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Code Issues Releases Packages Activity

Everywhere account when no-runmerging for single libs

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This commit is contained in:
James Fellows Yates 2023-04-04 18:36:37 +02:00
parent e5e0aab59d
commit 94e88d788d
1 changed files with 22 additions and 19 deletions
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41
conf/modules.config
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@ -76,7 +76,9 @@ 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.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs 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 }
] ]
] ]
} }
@ -110,7 +112,8 @@ process {
path: { "${params.outdir}/analysis_ready_fastqs" }, path: { "${params.outdir}/analysis_ready_fastqs" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
pattern: params.shortread_qc_mergepairs ? '*merged.fastq.gz' : '*.fastp.fastq.gz', pattern: params.shortread_qc_mergepairs ? '*merged.fastq.gz' : '*.fastp.fastq.gz',
enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs 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 }
] ]
] ]
} }
@ -139,7 +142,8 @@ process {
path: { "${params.outdir}/analysis_ready_fastqs" }, path: { "${params.outdir}/analysis_ready_fastqs" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
pattern: '*truncated.fastq.gz', pattern: '*truncated.fastq.gz',
enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs 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 }
] ]
] ]
} }
@ -171,7 +175,8 @@ process {
path: { "${params.outdir}/analysis_ready_fastqs" }, path: { "${params.outdir}/analysis_ready_fastqs" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
pattern: '*{truncated.fastq,singleton.truncated}.gz', 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 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}
] ]
] ]
} }
@ -184,7 +189,8 @@ 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: '*.fastq.gz',
enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs 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 }
] ]
] ]
} }
@ -207,7 +213,8 @@ process {
path: { "${params.outdir}/analysis_ready_fastqs" }, path: { "${params.outdir}/analysis_ready_fastqs" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
pattern: '*_porechopped.fastq.gz', pattern: '*_porechopped.fastq.gz',
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 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 }
] ]
] ]
} }
@ -236,7 +243,8 @@ 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: '*.fastq.gz',
enabled: !params.perform_runmerging && !params.perform_longread_hostremoval && !params.longread_qc_skipqualityfilter && params.perform_longread_qc && params.save_analysis_ready_fastqs 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 }
] ]
] ]
} }
@ -252,7 +260,7 @@ process {
[ [
path: { "${params.outdir}/bbduk/" }, path: { "${params.outdir}/bbduk/" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
pattern: '*.{fastq.gz,log}', pattern: '*.{fastq.gz}',
enabled: params.save_complexityfiltered_reads enabled: params.save_complexityfiltered_reads
], ],
[ [
@ -264,7 +272,8 @@ 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: '*.fastq.gz',
enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && params.shortread_complexityfilter_tool && params.save_analysis_ready_fastqs 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 }
] ]
] ]
} }
@ -290,8 +299,9 @@ 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: '*{_good_out.fastq.gz,_good_out_R1.fastq.gz,_good_out_R2.fastq.gz}',
enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && params.shortread_complexityfilter_tool && params.save_analysis_ready_fastqs 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 }
] ]
] ]
} }
@ -303,12 +313,6 @@ process {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
pattern: 'bowtie2', pattern: 'bowtie2',
enabled: params.save_hostremoval_index enabled: params.save_hostremoval_index
],
[
path: { "${params.outdir}/analysis_ready_fastqs" },
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.shortread_complexityfilter_tool && !params.perform_shortread_qc && params.save_analysis_ready_fastqs
] ]
] ]
} }
@ -339,7 +343,7 @@ process {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
enabled: params.perform_shortread_hostremoval, enabled: params.perform_shortread_hostremoval,
pattern: '*.fastq.gz', pattern: '*.fastq.gz',
// Don't know why `!` doesn't work here, but `== false` makes it work... 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 }
] ]
] ]
@ -384,7 +388,6 @@ process {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
pattern: '*.fq.gz', pattern: '*.fq.gz',
enabled: params.save_analysis_ready_fastqs, enabled: params.save_analysis_ready_fastqs,
// Don't know why `!` doesn't work here, but `== false` makes it work...
saveAs: { ( !params.perform_runmerging || params.perform_runmerging && !meta.is_multirun ) && params.perform_longread_hostremoval && params.save_analysis_ready_fastqs ? it : null } saveAs: { ( !params.perform_runmerging || params.perform_runmerging && !meta.is_multirun ) && params.perform_longread_hostremoval && params.save_analysis_ready_fastqs ? it : null }
] ]
] ]