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taxprofiler
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Logic safety!

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dev
James Fellows Yates 1 year ago
parent 0245c4880b
commit 5d90c775e9
1 changed files with 10 additions and 10 deletions
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20
conf/modules.config
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@ -78,7 +78,7 @@ process {
pattern: '*.fastq.gz',
enabled: params.save_analysis_ready_fastqs,
// Don't know why `!` doesn't work here, but `== false` makes it work...
saveAs: { ( params.perform_runmerging == false || params.perform_runmerging && !meta.is_multirun ) && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs ? it : null }
saveAs: { ( params.perform_runmerging == false || ( params.perform_runmerging && !meta.is_multirun ) ) && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs ? it : null }
]
]
}
@ -113,7 +113,7 @@ process {
mode: params.publish_dir_mode,
pattern: params.shortread_qc_mergepairs ? '*merged.fastq.gz' : '*.fastp.fastq.gz',
enabled: params.save_analysis_ready_fastqs,
saveAs: { ( params.perform_runmerging == false || params.perform_runmerging && !meta.is_multirun ) && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs ? it : null }
saveAs: { ( params.perform_runmerging == false || ( params.perform_runmerging && !meta.is_multirun ) ) && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs ? it : null }
]
]
}
@ -143,7 +143,7 @@ process {
mode: params.publish_dir_mode,
pattern: '*truncated.fastq.gz',
enabled: params.save_analysis_ready_fastqs,
saveAs: { ( params.perform_runmerging == false || params.perform_runmerging && !meta.is_multirun ) && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs ? it : null }
saveAs: { ( params.perform_runmerging == false || ( params.perform_runmerging && !meta.is_multirun ) ) && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs ? it : null }
]
]
}
@ -176,7 +176,7 @@ process {
mode: params.publish_dir_mode,
pattern: '*{truncated.fastq,singleton.truncated}.gz',
enabled: params.save_analysis_ready_fastqs,
saveAs: { ( params.perform_runmerging == false || params.perform_runmerging && !meta.is_multirun ) && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && !params.shortread_qc_mergepairs && params.save_analysis_ready_fastqs ? it : null}
saveAs: { ( params.perform_runmerging == false || ( params.perform_runmerging && !meta.is_multirun ) ) && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && !params.shortread_qc_mergepairs && params.save_analysis_ready_fastqs ? it : null}
]
]
}
@ -190,7 +190,7 @@ process {
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
enabled: params.save_analysis_ready_fastqs,
saveAs: { ( params.perform_runmerging == false || params.perform_runmerging && !meta.is_multirun ) && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs ? it : null }
saveAs: { ( params.perform_runmerging == false || ( params.perform_runmerging && !meta.is_multirun ) ) && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs ? it : null }
]
]
}
@ -214,7 +214,7 @@ process {
mode: params.publish_dir_mode,
pattern: '*_porechopped.fastq.gz',
enabled: params.save_analysis_ready_fastqs,
saveAs: { ( params.perform_runmerging == false || params.perform_runmerging && !meta.is_multirun ) && !params.perform_longread_hostremoval && params.longread_qc_skipqualityfilter && !params.longread_qc_skipadaptertrim && params.perform_longread_qc && params.save_analysis_ready_fastqs ? it : null }
saveAs: { ( params.perform_runmerging == false || ( params.perform_runmerging && !meta.is_multirun ) ) && !params.perform_longread_hostremoval && params.longread_qc_skipqualityfilter && !params.longread_qc_skipadaptertrim && params.perform_longread_qc && params.save_analysis_ready_fastqs ? it : null }
]
]
}
@ -244,7 +244,7 @@ process {
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
enabled: params.save_analysis_ready_fastqs,
saveAs: { ( params.perform_runmerging == false || params.perform_runmerging && !meta.is_multirun ) && !params.perform_longread_hostremoval && !params.longread_qc_skipqualityfilter && params.perform_longread_qc && params.save_analysis_ready_fastqs ? it : null }
saveAs: { ( params.perform_runmerging == false || ( params.perform_runmerging && !meta.is_multirun ) ) && !params.perform_longread_hostremoval && !params.longread_qc_skipqualityfilter && params.perform_longread_qc && params.save_analysis_ready_fastqs ? it : null }
]
]
}
@ -273,7 +273,7 @@ process {
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
enabled: params.save_analysis_ready_fastqs,
saveAs: { ( params.perform_runmerging == false || params.perform_runmerging && !meta.is_multirun ) && !params.perform_shortread_hostremoval && params.shortread_complexityfilter_tool && params.save_analysis_ready_fastqs ? it : null }
saveAs: { ( params.perform_runmerging == false || ( params.perform_runmerging && !meta.is_multirun ) ) && !params.perform_shortread_hostremoval && params.shortread_complexityfilter_tool && params.save_analysis_ready_fastqs ? it : null }
]
]
}
@ -301,7 +301,7 @@ process {
mode: params.publish_dir_mode,
pattern: '*{_good_out.fastq.gz,_good_out_R1.fastq.gz,_good_out_R2.fastq.gz}',
enabled: params.save_analysis_ready_fastqs,
saveAs: { ( params.perform_runmerging == false || params.perform_runmerging && !meta.is_multirun ) && !params.perform_shortread_hostremoval && params.shortread_complexityfilter_tool && params.save_analysis_ready_fastqs ? it : null }
saveAs: { ( params.perform_runmerging == false || ( params.perform_runmerging && !meta.is_multirun ) ) && !params.perform_shortread_hostremoval && params.shortread_complexityfilter_tool && params.save_analysis_ready_fastqs ? it : null }
]
]
}
@ -344,7 +344,7 @@ process {
enabled: params.perform_shortread_hostremoval,
pattern: '*.fastq.gz',
enabled: params.save_analysis_ready_fastqs,
saveAs: { ( params.perform_runmerging == false || params.perform_runmerging && !meta.is_multirun ) && params.perform_shortread_hostremoval && params.save_analysis_ready_fastqs ? it : null }
saveAs: { ( params.perform_runmerging == false || ( params.perform_runmerging && !meta.is_multirun ) ) && params.perform_shortread_hostremoval && params.save_analysis_ready_fastqs ? it : null }
]
]
}

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