c1ae55",
"CpG_OT_Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,9712eef973883f44dcc0a307af28ba70",
"CpG_OT_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,63e737eef999e2d6348e7ed2a7ce4402"
],
"Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.bismark.cov.gz:md5,474c1291d09b023e91ed892b5a09ba80",
"SRR389222_trimmed_bismark_hisat2.deduplicated.bismark.cov.gz:md5,e58cba79f419cb411a77b656173d48ea",
"Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated_splitting_report.txt:md5,a5dc04c52facdb5221a06ae7f3bca2e4",
"Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.bismark.cov.gz:md5,d8342eca72089408d8e4d7c5ec5e95bf",
"SRR389222_trimmed_bismark_hisat2.deduplicated.bismark.cov.gz:md5,ad7a19cb9908844c47b7b871ff1223c2",
"Ecoli_1_val_1_bismark_hisat2_pe.deduplicated_splitting_report.txt:md5,bc2284d712455231a2dd772098ca8dd9",
"SRR389222_trimmed_bismark_hisat2.deduplicated_splitting_report.txt:md5,1f792e1fddb17140947f14008e1f9ffd",
"SRR389222.merged.fastq.gz:md5,ba5df0639e25988059a6f5bf309dbb6e",
"genome_results.txt:md5,f272f759bfed7e8a30ec2719e0b518aa",
"SRR389222.merged.fastq.gz:md5,47e1d7461d511a970e80085dd6454775",
"genome_results.txt:md5,3703ab8cc04a6f3307ea1ffcfe23479a",
"genome_results.txt:md5,7706d3790aee0e9244c490941ecd394f"
],
"timestamp": "2023-08-28T10:04:42+0000"
"timestamp": "2023-12-20T02:58:11.727470144"
},
"single_end_rrbs": {
"content": [
"Ecoli_10K_methylated_R1_bismark_hisat2_pe.bam:md5,53c34edee0bc7f34c9f4e9a3685dd706",
"SRR389222.merged_bismark_hisat2.bam:md5,204123a5f7cd77cba3a90b904443c7eb",
"Ecoli_10K_methylated_R1_bismark_hisat2_pe.bedGraph.gz:md5,539b06719ca6dcccaf2b86d8be571ace",
"SRR389222.merged_bismark_hisat2.bedGraph.gz:md5,2b41ebc929eec351e21a16eec6f8fdd9",
"Ecoli_10K_methylated_R1_bismark_hisat2_pe.bedGraph.gz:md5,357196071c54757566cdd0bb7ab79fa8",
"SRR389222.merged_bismark_hisat2.bedGraph.gz:md5,d509b1e8e4ec03dcde48a127cf976594",
"Ecoli_10K_methylated_R1_bismark_hisat2_pe.M-bias.txt:md5,5fd8655f4b9dba2249a52b769fe50faf",
"SRR389222.merged_bismark_hisat2.M-bias.txt:md5,ea90b0495446d03e375aad42d598a9f9",
[
"CHG_OB_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,c2144bcfb7850b8c10bb8296dd2e09c1",
"CHG_OB_SRR389222.merged_bismark_hisat2.txt.gz:md5,3fcc7974fd6c5cbacf231835f58d949b",
"CHG_OT_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,7f49ecab1843458c28c3d6fe6a85149e",
"CHG_OT_SRR389222.merged_bismark_hisat2.txt.gz:md5,e924ba0137252d4b470532cfc36524c2",
"CHH_OB_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,4e8f5b27fbb933c572f269688004be38",
"CHH_OB_SRR389222.merged_bismark_hisat2.txt.gz:md5,2fb870b779750951bec579ce7562736e",
"CHH_OT_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,d173808471dbb7c50ef43eb1f5f29faa",
"CHH_OT_SRR389222.merged_bismark_hisat2.txt.gz:md5,6e1d89e988f10fa528398b117a554fb1",
"CpG_OB_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,3f58d13a3b47d639696dbb4478a39488",
"CpG_OB_SRR389222.merged_bismark_hisat2.txt.gz:md5,6537b18418e62410d9ae617480702c54",
"CpG_OT_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,6dfc57a2892d7cd3bebb7cbc0878196b",
"CpG_OT_SRR389222.merged_bismark_hisat2.txt.gz:md5,b07add9bb5ebc7d404e1505deb960654"
"CHG_OB_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,6d2ca2e6548640e3885c94a3ca6beae0",
"CHG_OB_SRR389222.merged_bismark_hisat2.txt.gz:md5,eeb08e87d7e3dca0acbb2c5ba2be66fb",
"CHG_OT_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,5e5aefaa3f63e73f30342ad843eb210b",
"CHG_OT_SRR389222.merged_bismark_hisat2.txt.gz:md5,7add3136b9f74de6aa83d38dde191060",
"CHH_OB_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,abd48ddf1c9e844d8164de5150850d10",
"CHH_OB_SRR389222.merged_bismark_hisat2.txt.gz:md5,a135c7e8a6c1b909a318ef17d47dca94",
"CHH_OT_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,978ad87fef01e39283a620253320ee45",
"CHH_OT_SRR389222.merged_bismark_hisat2.txt.gz:md5,8f1910f962b724592546a6187ad0a677",
"CpG_OB_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,51f8b079b9fd91e23e495d9e0e289530",
"CpG_OB_SRR389222.merged_bismark_hisat2.txt.gz:md5,b8b2de10044869b6c1097afc21c878a0",
"CpG_OT_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,9712eef973883f44dcc0a307af28ba70",
"CpG_OT_SRR389222.merged_bismark_hisat2.txt.gz:md5,877b026664516cb8851c1d80bf0d8495"
],
"Ecoli_10K_methylated_R1_bismark_hisat2_pe.bismark.cov.gz:md5,474c1291d09b023e91ed892b5a09ba80",
"SRR389222.merged_bismark_hisat2.bismark.cov.gz:md5,626edb040f82e57c1f521bdb72618407",
"Ecoli_10K_methylated_R1_bismark_hisat2_pe.bismark.cov.gz:md5,d8342eca72089408d8e4d7c5ec5e95bf",
"SRR389222.merged_bismark_hisat2.bismark.cov.gz:md5,29943eb00da6057a67e5530580668130",
"Ecoli_10K_methylated_R1_bismark_hisat2_pe_splitting_report.txt:md5,76868c2015864a3f7c2b4cd1738e4765",
"SRR389222.merged_bismark_hisat2_splitting_report.txt:md5,4a9e54ffb48c9bb1e5ac33aa77b25f5c",
"SRR389222.merged.fastq.gz:md5,ba5df0639e25988059a6f5bf309dbb6e",
"genome_results.txt:md5,13a70a3885acd9d55014aa1ad66e2bbb",
"SRR389222.merged.fastq.gz:md5,47e1d7461d511a970e80085dd6454775",
"genome_results.txt:md5,58bf4e22f697120806f09b48d9ffdc9e",
"genome_results.txt:md5,ae5b10e9a3ffa1ac7a4f4e736228ec49"
],
"timestamp": "2023-08-28T10:04:42+0000"
"timestamp": "2023-12-20T03:00:29.750687681"
}
}
}
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