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Update samshee #275

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merged 12 commits into from
Oct 22, 2024
Merged

Update samshee #275

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3d9dfa9
tmp
Oct 10, 2024
54a98cb
Adding samshee
nschcolnicov Oct 10, 2024
ff60023
Docs and changelog update
nschcolnicov Oct 10, 2024
4d305f1
Docs
nschcolnicov Oct 10, 2024
6e615b9
pulled from modules
nschcolnicov Oct 15, 2024
9b33143
PR comments on module
nschcolnicov Oct 15, 2024
1c87181
Update samshee
nschcolnicov Oct 15, 2024
978e3fe
revert unwanted changes
nschcolnicov Oct 15, 2024
2415665
Installed samshee from nf-core
nschcolnicov Oct 16, 2024
9adbcc2
Cleanup samshee modules.config
nschcolnicov Oct 16, 2024
ef5f6ab
Pulled from dev
nschcolnicov Oct 21, 2024
a12681f
Linting fix and changelog update
nschcolnicov Oct 21, 2024
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3 changes: 3 additions & 0 deletions conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -234,6 +234,9 @@ process {
}

withName: SAMSHEE {
ext.json_schema_validator = { params.json_schema_validator ? "--schema '${params.json_schema_validator}'" : "" }
ext.name_schema_validator = { params.name_schema_validator ? "--schema '${params.name_schema_validator}'" : "" }
ext.v1 = { params.v1_schema ? "--output-format sectioned" : "" }
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I think we can put all that in a ext.args and not ressort to creating non standard ext

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@nschcolnicov nschcolnicov Oct 15, 2024 •
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Yes, I agree, this is still a draft

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Sorry for checking in on a draft, just working on a PR on this repo too, and I saw this one appeared and was curious

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Haha no worries! 😄 .Don't want you to waste your time reviewing something that might change regardless, but any help is always appreciated!

errorStrategy = "terminate"
publishDir = [
path: { "${params.outdir}/" },
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2 changes: 1 addition & 1 deletion conf/test_full.config
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Expand Up @@ -17,5 +17,5 @@ params {
// Input data
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/samplesheet/1.3.0/samplesheet_full.csv'
demultiplexer = 'bcl2fastq'
skip_tools = 'samshee'
v1_schema = true
}
20 changes: 9 additions & 11 deletions modules/nf-core/samshee/main.nf
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8 changes: 1 addition & 7 deletions modules/nf-core/samshee/meta.yml
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4 changes: 0 additions & 4 deletions workflows/demultiplex.nf
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Expand Up @@ -63,8 +63,6 @@ workflow DEMULTIPLEX {
ch_multiqc_files = Channel.empty()
ch_multiqc_reports = Channel.empty()
checkqc_config = params.checkqc_config ? Channel.fromPath(params.checkqc_config, checkIfExists: true) : [] // file checkqc_config.yaml
ch_json_schema_validator = params.json_schema_validator ? Channel.value(params.json_schema_validator) : [] // string schema in json format
ch_name_schema_validator = params.name_schema_validator ? Channel.value(params.name_schema_validator) : [] // string schema name
ch_file_schema_validator = params.file_schema_validator ? Channel.fromPath(params.file_schema_validator, checkIfExists: true) : [] // file schema.json

// Remove adapter from Illumina samplesheet to avoid adapter trimming in demultiplexer tools
Expand Down Expand Up @@ -94,8 +92,6 @@ workflow DEMULTIPLEX {
if (!("samshee" in skip_tools) && (params.demultiplexer in ["bcl2fastq", "bclconvert", "mkfastq"])){
SAMSHEE (
ch_samplesheet.map{ meta, samplesheet, flowcell, lane -> [meta,samplesheet] },
ch_json_schema_validator,
ch_name_schema_validator,
ch_file_schema_validator
)
ch_versions = ch_versions.mix(SAMSHEE.out.versions)
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