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Reditools3: logging and threads #23

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Merged
eascarrunz merged 2 commits into from
Jun 3, 2025
Merged

Reditools3: logging and threads #23

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b88c191
fix output file name
eascarrunz Jun 3, 2025
d9a04b0
emit log and set thread numbers for reditools3
eascarrunz Jun 3, 2025
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4 changes: 4 additions & 0 deletions config/ressources/hpc.config
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Original file line number Diff line number Diff line change
Expand Up @@ -28,4 +28,8 @@ process {
cpus = 8
time = '4d'
}
withName: 'reditools3' {
cpus = 6
time = '4d'
}
}
11 changes: 11 additions & 0 deletions config/ressources/local.config
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Expand Up @@ -18,6 +18,11 @@ process {
memory = "4G"
time = '1d'
}
withLabel: 'agat' {
cpus = 1
memory = "2G"
time = '1d'
}
withLabel: 'hisat2_index' {
cpus = 4
time = '1h'
Expand All @@ -35,7 +40,13 @@ process {
time = '1d'
}
withLabel: 'bamutil' {
cpus = 1
time = '1d'
memory="12G"
}
withLabel: 'reditools3' {
cpus = 2
time = '1d'
memory="4G"
}
}
6 changes: 4 additions & 2 deletions modules/reditools3.nf
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Expand Up @@ -8,7 +8,8 @@ process reditools3 {
path genome

output:
tuple(val(meta), path("edit_table.txt"), emit: tuple_sample_serial_table)
tuple(val(meta), path("${base_name}.site_edits_reditools3.txt"), emit: tuple_sample_serial_table)
path("${base_name}.reditools3.log", emit: log)

script:
// Set the strand orientation parameter from the library type parameter
Expand All @@ -27,8 +28,9 @@ process reditools3 {
// the reditools error message
strand_orientation = meta.libtype
}
base_name = bam.BaseName

"""
python -m reditools analyze ${bam} --reference ${genome} --strand ${strand_orientation} --output-file edit_table.txt
python -m reditools analyze ${bam} --reference ${genome} --strand ${strand_orientation} --output-file ${base_name}.site_edits_reditools3.txt --threads ${task.cpus} --verbose > ${base_name}.reditools3.log
"""
}