diff --git a/CHANGELOG.md b/CHANGELOG.md index 6a52598..831f117 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [[PR #111](https://github.com/nf-core/pixelator/pull/111)] - Template update for nf-core/tools v3.0.2 - [[PR #112](https://github.com/nf-core/pixelator/pull/112)] - Add graph refinement options for pixelator 0.19 - [[PR #113](https://github.com/nf-core/pixelator/pull/113)] - Fix validation issues after nf-core/tools v3.0.2 update +- [[PR #114](https://github.com/nf-core/pixelator/pull/114)] - Remove `--save_recovered_components` options for graph outputs ### Parameters @@ -23,6 +24,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | `--validationShowHiddenParams` | | | `--leiden_iterations` | `--graph_max_refinement_recursion_depth` | | | `--graph_max_edges_to_split` | +| | `--graph_max_edges_to_split` | +| `--save_recovered_components` | | > [!NOTE] > Parameter has been **updated** if both old and new parameter information is present. diff --git a/conf/modules.config b/conf/modules.config index 06d17e9..a0e7414 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -228,12 +228,6 @@ process { } publishDir = [ - [ - path: { "${params.outdir}/pixelator" }, - mode: params.publish_dir_mode, - pattern: 'graph/*.components_recovered.csv', - saveAs: { (params.save_recovered_components || params.save_all) ? it : null } - ], [ path: { "${params.outdir}/pixelator" }, mode: params.publish_dir_mode, diff --git a/conf/test.config b/conf/test.config index 0952ac7..d968327 100644 --- a/conf/test.config +++ b/conf/test.config @@ -30,8 +30,9 @@ params { input_basedir = params.pipelines_testdata_base_path + 'pixelator/testdata' multiplet_recovery = true - min_size = 2 + min_size = null max_size = 100000 + dynamic_filter = null compute_polarization = true use_full_bipartite = true colocalization_min_region_count = 0 diff --git a/conf/test_panel_v2.config b/conf/test_panel_v2.config index 3e2c3d2..7707d12 100644 --- a/conf/test_panel_v2.config +++ b/conf/test_panel_v2.config @@ -33,6 +33,7 @@ params { multiplet_recovery = true min_size = 2 max_size = 100000 + dynamic_filter = null compute_polarization = true use_full_bipartite = true colocalization_min_region_count = 0 diff --git a/docs/output.md b/docs/output.md index 7d3f5d0..70b5e72 100644 --- a/docs/output.md +++ b/docs/output.md @@ -156,9 +156,7 @@ When graphs are computed and identified, their ID names are added back to the ed The graph command has the option to recover components (technical multiplets) into smaller components using community detection to find and remove problematic edges -(see `--multiplet_recovery`). These new component IDs are then stored in the "component" column. The information to keep track of the original and -newly recovered components are stored in a file (components_recovered.csv). -This file is not included in the output folder by default, but can be included by passing `--save_recovered_components`. +(see `--multiplet_recovery`). These new component IDs are then stored in the "component" column. The edge list is intermediate and by default not placed in the output folder with the final files delivered to users. Set `--save_edgelist` to enable publishing of these file. diff --git a/modules/local/pixelator/single-cell/graph/main.nf b/modules/local/pixelator/single-cell/graph/main.nf index b26b8e4..4cd5db8 100644 --- a/modules/local/pixelator/single-cell/graph/main.nf +++ b/modules/local/pixelator/single-cell/graph/main.nf @@ -13,7 +13,6 @@ process PIXELATOR_GRAPH { output: tuple val(meta), path("graph/*.edgelist.parquet") , emit: edgelist - tuple val(meta), path("graph/*.components_recovered.csv"), emit: components_recovered, optional: true tuple val(meta), path("graph/*.report.json") , emit: report_json tuple val(meta), path("graph/*.meta.json") , emit: input_params tuple val(meta), path("graph/*") , emit: all_results diff --git a/nextflow.config b/nextflow.config index fa151d0..a7ae971 100644 --- a/nextflow.config +++ b/nextflow.config @@ -70,7 +70,6 @@ params { save_demux_processed_reads = false save_demux_failed_reads = false save_collapsed_reads = false - save_recovered_components = false save_edgelist = false save_annotate_dataset = false save_raw_component_metrics = false diff --git a/nextflow_schema.json b/nextflow_schema.json index c7e57cb..9d6335a 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -260,13 +260,6 @@ "default": false, "description": "Save an intermediate CSV file containing the unfiltered graph edge list.", "help": "By default, the unfiltered edge list will not be saved to the results directory. Specify this flag (or set to `true` in your config file) to copy these files to the results directory when complete." - }, - "save_recovered_components": { - "fa_icon": "fas fa-save", - "type": "boolean", - "default": false, - "description": "Save an intermediate CSV file containing the recovered components after multiplet recovery.", - "help": "By default, the recovered component will not be saved to the results directory. Specify this flag (or set to `true` in your config file) to copy these files to the results directory when complete." } } }, @@ -283,7 +276,8 @@ "type": "integer" }, "dynamic_filter": { - "description": " Enable the estimation of dynamic size filters using a log-rank approach both: estimate both min and max size, min: estimate min size (--min-size), max: estimate max size (--max-size)", + "description": "Enable the estimation of dynamic size filters using a log-rank approach.", + "help_text": "Following options are available:\n- both: estimates both minimum and maximum component size\n- min: estimates the minimum component size (or uses {MINIMUM_N_EDGES_CELL_SIZE} edges, whichever is smallest)\n- max: estimates the maximum component size.\n\nNote that this cannot be set at the same time as `--min-size` or `--max-size`.", "type": "string", "enum": ["both", "min", "max"], "default": "min" @@ -435,7 +429,7 @@ "type": "boolean", "default": false, "description": "Save all intermediate results.", - "help": "This option is equivalent to passing:\n`--save_amplicon_reads --save_qc_passed_reads --save_qc_failed_reads --save_demux_processed_reads --save_demux_failed_reads --save_collapsed_reads --save_edgelist --save_recovered_components --save_annotate_dataset --save_analysis_dataset`" + "help": "This option is equivalent to passing:\n`--save_amplicon_reads --save_qc_passed_reads --save_qc_failed_reads --save_demux_processed_reads --save_demux_failed_reads --save_collapsed_reads --save_edgelist --save_annotate_dataset --save_analysis_dataset`" } } }, diff --git a/subworkflows/local/utils_nfcore_pixelator_pipeline/main.nf b/subworkflows/local/utils_nfcore_pixelator_pipeline/main.nf index 82872b8..bcad4b4 100644 --- a/subworkflows/local/utils_nfcore_pixelator_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_pixelator_pipeline/main.nf @@ -100,13 +100,13 @@ workflow PIPELINE_INITIALISATION { // Create a set of valid pixelator options to pass to --design ch_design_options = PIXELATOR_LIST_OPTIONS.out.designs .splitText() - .map( text -> text.trim()) + .map { it.trim() } .reduce( new HashSet() ) { prev, curr -> prev << curr } // Create a set of valid pixelator panel keys to pass using --panel ch_panel_options = PIXELATOR_LIST_OPTIONS.out.panels .splitText() - .map( text -> text.trim()) + .map { it.trim() } .reduce( new HashSet() ) { prev, curr -> prev << curr } //