mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-13 07:23:10 +00:00
Everywhere account when no-runmerging for single libs
This commit is contained in:
parent
e5e0aab59d
commit
94e88d788d
1 changed files with 22 additions and 19 deletions
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@ -76,7 +76,9 @@ process {
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path: { "${params.outdir}/analysis_ready_fastqs" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs
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enabled: params.save_analysis_ready_fastqs,
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// Don't know why `!` doesn't work here, but `== false` makes it work...
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saveAs: { ( params.perform_runmerging == false || params.perform_runmerging && !meta.is_multirun ) && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs ? it : null }
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]
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]
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}
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@ -110,7 +112,8 @@ process {
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path: { "${params.outdir}/analysis_ready_fastqs" },
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mode: params.publish_dir_mode,
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pattern: params.shortread_qc_mergepairs ? '*merged.fastq.gz' : '*.fastp.fastq.gz',
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enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs
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enabled: params.save_analysis_ready_fastqs,
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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 }
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]
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]
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}
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@ -139,7 +142,8 @@ process {
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path: { "${params.outdir}/analysis_ready_fastqs" },
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mode: params.publish_dir_mode,
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pattern: '*truncated.fastq.gz',
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enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs
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enabled: params.save_analysis_ready_fastqs,
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saveAs: { ( params.perform_runmerging == false || params.perform_runmerging && !meta.is_multirun ) && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs ? it : null }
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]
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]
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}
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@ -171,7 +175,8 @@ process {
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path: { "${params.outdir}/analysis_ready_fastqs" },
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mode: params.publish_dir_mode,
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pattern: '*{truncated.fastq,singleton.truncated}.gz',
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enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && !params.shortread_qc_mergepairs && params.save_analysis_ready_fastqs
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enabled: params.save_analysis_ready_fastqs,
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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}
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]
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]
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}
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@ -184,7 +189,8 @@ process {
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path: { "${params.outdir}/analysis_ready_fastqs" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs
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enabled: params.save_analysis_ready_fastqs,
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saveAs: { ( params.perform_runmerging == false || params.perform_runmerging && !meta.is_multirun ) && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs ? it : null }
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]
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]
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}
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@ -207,7 +213,8 @@ process {
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path: { "${params.outdir}/analysis_ready_fastqs" },
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mode: params.publish_dir_mode,
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pattern: '*_porechopped.fastq.gz',
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enabled: !params.perform_runmerging && !params.perform_longread_hostremoval && params.longread_qc_skipqualityfilter && !params.longread_qc_skipadaptertrim && params.perform_longread_qc && params.save_analysis_ready_fastqs
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enabled: params.save_analysis_ready_fastqs,
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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 }
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]
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]
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}
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@ -236,7 +243,8 @@ process {
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path: { "${params.outdir}/analysis_ready_fastqs" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: !params.perform_runmerging && !params.perform_longread_hostremoval && !params.longread_qc_skipqualityfilter && params.perform_longread_qc && params.save_analysis_ready_fastqs
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enabled: params.save_analysis_ready_fastqs,
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saveAs: { ( params.perform_runmerging == false || params.perform_runmerging && !meta.is_multirun ) && !params.perform_longread_hostremoval && !params.longread_qc_skipqualityfilter && params.perform_longread_qc && params.save_analysis_ready_fastqs ? it : null }
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]
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]
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}
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@ -252,7 +260,7 @@ process {
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[
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path: { "${params.outdir}/bbduk/" },
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mode: params.publish_dir_mode,
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pattern: '*.{fastq.gz,log}',
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pattern: '*.{fastq.gz}',
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enabled: params.save_complexityfiltered_reads
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],
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[
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@ -264,7 +272,8 @@ process {
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path: { "${params.outdir}/analysis_ready_fastqs" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && params.shortread_complexityfilter_tool && params.save_analysis_ready_fastqs
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enabled: params.save_analysis_ready_fastqs,
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saveAs: { ( params.perform_runmerging == false || params.perform_runmerging && !meta.is_multirun ) && !params.perform_shortread_hostremoval && params.shortread_complexityfilter_tool && params.save_analysis_ready_fastqs ? it : null }
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]
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]
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}
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@ -290,8 +299,9 @@ process {
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[
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path: { "${params.outdir}/analysis_ready_fastqs" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && params.shortread_complexityfilter_tool && params.save_analysis_ready_fastqs
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pattern: '*{_good_out.fastq.gz,_good_out_R1.fastq.gz,_good_out_R2.fastq.gz}',
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enabled: params.save_analysis_ready_fastqs,
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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 }
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]
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]
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}
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@ -303,12 +313,6 @@ process {
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mode: params.publish_dir_mode,
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pattern: 'bowtie2',
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enabled: params.save_hostremoval_index
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],
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[
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path: { "${params.outdir}/analysis_ready_fastqs" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.shortread_complexityfilter_tool && !params.perform_shortread_qc && params.save_analysis_ready_fastqs
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]
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]
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}
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@ -339,7 +343,7 @@ process {
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mode: params.publish_dir_mode,
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enabled: params.perform_shortread_hostremoval,
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pattern: '*.fastq.gz',
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// Don't know why `!` doesn't work here, but `== false` makes it work...
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enabled: params.save_analysis_ready_fastqs,
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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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]
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]
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@ -384,7 +388,6 @@ process {
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mode: params.publish_dir_mode,
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pattern: '*.fq.gz',
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enabled: params.save_analysis_ready_fastqs,
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// Don't know why `!` doesn't work here, but `== false` makes it work...
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saveAs: { ( !params.perform_runmerging || params.perform_runmerging && !meta.is_multirun ) && params.perform_longread_hostremoval && params.save_analysis_ready_fastqs ? it : null }
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]
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]
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