1
0
Fork 0
mirror of https://github.com/MillironX/taxprofiler.git synced 2024-11-13 07:13:10 +00:00

Further fixes

This commit is contained in:
James Fellows Yates 2023-04-04 15:52:23 +02:00
parent 6895e45768
commit ca9c0cf8fd

View file

@ -76,7 +76,7 @@ process {
path: { "${params.outdir}/analysis_ready_fastqs" },
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.shortread_complexityfilter_tool && params.perform_shortread_qc && params.save_analysis_ready_fastqs
enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs
]
]
}
@ -109,8 +109,8 @@ process {
[
path: { "${params.outdir}/analysis_ready_fastqs" },
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
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
]
]
}
@ -138,8 +138,8 @@ process {
[
path: { "${params.outdir}/analysis_ready_fastqs" },
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.shortread_complexityfilter_tool && params.perform_shortread_qc && params.save_analysis_ready_fastqs
pattern: '*truncated.fastq.gz',
enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs
]
]
}
@ -166,6 +166,12 @@ process {
path: { "${params.outdir}/adapterremoval" },
mode: params.publish_dir_mode,
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" },
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
enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs
]
]
}