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Remove duplicate config and sync longread fastqc

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This commit is contained in:
James Fellows Yates 2022-03-25 15:28:30 +01:00
parent b763bfa2c0
commit ede362dbf9
2 changed files with 1 additions and 11 deletions
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10
conf/modules.config
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@ -90,16 +90,6 @@ process {
] ]
} }
withName: FASTQC_POST {
ext.args = '--quiet'
ext.prefix = { "${meta.id}_${meta.run_accession}_processed" }
publishDir = [
path: { "${params.outdir}/fastqc/processed" },
mode: 'copy',
pattern: '*.html'
]
}
withName: CAT_FASTQ { withName: CAT_FASTQ {
publishDir = [ publishDir = [
path: { "${params.outdir}/prepared_sequences" }, path: { "${params.outdir}/prepared_sequences" },

2
subworkflows/local/longread_preprocessing.nf
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@ -24,7 +24,7 @@ workflow LONGREAD_PREPROCESSING {
[ meta_new, reads ] [ meta_new, reads ]
} }
FASTQC_POST ( PORECHOP.out.reads ) FASTQC_PROCESSED ( PORECHOP.out.reads )
ch_versions = ch_versions.mix(PORECHOP.out.versions.first()) ch_versions = ch_versions.mix(PORECHOP.out.versions.first())
ch_multiqc_files = ch_multiqc_files.mix( FASTQC_PROCESSED.out.zip.collect{it[1]} ) ch_multiqc_files = ch_multiqc_files.mix( FASTQC_PROCESSED.out.zip.collect{it[1]} )