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use nft-bam plugin - init default
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@sateeshperi
sateeshperi committed Sep 19, 2024
1 parent 916a47a commit 428ae98
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83 changes: 83 additions & 0 deletions tests/default.nf.test
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nextflow_pipeline {

name "Test Workflow main.nf"
script "../main.nf"
config "./nextflow.config"

test("Bismark Single-End") {
when {
params {
aligner = "bismark"
save_reference = true
save_align_intermeds = true
outdir = "$outputDir"
}
}

then {
assertAll(
{ assert workflow.success },
{ assert snapshot(
bam("$outputDir/bismark/alignments/Ecoli_1_val_1_bismark_bt2_pe.bam").getReadsMD5(),
bam("$outputDir/bismark/alignments/Ecoli.sorted.bam").getReadsMD5(),
bam("$outputDir/bismark/alignments/SRR389222_sub1.sorted.bam").getReadsMD5(),
bam("$outputDir/bismark/alignments/SRR389222_sub1_trimmed_bismark_bt2.bam").getReadsMD5(),
bam("$outputDir/bismark/alignments/SRR389222_sub2.sorted.bam").getReadsMD5(),
bam("$outputDir/bismark/alignments/SRR389222_sub2_trimmed_bismark_bt2.bam").getReadsMD5(),
bam("$outputDir/bismark/alignments/SRR389222_sub3.sorted.bam").getReadsMD5(),
bam("$outputDir/bismark/alignments/SRR389222_sub3_trimmed_bismark_bt2.bam").getReadsMD5(),

path("$outputDir/bismark/deduplicated/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bam"),
path("$outputDir/bismark/deduplicated/SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bam"),
path("$outputDir/bismark/deduplicated/SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bam"),
path("$outputDir/bismark/deduplicated/SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bam"),
path("$outputDir/bismark/methylation_calls/bedGraph/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz"),
path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bedGraph.gz"),
path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bedGraph.gz"),
path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bedGraph.gz"),
path("$outputDir/bismark/methylation_calls/mbias/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt"),
path("$outputDir/bismark/methylation_calls/mbias/SRR389222_sub1_trimmed_bismark_bt2.deduplicated.M-bias.txt"),
path("$outputDir/bismark/methylation_calls/mbias/SRR389222_sub2_trimmed_bismark_bt2.deduplicated.M-bias.txt"),
path("$outputDir/bismark/methylation_calls/mbias/SRR389222_sub3_trimmed_bismark_bt2.deduplicated.M-bias.txt"),
path("$outputDir/bismark/methylation_calls/methylation_coverage/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz"),
path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bismark.cov.gz"),
path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bismark.cov.gz"),
path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bismark.cov.gz"),
path("$outputDir/bismark/methylation_calls/methylation_calls/").list(),
path("$outputDir/bismark/methylation_calls/splitting_report/Ecoli_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt"),
path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_sub1_trimmed_bismark_bt2.deduplicated_splitting_report.txt"),
path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_sub2_trimmed_bismark_bt2.deduplicated_splitting_report.txt"),
path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_sub3_trimmed_bismark_bt2.deduplicated_splitting_report.txt"),
path("$outputDir/bismark/reference_genome/BismarkIndex/").list(),
path("$outputDir/qualimap/Ecoli/genome_results.txt"),
path("$outputDir/qualimap/SRR389222_sub1/genome_results.txt"),
path("$outputDir/qualimap/SRR389222_sub2/genome_results.txt"),
path("$outputDir/qualimap/SRR389222_sub3/genome_results.txt")
).match("single_end") },
{ assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_software_versions") },
{ assert new File("$outputDir/bismark/alignments/logs/Ecoli_1_val_1_bismark_bt2_PE_report.txt").exists() },
{ assert new File("$outputDir/bismark/alignments/logs/SRR389222_sub1_trimmed_bismark_bt2_SE_report.txt").exists() },
{ assert new File("$outputDir/bismark/alignments/logs/SRR389222_sub2_trimmed_bismark_bt2_SE_report.txt").exists() },
{ assert new File("$outputDir/bismark/alignments/logs/SRR389222_sub3_trimmed_bismark_bt2_SE_report.txt").exists() },
{ assert new File("$outputDir/bismark/reports/Ecoli_1_val_1_bismark_bt2_PE_report.html").exists() },
{ assert new File("$outputDir/bismark/reports/SRR389222_sub1_trimmed_bismark_bt2_SE_report.html").exists() },
{ assert new File("$outputDir/bismark/reports/SRR389222_sub2_trimmed_bismark_bt2_SE_report.html").exists() },
{ assert new File("$outputDir/bismark/reports/SRR389222_sub3_trimmed_bismark_bt2_SE_report.html").exists() },
{ assert new File("$outputDir/bismark/summary/bismark_summary_report.html").exists() },
{ assert new File("$outputDir/bismark/summary/bismark_summary_report.txt").exists() },
{ assert new File("$outputDir/fastqc/Ecoli_1_fastqc.html").exists() },
{ assert new File("$outputDir/fastqc/Ecoli_2_fastqc.html").exists() },
{ assert new File("$outputDir/fastqc/SRR389222_sub1_fastqc.html").exists() },
{ assert new File("$outputDir/fastqc/SRR389222_sub2_fastqc.html").exists() },
{ assert new File("$outputDir/fastqc/SRR389222_sub3_fastqc.html").exists() },
{ assert new File("$outputDir/multiqc/bismark/multiqc_report.html").exists() },
{ assert new File("$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_sub1.fastq.gz_trimming_report.txt").exists() },
{ assert new File("$outputDir/trimgalore/logs/SRR389222_sub2.fastq.gz_trimming_report.txt").exists() },
{ assert new File("$outputDir/trimgalore/logs/SRR389222_sub3.fastq.gz_trimming_report.txt").exists() }
)
}
}

}
122 changes: 122 additions & 0 deletions tests/default.nf.test.snap
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{
"single_end_software_versions": {
"content": [
{
"BISMARK_ALIGN": {
"bismark": "0.24.0"
},
"BISMARK_GENOMEPREPARATION": {
"bismark": "0.24.0"
},
"FASTQC": {
"fastqc": "0.12.1"
},
"QUALIMAP_BAMQC": {
"qualimap": 2.3
},
"TRIMGALORE": {
"trimgalore": "0.6.7",
"cutadapt": 3.4
},
"Workflow": {
"nf-core/methylseq": "v2.7.0dev"
}
}
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-09-18T19:08:58.67297311"
},
"single_end": {
"content": [
"fad4414ebdaafdb15e0584b393400b27",
"a54ab7c96f9523a4ccd25fd69f6905f8",
"3f11ef5fbbda3797fd6217728e4f00d3",
"934288bfc59d40ff7e73706d07815fb",
"b01f29fc1d8d46922a69df09c636b4c4",
"a94aeadc2acebd0a46647bb95acf2d55",
"347195c04c9ffd2a2b10967a6682fc69",
"6579ca7e49b9d7760ea5b3f3456739a1",
"Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bam:md5,caa027599dac71c50c24de1857dbf5c7",
"SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bam:md5,66b4244c9f75ee798a77b0a1e47214ea",
"SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bam:md5,79e4d27508ee03d74bf4c79d23d439fd",
"SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bam:md5,d627ec0448a0bba875895615b90beab6",
"Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz:md5,58c9ba98d0638c26a30233b006a81172",
"SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,d31df76c1c9128299367ebfe740357b9",
"SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,010f32001bbc7805f8e041f3ef0d9ea9",
"SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,d42e09af121ae14f6e0de5779e317b0b",
"Ecoli_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt:md5,29f3b882a51b63ce77d3d9c69b0e5f85",
"SRR389222_sub1_trimmed_bismark_bt2.deduplicated.M-bias.txt:md5,ed28b3cce432eecfae73bc4a071ec4ee",
"SRR389222_sub2_trimmed_bismark_bt2.deduplicated.M-bias.txt:md5,b06ce0084e54193ff8c9b9dd0ec9757b",
"SRR389222_sub3_trimmed_bismark_bt2.deduplicated.M-bias.txt:md5,b865b7fb6e1225feeb6aef3372ef0b1d",
"Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz:md5,8e6ba6fe66416d73e7f94b4da9ca77b1",
"SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bismark.cov.gz:md5,5377d9fff4f1bf5b98dc2310fbeb6ec9",
"SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bismark.cov.gz:md5,4713bda7b4f2bb16ce23853aea763cbd",
"SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bismark.cov.gz:md5,f9a07c3e11e0caad6df3cd2e4d94d8ac",
[
"CHG_OB_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,9c2248d95d96d6c315c65f1b8dc3bc39",
"CHG_OB_SRR389222_sub1_trimmed_bismark_bt2.deduplicated.txt.gz:md5,a10f4263bf7b9b1985b16ff3c1041240",
"CHG_OB_SRR389222_sub2_trimmed_bismark_bt2.deduplicated.txt.gz:md5,1b036ec35b09e0d3b748040381cb1fd5",
"CHG_OB_SRR389222_sub3_trimmed_bismark_bt2.deduplicated.txt.gz:md5,929b960ad908ec05687540b684106de0",
"CHG_OT_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,5e5aefaa3f63e73f30342ad843eb210b",
"CHG_OT_SRR389222_sub1_trimmed_bismark_bt2.deduplicated.txt.gz:md5,87d488061e2d43db2060a37874c346cc",
"CHG_OT_SRR389222_sub2_trimmed_bismark_bt2.deduplicated.txt.gz:md5,2013c67301066dde516bb950731fb04a",
"CHG_OT_SRR389222_sub3_trimmed_bismark_bt2.deduplicated.txt.gz:md5,e4d5f53c056424471038f28ffd49b2df",
"CHH_OB_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,65f2afc6b1c76209af1acd1d4277a1cc",
"CHH_OB_SRR389222_sub1_trimmed_bismark_bt2.deduplicated.txt.gz:md5,172b329b6aabf8d07c8255a152d4105a",
"CHH_OB_SRR389222_sub2_trimmed_bismark_bt2.deduplicated.txt.gz:md5,82e84337d3a4c5ca20260e7455c53022",
"CHH_OB_SRR389222_sub3_trimmed_bismark_bt2.deduplicated.txt.gz:md5,d06408d5bb2071ae66a4d4260a73c491",
"CHH_OT_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,978ad87fef01e39283a620253320ee45",
"CHH_OT_SRR389222_sub1_trimmed_bismark_bt2.deduplicated.txt.gz:md5,20038a010d4258a2a76aa389e05b84ba",
"CHH_OT_SRR389222_sub2_trimmed_bismark_bt2.deduplicated.txt.gz:md5,e585363a40c045ea66c16257e507d3de",
"CHH_OT_SRR389222_sub3_trimmed_bismark_bt2.deduplicated.txt.gz:md5,9b529b04d321e5fc11dcb023345fd136",
"CpG_OB_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,54def6bf13e27f38adbbd3dd06297596",
"CpG_OB_SRR389222_sub1_trimmed_bismark_bt2.deduplicated.txt.gz:md5,d581258ecd66c080c70caeea30e31ca2",
"CpG_OB_SRR389222_sub2_trimmed_bismark_bt2.deduplicated.txt.gz:md5,dee4913db39eef1e706167d6c0f0c389",
"CpG_OB_SRR389222_sub3_trimmed_bismark_bt2.deduplicated.txt.gz:md5,74a9c8092dbd8c2f27d54bb627993f90",
"CpG_OT_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,9712eef973883f44dcc0a307af28ba70",
"CpG_OT_SRR389222_sub1_trimmed_bismark_bt2.deduplicated.txt.gz:md5,ff50e21971733216ea1315ba772bef09",
"CpG_OT_SRR389222_sub2_trimmed_bismark_bt2.deduplicated.txt.gz:md5,94302d0daeb2b275b015622a9a10ac25",
"CpG_OT_SRR389222_sub3_trimmed_bismark_bt2.deduplicated.txt.gz:md5,e2fb1e0f57f5eaf10347b1221e6cd47c"
],
"Ecoli_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt:md5,b759f31785293e8d952f1dd3246f9a7b",
"SRR389222_sub1_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,d70ee229a29b68db8634fa7d568b7c53",
"SRR389222_sub2_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,6cc81c365aa59992d510cdce467230d6",
"SRR389222_sub3_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,13883f84bb3b1cec4593541749571c12",
[
[
[
"BS_CT.1.bt2:md5,d53bef7d951c7d08e327944581c911eb",
"BS_CT.2.bt2:md5,752a03fc364115fc910e5a28ae154382",
"BS_CT.3.bt2:md5,b41e72eefad74e8ede411c78a5bd5dee",
"BS_CT.4.bt2:md5,02b3d1855a67fd9cbb4c411406a22fde",
"BS_CT.rev.1.bt2:md5,52ae603fff473b3b25eecd36c533edb9",
"BS_CT.rev.2.bt2:md5,0e290e05f7dae065cae54e29ed97afe5",
"genome_mfa.CT_conversion.fa:md5,4dd181b65f1f3549f4132c9a3759eee8"
],
[
"BS_GA.1.bt2:md5,9aff51b1712758b891b0c427a988977f",
"BS_GA.2.bt2:md5,579241d95941538b2e75bbdb6cfaa73d",
"BS_GA.3.bt2:md5,b41e72eefad74e8ede411c78a5bd5dee",
"BS_GA.4.bt2:md5,6b64fa496ffa2af2af235e1c87f06a25",
"BS_GA.rev.1.bt2:md5,dabf2d6f80ba7e8fc96dfdc203f6bbfd",
"BS_GA.rev.2.bt2:md5,fac2f8b39b0e15dec7aa79a0ecf12b49",
"genome_mfa.GA_conversion.fa:md5,3dee732bc344fd620c3a7322f52c6a5f"
]
],
"genome.fa:md5,923a0a268ad29fee3c3437d00f9970de"
],
"genome_results.txt:md5,886ffc763d05a84ead7f80a1d1db1fa2",
"genome_results.txt:md5,79287f69ff6c8a308f0bb988c97f0e15",
"genome_results.txt:md5,7838069da6060f756821c776cc3a4929",
"genome_results.txt:md5,41aa314da188306ead441ddcb14f79b2"
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-09-18T19:11:13.763004169"
}
}
2 changes: 1 addition & 1 deletion tests/lib/UTILS.groovy
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
// Function to remove Nextflow version from software_versions.yml

class UTILS {
public static String removeNextflowVersion(outputDir) {
public static Object removeNextflowVersion(outputDir) {
def softwareVersions = path("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml").yaml
if (softwareVersions.containsKey("Workflow")) {
softwareVersions.Workflow.remove("Nextflow")
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