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Code Issues Releases Packages Activity

Further fixes

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This commit is contained in:
James Fellows Yates 2023-04-04 15:52:23 +02:00
parent 6895e45768
commit ca9c0cf8fd
1 changed files with 12 additions and 6 deletions
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18
conf/modules.config
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@ -76,7 +76,7 @@ process {
path: { "${params.outdir}/analysis_ready_fastqs" }, path: { "${params.outdir}/analysis_ready_fastqs" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
pattern: '*.fastq.gz', pattern: '*.fastq.gz',
enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.shortread_complexityfilter_tool && params.perform_shortread_qc && params.save_analysis_ready_fastqs enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs
] ]
] ]
} }
@ -109,8 +109,8 @@ process {
[ [
path: { "${params.outdir}/analysis_ready_fastqs" }, path: { "${params.outdir}/analysis_ready_fastqs" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
pattern: '*.fastq.gz', pattern: params.shortread_qc_mergepairs ? '*merged.fastq.gz' : '*.fastp.fastq.gz',
enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.shortread_complexityfilter_tool && params.perform_shortread_qc && params.save_analysis_ready_fastqs enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs
] ]
] ]
} }
@ -138,8 +138,8 @@ process {
[ [
path: { "${params.outdir}/analysis_ready_fastqs" }, path: { "${params.outdir}/analysis_ready_fastqs" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
pattern: '*.fastq.gz', pattern: '*truncated.fastq.gz',
enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.shortread_complexityfilter_tool && params.perform_shortread_qc && params.save_analysis_ready_fastqs enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs
] ]
] ]
} }
@ -166,6 +166,12 @@ process {
path: { "${params.outdir}/adapterremoval" }, path: { "${params.outdir}/adapterremoval" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
pattern: '*.settings' pattern: '*.settings'
],
[
path: { "${params.outdir}/analysis_ready_fastqs" },
mode: params.publish_dir_mode,
pattern: '*{truncated.fastq,singleton.truncated}.gz',
enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && !params.shortread_qc_mergepairs && params.save_analysis_ready_fastqs
] ]
] ]
} }
@ -178,7 +184,7 @@ process {
path: { "${params.outdir}/analysis_ready_fastqs" }, path: { "${params.outdir}/analysis_ready_fastqs" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
pattern: '*.fastq.gz', pattern: '*.fastq.gz',
enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.shortread_complexityfilter_tool && params.perform_shortread_qc && params.save_analysis_ready_fastqs enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs
] ]
] ]
} }