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Further fixes
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parent
6895e45768
commit
ca9c0cf8fd
1 changed files with 12 additions and 6 deletions
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@ -76,7 +76,7 @@ process {
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path: { "${params.outdir}/analysis_ready_fastqs" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.shortread_complexityfilter_tool && params.perform_shortread_qc && params.save_analysis_ready_fastqs
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enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs
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]
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]
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}
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@ -109,8 +109,8 @@ process {
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[
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path: { "${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.perform_shortread_qc && params.save_analysis_ready_fastqs
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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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]
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]
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}
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@ -138,8 +138,8 @@ process {
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[
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path: { "${params.outdir}/analysis_ready_fastqs" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.shortread_complexityfilter_tool && params.perform_shortread_qc && params.save_analysis_ready_fastqs
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pattern: '*truncated.fastq.gz',
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enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs
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]
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]
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}
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@ -166,6 +166,12 @@ process {
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path: { "${params.outdir}/adapterremoval" },
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mode: params.publish_dir_mode,
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pattern: '*.settings'
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],
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[
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path: { "${params.outdir}/analysis_ready_fastqs" },
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mode: params.publish_dir_mode,
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pattern: '*{truncated.fastq,singleton.truncated}.gz',
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enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && !params.shortread_qc_mergepairs && params.save_analysis_ready_fastqs
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]
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]
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}
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@ -178,7 +184,7 @@ process {
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path: { "${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.perform_shortread_qc && params.save_analysis_ready_fastqs
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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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]
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]
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}
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