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Merge pull request #45 from aertslab/hotfixes
Hotfixes Former-commit-id: 840d5d3
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,23 +1,26 @@ | ||
| nextflow.preview.dsl=2 | ||
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| include getBaseName from '../../utils/processes/files.nf' | ||
| if(!params.containsKey("test")) { | ||
| binDir = "${workflow.projectDir}/src/scanpy/bin/" | ||
| } else { | ||
| binDir = "" | ||
| } | ||
|
|
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| process SC__SCANPY__CLUSTERING { | ||
|
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| container params.sc.scanpy.container | ||
| publishDir "${params.outdir}/data/intermediate", mode: 'symlink', overwrite: true | ||
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| input: | ||
| file(f) | ||
| tuple val(id), file(f) | ||
| output: | ||
| file "${getBaseName(f)}.SC__SCANPY__CLUSTERING.${params.off}" | ||
| tuple val(id), file("${id}.SC__SCANPY__CLUSTERING.${params.off}") | ||
| script: | ||
| """ | ||
| ${workflow.projectDir}/src/scanpy/bin/cluster/sc_clustering.py \ | ||
| ${binDir}cluster/sc_clustering.py \ | ||
| ${(params.containsKey('clusteringMethod')) ? '--method ' + params.clusteringMethod : ''} \ | ||
| ${(params.containsKey('resolution')) ? '--resolution ' + params.resolution : ''} \ | ||
| $f \ | ||
| "${getBaseName(f)}.SC__SCANPY__CLUSTERING.${params.off}" | ||
| "${id}.SC__SCANPY__CLUSTERING.${params.off}" | ||
| """ | ||
| } | ||
|
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,26 +1,30 @@ | ||
| nextflow.preview.dsl=2 | ||
|
|
||
| include getBaseName from '../../utils/processes/files.nf' | ||
| if(!params.containsKey("test")) { | ||
| binDir = "${workflow.projectDir}/src/scanpy/bin/" | ||
| } else { | ||
| binDir = "" | ||
| } | ||
|
|
||
| process SC__SCANPY__FEATURE_SELECTION { | ||
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| container params.sc.scanpy.container | ||
| publishDir "${params.outdir}/data/intermediate", mode: 'symlink', overwrite: true | ||
|
|
||
| input: | ||
| file(f) | ||
| tuple val(id), file(f) | ||
| output: | ||
| file "${getBaseName(f)}.SC__SCANPY__FEATURE_SELECTION.${params.off}" | ||
| tuple val(id), file("${id}.SC__SCANPY__FEATURE_SELECTION.${params.off}") | ||
| script: | ||
| """ | ||
| ${workflow.projectDir}/src/scanpy/bin/feature_selection/sc_select_variable_genes.py \ | ||
| ${binDir}feature_selection/sc_select_variable_genes.py \ | ||
| --method $params.featureSelectionMethod \ | ||
| ${(params.containsKey('featureSelectionMinMean')) ? '--min-mean ' + params.featureSelectionMinMean : ''} \ | ||
| ${(params.containsKey('featureSelectionMaxMean')) ? '--max-mean ' + params.featureSelectionMaxMean : ''} \ | ||
| ${(params.containsKey('featureSelectionMinDisp')) ? '--min-disp ' + params.featureSelectionMinDisp : ''} \ | ||
| ${(params.containsKey('featureSelectionMaxDisp')) ? '--max-disp ' + params.featureSelectionMaxDisp : ''} \ | ||
| $f \ | ||
| "${getBaseName(f)}.SC__SCANPY__FEATURE_SELECTION.${params.off}" | ||
| "${id}.SC__SCANPY__FEATURE_SELECTION.${params.off}" | ||
| """ | ||
| } | ||
|
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,24 +1,28 @@ | ||
| nextflow.preview.dsl=2 | ||
|
|
||
| include getBaseName from '../../utils/processes/files.nf' | ||
| if(!params.containsKey("test")) { | ||
| binDir = "${workflow.projectDir}/src/scanpy/bin/" | ||
| } else { | ||
| binDir = "" | ||
| } | ||
|
|
||
| process SC__SCANPY__MARKER_GENES { | ||
|
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| container params.sc.scanpy.container | ||
| publishDir "${params.outdir}/data/intermediate", mode: 'symlink', overwrite: true | ||
|
|
||
| input: | ||
| file(f) | ||
| tuple val(id), file(f) | ||
| output: | ||
| file "${getBaseName(f)}.SC__SCANPY__MARKER_GENES.${params.off}" | ||
| tuple val(id), file("${id}.SC__SCANPY__MARKER_GENES.${params.off}") | ||
| script: | ||
| """ | ||
| ${workflow.projectDir}/src/scanpy/bin/cluster/sc_marker_genes.py \ | ||
| ${binDir}cluster/sc_marker_genes.py \ | ||
| ${(params.containsKey('method')) ? '--method ' + params.method : ''} \ | ||
| ${(params.containsKey('groupby')) ? '--groupby ' + params.groupby : ''} \ | ||
| ${(params.containsKey('ngenes')) ? '--ngenes ' + params.ngenes : ''} \ | ||
| $f \ | ||
| "${getBaseName(f)}.SC__SCANPY__MARKER_GENES.${params.off}" | ||
| "${id}.SC__SCANPY__MARKER_GENES.${params.off}" | ||
| """ | ||
| } | ||
|
|
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