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Updated mkfastq and removed customdumpsoftware from modules.json
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zxBIB Schcolnicov committed Aug 15, 2024
1 parent 24edd51 commit 4b9de28
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Showing 8 changed files with 164 additions and 66 deletions.
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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Original file line number Diff line number Diff line change
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'
}
89 changes: 62 additions & 27 deletions modules.json
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Original file line number Diff line number Diff line change
Expand Up @@ -8,82 +8,107 @@
"bases2fastq": {
"branch": "master",
"git_sha": "c651992bf8425fecefe14085ff486f42172cba77",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"bcl2fastq": {
"branch": "master",
"git_sha": "22261833fced91665b986c6833e91a4a5cccb0a9",
"installed_by": ["bcl_demultiplex"]
"installed_by": [
"bcl_demultiplex"
]
},
"bclconvert": {
"branch": "master",
"git_sha": "22261833fced91665b986c6833e91a4a5cccb0a9",
"installed_by": ["bcl_demultiplex"]
"installed_by": [
"bcl_demultiplex"
]
},
"cellranger/mkfastq": {
"branch": "master",
"git_sha": "d89faad13503f47372b8706008f7cdb2c4f1d859",
"installed_by": ["modules"]
"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"]
"installed_by": [
"modules"
]
},
"falco": {
"branch": "master",
"git_sha": "a236d2c2ec9e68db9b8501105d804acb359552b5",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"fastp": {
"branch": "master",
"git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"fastqc": {
"branch": "master",
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"fqtk": {
"branch": "master",
"git_sha": "c60c14b285b89bdd0607e371417dadb80385ad6e",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"kraken2/kraken2": {
"branch": "master",
"git_sha": "a13d5d945742a60bbef6e5c177e81cda540f75dc",
"installed_by": ["fastq_contam_seqtk_kraken"]
"installed_by": [
"fastq_contam_seqtk_kraken"
]
},
"md5sum": {
"branch": "master",
"git_sha": "1164836d4d3922ab937865b17086485f0f472748",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"multiqc": {
"branch": "master",
"git_sha": "b80f5fd12ff7c43938f424dd76392a2704fa2396",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"seqtk/sample": {
"branch": "master",
"git_sha": "730f3aee80d5f8d0b5fc532202ac59361414d006",
"installed_by": ["fastq_contam_seqtk_kraken"]
"installed_by": [
"fastq_contam_seqtk_kraken"
]
},
"sgdemux": {
"branch": "master",
"git_sha": "574074e6ea2497b53df1f226473a8c71524af0d0",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"untar": {
"branch": "master",
"git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
}
}
},
Expand All @@ -92,30 +117,40 @@
"bcl_demultiplex": {
"branch": "master",
"git_sha": "22261833fced91665b986c6833e91a4a5cccb0a9",
"installed_by": ["subworkflows"]
"installed_by": [
"subworkflows"
]
},
"fastq_contam_seqtk_kraken": {
"branch": "master",
"git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
"installed_by": ["subworkflows"]
"installed_by": [
"subworkflows"
]
},
"utils_nextflow_pipeline": {
"branch": "master",
"git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
"installed_by": ["subworkflows"]
"installed_by": [
"subworkflows"
]
},
"utils_nfcore_pipeline": {
"branch": "master",
"git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
"installed_by": ["subworkflows"]
"installed_by": [
"subworkflows"
]
},
"utils_nfvalidation_plugin": {
"branch": "master",
"git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
"installed_by": ["subworkflows"]
"installed_by": [
"subworkflows"
]
}
}
}
}
}
}
}
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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