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Move out integration processes #597

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merged 10 commits into from
Dec 4, 2023
Merged

Move out integration processes #597

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20de27c
move fastmnn and harmony functions into new file in modules
sjspielman Nov 28, 2023
237b765
add comment that they are unused right now
sjspielman Nov 28, 2023
e560d1a
Merge branch 'development' into sjspielman/592-move-processes
sjspielman Nov 28, 2023
6af22b6
rename workflow file
sjspielman Nov 28, 2023
7ffc2c2
Update code with merge language instead of integrate, and leave some …
sjspielman Nov 28, 2023
f4262cc
Merge branch 'development' into sjspielman/592-move-processes
sjspielman Nov 28, 2023
a52d296
replace a few more integration words with merge
sjspielman Nov 28, 2023
7b4125a
Update merge.nf
sjspielman Dec 4, 2023
8212463
Merge branch 'development' into sjspielman/592-move-processes
sjspielman Dec 4, 2023
90197cf
Apply suggestions from code review
sjspielman Dec 4, 2023
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52 changes: 0 additions & 52 deletions integrate.nf
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Do you want to rename this while you are at it, since it isn't integration at all now?

Original file line number Diff line number Diff line change
Expand Up @@ -54,57 +54,6 @@ process merge_sce {

}

// integrate with fastMNN
process integrate_fastmnn {
container params.SCPCATOOLS_CONTAINER
label 'mem_16'
label 'cpus_4'
input:
tuple val(integration_group), path(merged_sce_file)
output:
tuple val(integration_group), path(integrated_sce_file)
script:
integrated_sce_file = "${integration_group}.rds"
"""
integrate_sce.R \
--input_sce_file "${merged_sce_file}" \
--output_sce_file "${integrated_sce_file}" \
--method "fastMNN" \
--seed ${params.seed} \
--threads ${task.cpus}
"""
stub:
integrated_sce_file = "${integration_group}.rds"
"""
touch ${integrated_sce_file}
"""
}

// integrate with fastMNN
process integrate_harmony {
container params.SCPCATOOLS_CONTAINER
publishDir "${params.results_dir}/integration/${integration_group}"
label 'mem_16'
input:
tuple val(integration_group), path(merged_sce_file)
output:
tuple val(integration_group), path(integrated_sce_file)
script:
integrated_sce_file = "${integration_group}.rds"
"""
integrate_sce.R \
--input_sce_file "${merged_sce_file}" \
--output_sce_file "${integrated_sce_file}" \
--method "harmony" \
--seed ${params.seed}
"""
stub:
integrated_sce_file = "${integration_group}.rds"
"""
touch ${integrated_sce_file}
"""
}

// create integrated report and single object
process integration_report {
container params.SCPCATOOLS_CONTAINER
Expand Down Expand Up @@ -180,4 +129,3 @@ workflow {
// generate integration report
integration_report(integrate_harmony.out, file(integration_template))
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Probably want to rename this report, and we need to get rid of the integration process calls above here?

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Maybe just comment this out for now, since we also don't have the rmd yet?

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Yeah, I'm fine with just commenting out most of this. I just don't like the idea of merging in changes that by their nature break the workflow.

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and we need to get rid of the integration process calls above here?

Ah, I totally missed this 🙃. I blame my long 🦃 break. These lines are gone now!

}

52 changes: 52 additions & 0 deletions modules/integrate-sces.nf
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Original file line number Diff line number Diff line change
@@ -0,0 +1,52 @@
// These processes are not currently used by any workflow.

// Process to integrate SCEs with fastMNN
process integrate_fastmnn {
container params.SCPCATOOLS_CONTAINER
label 'mem_16'
label 'cpus_4'
input:
tuple val(integration_group), path(merged_sce_file)
output:
tuple val(integration_group), path(integrated_sce_file)
script:
integrated_sce_file = "${integration_group}.rds"
"""
integrate_sce.R \
--input_sce_file "${merged_sce_file}" \
--output_sce_file "${integrated_sce_file}" \
--method "fastMNN" \
--seed ${params.seed} \
--threads ${task.cpus}
"""
stub:
integrated_sce_file = "${integration_group}.rds"
"""
touch ${integrated_sce_file}
"""
}

// Process to integrate SCEs with Harmony
process integrate_harmony {
container params.SCPCATOOLS_CONTAINER
publishDir "${params.results_dir}/integration/${integration_group}"
label 'mem_16'
input:
tuple val(integration_group), path(merged_sce_file)
output:
tuple val(integration_group), path(integrated_sce_file)
script:
integrated_sce_file = "${integration_group}.rds"
"""
integrate_sce.R \
--input_sce_file "${merged_sce_file}" \
--output_sce_file "${integrated_sce_file}" \
--method "harmony" \
--seed ${params.seed}
"""
stub:
integrated_sce_file = "${integration_group}.rds"
"""
touch ${integrated_sce_file}
"""
}