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Fix mkfastq #253

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merged 2 commits into from
Aug 19, 2024
Merged

Fix mkfastq #253

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4b9de28
Updated mkfastq and removed customdumpsoftware from modules.json
Aug 15, 2024
452e918
Ran pre-commit
nschcolnicov Aug 15, 2024
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9 changes: 8 additions & 1 deletion conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -203,7 +203,14 @@ process {
//Gather fastqs
path: { meta.lane ? "${params.outdir}/${meta.id}/L00${meta.lane}" : "${params.outdir}/${meta.id}" },
mode: params.publish_dir_mode,
pattern: "**/outs/fastq_path/**.fastq.gz",
pattern: "**/outs/fastq_path/**/*.fastq.gz",
saveAs: {filename -> filename.split("/")[-1] }
],
[
//Gather undetermined fastqs
path: { meta.lane ? "${params.outdir}/${meta.id}/L00${meta.lane}/undetermined" : "${params.outdir}/${meta.id}/undetermined" },
mode: params.publish_dir_mode,
pattern: "**/outs/fastq_path/*.fastq.gz",
saveAs: {filename -> filename.split("/")[-1] }
]
]
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4 changes: 2 additions & 2 deletions conf/test_mkfastq.config
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Expand Up @@ -20,7 +20,7 @@ params {
max_time = '1.h'

// Input data
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/samplesheet/1.3.0/mkfastq-samplesheet.csv'
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/samplesheet/cellranger_tiny/mkfastq_tiny_samplesheet.csv'
demultiplexer = 'mkfastq'
skip_tools = 'samshee'
skip_tools = 'samshee,falco'
}
7 changes: 1 addition & 6 deletions modules.json
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Original file line number Diff line number Diff line change
Expand Up @@ -22,19 +22,14 @@
},
"cellranger/mkfastq": {
"branch": "master",
"git_sha": "d89faad13503f47372b8706008f7cdb2c4f1d859",
"git_sha": "61123e49c6034920eb6f312ad71e4815a7853257",
"installed_by": ["modules"]
},
"checkqc": {
"branch": "master",
"git_sha": "337bc962d03c2e08a728c9bf731a2148e323e731",
"installed_by": ["modules"]
},
"custom/dumpsoftwareversions": {
"branch": "master",
"git_sha": "82024cf6325d2ee194e7f056d841ecad2f6856e9",
"installed_by": ["modules"]
},
"falco": {
"branch": "master",
"git_sha": "a236d2c2ec9e68db9b8501105d804acb359552b5",
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24 changes: 17 additions & 7 deletions modules/nf-core/cellranger/mkfastq/main.nf
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3 changes: 3 additions & 0 deletions modules/nf-core/cellranger/mkfastq/tests/main.nf.test
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41 changes: 35 additions & 6 deletions modules/nf-core/cellranger/mkfastq/tests/main.nf.test.snap
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29 changes: 18 additions & 11 deletions tests/pipeline/mkfastq.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -18,25 +18,32 @@ nextflow_pipeline {
assertAll(
{ assert workflow.success },
{ assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") },
{ assert workflow.trace.succeeded().size() == 7 },
{ assert workflow.trace.succeeded().size() == 10 },
// How many directories were produced?
{assert path("${outputDir}").list().size() == 6},
// How many files were produced?
{assert path("$outputDir/220422_M11111_0222_000000000-K9H97_mkfastq/").list().size() == 2},
{assert path("$outputDir/cellranger-tiny-bcl-simple/").list().size() == 2},
{assert path("$outputDir/multiqc/").list().size() == 3},
{assert path("$outputDir/pipeline_info/").list().size() == 5},
// File assertions: Files that should be exactly the same with every pipeline execution.
{assert snapshot(
//Check output files
path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/L001/Sample1_S1_L001_summary.txt"),
path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/L001/Sample1_S1_L001_report.html").exists(),
path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/L001/Sample1_S1_L001_R1_001.fastq.gz"),
path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/L001/Sample1_S1_L001_fastqc_data.txt"),
path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/L001/Sample1_S1_L001.fastp.json"),
path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/L001/Sample1_S1_L001.fastp.html").exists(),
path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/L001/Sample1_S1_L001.fastp.fastq.gz.md5"),
path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/L001/Sample1_S1_L001.fastp.fastq.gz"),
path("${outputDir}/220422_M11111_0222_000000000-K9H97_mkfastq/InterOp/IndexMetricsOut.bin")
path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_1.fastp.fastq.gz"),
path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_1.fastp.fastq.gz.md5"),
path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_2.fastp.fastq.gz"),
path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_2.fastp.fastq.gz.md5"),
path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_I1_001.fastp.fastq.gz.md5"),
path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_I1_001.fastq.gz"),
path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_R1_001.fastq.gz"),
path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_R2_001.fastq.gz"),
path("${outputDir}/cellranger-tiny-bcl-simple/L001/undetermined/Undetermined_S0_L001_I1_001.fastq.gz"),
path("${outputDir}/cellranger-tiny-bcl-simple/L001/undetermined/Undetermined_S0_L001_R1_001.fastq.gz"),
path("${outputDir}/cellranger-tiny-bcl-simple/L001/undetermined/Undetermined_S0_L001_R2_001.fastq.gz"),
path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_I1_001.fastp.html").exists(),
path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001.fastp.html").exists(),
path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001.fastp.json"),
path("${outputDir}/cellranger-tiny-bcl-simple/L001/test_sample_S1_L001_I1_001.fastp.json"),
path("${outputDir}/cellranger-tiny-bcl-simple/InterOp/IndexMetricsOut.bin")
).match("file_assertions_mkfastq")}
)
}
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31 changes: 19 additions & 12 deletions tests/pipeline/mkfastq.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,30 +1,37 @@
{
"software_versions": {
"content": [
"{CELLRANGER_MKFASTQ={cellranger=8.0.0}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, MD5SUM={md5sum=8.3}, UNTAR_FLOWCELL={untar=1.34}, Workflow={nf-core/demultiplex=v1.5.1dev}}"
"{CELLRANGER_MKFASTQ={cellranger=8.0.0}, FASTP={fastp=0.23.4}, MD5SUM={md5sum=8.3}, UNTAR_FLOWCELL={untar=1.34}, Workflow={nf-core/demultiplex=v1.5.1dev}}"
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "23.10.0"
"nextflow": "24.04.3"
},
"timestamp": "2024-08-02T20:09:53.707554042"
"timestamp": "2024-08-15T17:36:35.551329"
},
"file_assertions_mkfastq": {
"content": [
"Sample1_S1_L001_summary.txt:md5,510c6b8a26ff8d530950c05b3ca5a1c6",
"test_sample_S1_L001_1.fastp.fastq.gz:md5,b348491a3b1afa096fde514dbdf55215",
"test_sample_S1_L001_1.fastp.fastq.gz.md5:md5,43d7882f3aaae47b56df56da6c802236",
"test_sample_S1_L001_2.fastp.fastq.gz:md5,1c60f1f3958b8b2b0255b9fae6df0b3d",
"test_sample_S1_L001_2.fastp.fastq.gz.md5:md5,01d742cc56639c476b0bac0c094eba4b",
"test_sample_S1_L001_I1_001.fastp.fastq.gz.md5:md5,82e397b4a2418f27269a30f6ca0e349e",
"test_sample_S1_L001_I1_001.fastq.gz:md5,018b0dbd8daf76fb9f6dfa4729ea0453",
"test_sample_S1_L001_R1_001.fastq.gz:md5,df3ddf85d83bd722219c646c7815dbdc",
"test_sample_S1_L001_R2_001.fastq.gz:md5,c8a387b517ff5b7e56b85ccbf882efd2",
"Undetermined_S0_L001_I1_001.fastq.gz:md5,c93946d67bdb1d5b2ab955fd1dc9cb31",
"Undetermined_S0_L001_R1_001.fastq.gz:md5,faa79ce215ae72fdc3375cda066c6757",
"Undetermined_S0_L001_R2_001.fastq.gz:md5,d8955db4dfbf7aee89b6bdc3b7629f8f",
true,
"Sample1_S1_L001_R1_001.fastq.gz:md5,0675fb6365322eaafb33c0f8e862b54b",
"Sample1_S1_L001_fastqc_data.txt:md5,0adf4e2617f55fabba0663583c1f65b7",
"Sample1_S1_L001.fastp.json:md5,ed62c667631b03f5fd3b50454322b423",
true,
"Sample1_S1_L001.fastp.fastq.gz.md5:md5,c3cd96f3a22fb6afbaa1df324814d54c",
"Sample1_S1_L001.fastp.fastq.gz:md5,64639ff33d4b07d62a9079f88cbbd373",
"IndexMetricsOut.bin:md5,9e688c58a5487b8eaf69c9e1005ad0bf"
"test_sample_S1_L001.fastp.json:md5,f616058446c5822797048ea6c5d2393d",
"test_sample_S1_L001_I1_001.fastp.json:md5,42cad4ed99a3d577f100017cbe11d711",
"IndexMetricsOut.bin:md5,e2ac28695537336b53a509f48e93ed1f"
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.3"
},
"timestamp": "2024-07-23T23:50:42.910185053"
"timestamp": "2024-08-15T17:54:45.551098"
}
}
}
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