CI
bb7533583f
Build pipeline: vsh-ci-dev-gckj5
Source commit: da62b4ffe3
Source message: Add labels to qc_test component
351 lines
11 KiB
Plaintext
351 lines
11 KiB
Plaintext
nextflow.enable.dsl=2
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targetDir = params.rootDir + "/target/nextflow"
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include { remove_modality } from targetDir + '/filter/remove_modality/main.nf'
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include { move_layer } from targetDir + '/transform/move_layer/main.nf'
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include { process_samples } from targetDir + "/workflows/multiomics/process_samples/main.nf"
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params.resources_test = params.rootDir + "/resources_test"
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workflow test_wf {
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resources_test = file(params.resources_test)
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output_ch = Channel.fromList([
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[
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id: "mouse",
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input: resources_test.resolve("concat_test_data/e18_mouse_brain_fresh_5k_filtered_feature_bc_matrix_subset_unique_obs.h5mu"),
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publish_dir: "foo/",
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rna_min_counts: 2,
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output: "test.h5mu",
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],
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[
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id: "human",
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input: resources_test.resolve("concat_test_data/human_brain_3k_filtered_feature_bc_matrix_subset_unique_obs.h5mu"),
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publish_dir: "foo/",
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rna_min_counts: 2,
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output: "test.h5mu",
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]
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])
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| map{ state -> [state.id, state] }
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| process_samples
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| view { output ->
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assert output.size() == 2 : "outputs should contain two elements; [id, file]"
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assert output[1].output.toString().endsWith("test.h5mu") : "Output file should be a h5mu file. Found: ${output[1].output}"
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"Output: $output"
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}
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| toSortedList()
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| map { output_list ->
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assert output_list.size() == 1 : "output channel should contain one event"
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assert output_list[0][0] == "merged" : "Output ID should be 'merged'"
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}
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}
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workflow test_wf2 {
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resources_test = file(params.resources_test)
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output_ch = Channel.fromList([
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[
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id: "pbmc",
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input: resources_test.resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_filtered_feature_bc_matrix.h5mu"),
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var_name_mitochondrial_genes: 'mitochondrial',
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rna_min_counts: 2,
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prot_min_counts: 3,
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add_id_to_obs: true,
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add_id_make_observation_keys_unique: true,
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add_id_obs_output: "sample_id"
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],
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[
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id: "pbmc_with_more_args",
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input: resources_test.resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_filtered_feature_bc_matrix.h5mu"),
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rna_min_counts: 2,
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rna_max_counts: 1000000,
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rna_min_genes_per_cell: 1,
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rna_max_genes_per_cell: 1000000,
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rna_min_cells_per_gene: 1,
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rna_min_fraction_mito: 0.0,
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rna_max_fraction_mito: 1.0,
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prot_min_counts: 3,
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prot_max_counts: 1000000,
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prot_min_proteins_per_cell: 1,
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prot_max_proteins_per_cell: 1000000,
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prot_min_cells_per_protein: 1,
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var_name_mitochondrial_genes: 'mitochondrial',
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obs_name_mitochondrial_fraction: 'fraction_mitochondrial',
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add_id_to_obs: true,
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add_id_make_observation_keys_unique: true,
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add_id_obs_output: "sample_id"
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],
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])
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| map{ state -> [state.id, state] }
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| process_samples
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| view { output ->
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assert output.size() == 2 : "outputs should contain two elements; [id, file]"
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assert output[1].output.toString().endsWith(".h5mu") : "Output file should be a h5mu file. Found: ${output[1].output}"
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"Output: $output"
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}
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| toSortedList()
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| map { output_list ->
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// The result of this pipeline is always 1 merged sample, regardless of the number of input samples.
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assert output_list.size() == 1 : "output channel should contain one event"
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assert output_list[0][0] == "merged" : "Output ID should be 'merged'"
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}
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}
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workflow test_wf3 {
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resources_test = file(params.resources_test)
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input_ch = Channel.fromList([
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[
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id: "mouse",
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input: resources_test.resolve("concat_test_data/e18_mouse_brain_fresh_5k_filtered_feature_bc_matrix_subset_unique_obs.h5mu"),
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publish_dir: "foo/",
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rna_min_counts: 2,
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var_qc_metrics: "highly_variable",
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highly_variable_features_var_output: "highly_variable",
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],
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[
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id: "human",
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input: resources_test.resolve("concat_test_data/human_brain_3k_filtered_feature_bc_matrix_subset_unique_obs.h5mu"),
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publish_dir: "foo/",
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rna_min_counts: 2,
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var_qc_metrics: "highly_variable",
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highly_variable_features_var_output: "highly_variable",
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]
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])
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| map{ state -> [state.id, state] }
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human_ch = input_ch
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| filter{it[0] == "human"}
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| remove_modality.run(
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fromState: { id, state ->
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[
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"input": state.input,
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"modality": "atac"
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]
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},
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toState: ["input": "output"]
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)
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mouse_ch = input_ch
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| filter{it[0] == "mouse"}
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| remove_modality.run(
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fromState: { id, state ->
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[
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"input": state.input,
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"modality": "rna"
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]
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},
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toState: ["input": "output"]
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)
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output_ch_test_2 = human_ch.concat(mouse_ch)
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| process_samples
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| view { output ->
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assert output.size() == 2 : "outputs should contain two elements; [id, file]"
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assert output[1].output.toString().endsWith(".h5mu") : "Output file should be a h5mu file. Found: ${output[1].output}"
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"Output: $output"
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}
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| toSortedList()
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| map { output_list ->
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assert output_list.size() == 1 : "output channel should contain one event"
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assert output_list[0][0] == "merged" : "Output ID should be 'merged'"
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}
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}
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workflow test_wf4 {
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resources_test = file(params.resources_test)
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output_ch = Channel.fromList([
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[
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id: "10x_5k_lung_crispr",
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input: resources_test.resolve("10x_5k_lung_crispr/SC3_v3_NextGem_DI_CRISPR_A549_5K.h5mu"),
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rna_min_counts: 2,
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gdo_min_counts: 10,
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gdo_max_counts: 10000,
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add_id_to_obs: true,
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add_id_make_observation_keys_unique: true,
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add_id_obs_output: "sample_id"
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]
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])
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| map{ state -> [state.id, state] }
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| process_samples
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| view { output ->
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assert output.size() == 2 : "outputs should contain two elements; [id, file]"
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assert output[1].output.toString().endsWith(".h5mu") : "Output file should be a h5mu file. Found: ${output[1].output}"
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"Output: $output"
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}
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| toSortedList()
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| map { output_list ->
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// The result of this pipeline is always 1 merged sample, regardless of the number of input samples.
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assert output_list.size() == 1 : "output channel should contain one event"
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assert output_list[0][0] == "merged" : "Output ID should be 'merged'"
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}
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}
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workflow test_wf5 {
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resources_test = file(params.resources_test)
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output_ch = Channel.fromList([
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[
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id: "5k_human_antiCMV_T_TBNK_select_layer",
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input: resources_test.resolve("10x_5k_lung_crispr/SC3_v3_NextGem_DI_CRISPR_A549_5K.h5mu"),
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rna_min_counts: 2,
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rna_max_counts: 1000000,
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rna_min_genes_per_cell: 1,
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rna_max_genes_per_cell: 1000000,
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rna_min_cells_per_gene: 1,
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rna_min_fraction_mito: 0.0,
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rna_max_fraction_mito: 1.0,
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var_name_mitochondrial_genes: 'mitochondrial',
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obs_name_mitochondrial_fraction: 'fraction_mitochondrial',
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add_id_to_obs: true,
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add_id_make_observation_keys_unique: true,
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add_id_obs_output: "sample_id",
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rna_layer: "test_layer"
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],
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])
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| map{ state -> [state.id, state] }
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| move_layer.run(
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fromState: { id, state ->
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[
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"input": state.input,
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"output_layer": "test_layer",
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"modality": "rna"
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]
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},
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toState: ["input": "output"]
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)
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| process_samples
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| view { output ->
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assert output.size() == 2 : "outputs should contain two elements; [id, file]"
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assert output[1].output.toString().endsWith(".h5mu") : "Output file should be a h5mu file. Found: ${output[1].output}"
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"Output: $output"
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}
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| toSortedList()
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| map { output_list ->
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// The result of this pipeline is always 1 merged sample, regardless of the number of input samples.
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assert output_list.size() == 1 : "output channel should contain one event"
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assert output_list[0][0] == "merged" : "Output ID should be 'merged'"
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}
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}
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workflow test_wf6 {
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resources_test = file(params.resources_test)
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output_ch = Channel.fromList([
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[
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id: "pbmc_clr_axis_0",
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input: resources_test.resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_filtered_feature_bc_matrix.h5mu"),
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clr_axis: 1
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],
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[
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id: "pbmc_clr_axis_1",
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input: resources_test.resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_filtered_feature_bc_matrix.h5mu"),
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clr_axis: 1
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]
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])
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| map{ state -> [state.id, state] }
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| process_samples
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| view { output ->
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assert output.size() == 2 : "outputs should contain two elements; [id, file]"
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assert output[1].output.toString().endsWith(".h5mu") : "Output file should be a h5mu file. Found: ${output[1].output}"
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"Output: $output"
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}
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| toSortedList()
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| map { output_list ->
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assert output_list.size() == 1 : "output channel should contain one event"
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assert output_list[0][0] == "merged" : "Output ID should be 'merged'"
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}
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}
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// The following test is supposed to fail. It is used to test the error handling of the pipeline.
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// However, there is not way to catch the error originating from the workflow
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// workflow test_wf4 {
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// helpMessage(config)
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// // allow changing the resources_test dir
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// params.resources_test = params.rootDir + "/resources_test"
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// testParams = [
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// param_list: [
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// [
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// id: "pbmc",
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// input: params.resources_test + "/pbmc_1k_protein_v3/pbmc_1k_protein_v3_filtered_feature_bc_matrix.h5mu",
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// output: "foo.h5mu"
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// ],
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// [
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// id: "pbmc_with_more_args",
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// input: params.resources_test + "/pbmc_1k_protein_v3/pbmc_1k_protein_v3_filtered_feature_bc_matrix.h5mu",
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// output: "foo2.h5mu"
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// ],
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// ],
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// ]
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// output_ch = channelFromParams(testParams, config)
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// | run_wf
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// }
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workflow test_wf7 {
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resources_test = file(params.resources_test)
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output_ch = Channel.fromList([
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[
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id: "5k_human_antiCMV_T_TBNK_select_layer",
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input: resources_test.resolve("10x_5k_lung_crispr/SC3_v3_NextGem_DI_CRISPR_A549_5K.h5mu"),
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rna_min_counts: 2,
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rna_max_counts: 1000000,
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rna_min_genes_per_cell: 1,
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rna_max_genes_per_cell: 1000000,
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rna_min_cells_per_gene: 1,
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rna_min_fraction_mito: 0.0,
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rna_max_fraction_mito: 1.0,
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rna_enable_scaling: true,
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var_name_mitochondrial_genes: 'mitochondrial',
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obs_name_mitochondrial_fraction: 'fraction_mitochondrial',
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add_id_to_obs: true,
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add_id_make_observation_keys_unique: true,
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add_id_obs_output: "sample_id",
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rna_layer: "test_layer",
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],
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])
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| map{ state -> [state.id, state] }
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| move_layer.run(
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fromState: { id, state ->
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[
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"input": state.input,
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"output_layer": "test_layer",
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"modality": "rna"
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]
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},
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toState: ["input": "output"]
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)
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| process_samples
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| view { output ->
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assert output.size() == 2 : "outputs should contain two elements; [id, file]"
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assert output[1].output.toString().endsWith(".h5mu") : "Output file should be a h5mu file. Found: ${output[1].output}"
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"Output: $output"
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}
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| toSortedList()
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| map { output_list ->
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// The result of this pipeline is always 1 merged sample, regardless of the number of input samples.
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assert output_list.size() == 1 : "output channel should contain one event"
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assert output_list[0][0] == "merged" : "Output ID should be 'merged'"
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}
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}
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