diff --git a/tests_old/data/lane_result.html b/tests_old/data/lane_result.html index 6c757e89..1110cfd4 100644 --- a/tests_old/data/lane_result.html +++ b/tests_old/data/lane_result.html @@ -1,85 +1,92 @@ - - - - - -

C6L1WANXX / - [all projects] / - [all samples] / - [all barcodes]

show barcodes

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Flowcell Summary

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Clusters (Raw)Clusters(PF)Yield (MBases)
15,320,088,57612,662,815,7551,506,875
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Lane Summary

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% >= Q30bases% One mismatchbarcode% PFClusters% Perfectbarcode% of thelaneLaneMean QualityScorePF ClustersYield (Mbases)
95.44084.59100.00100.00136.233,239,634,349385,516
94.91080.36100.00100.00236.133,077,777,014366,255
94.80082.82100.00100.00336.113,171,906,422377,457
94.88082.86100.00100.00436.123,173,497,970377,646
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+

C6L1WANXX / [all projects] / [all samples] / [all barcodes]

+ 		+

+ show barcodes +

+
+

Flowcell Summary

+ + + + + + + + + + + +
Clusters (Raw)Clusters(PF)Yield (MBases)
15,320,088,57612,662,815,7551,506,875
+

Lane Summary

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
% >= Q30bases% One mismatchbarcode% PFClusters% Perfectbarcode% of thelaneLaneMean QualityScorePF ClustersYield (Mbases)
95.44084.59100.00100.00136.233,239,634,349385,516
94.91080.36100.00100.00236.133,077,777,014366,255
94.80082.82100.00100.00336.113,171,906,422377,457
94.88082.86100.00100.00436.123,173,497,970377,646
+

+ diff --git a/tests_old/data/taca_test_cfg.yaml b/tests_old/data/taca_test_cfg.yaml index 00c56401..5e5a5188 100644 --- a/tests_old/data/taca_test_cfg.yaml +++ b/tests_old/data/taca_test_cfg.yaml @@ -14,147 +14,146 @@ statusdb: xten_db: x_flowcells analysis: - status_dir: data/ - data_dir: data/test_data/ - deliver_runfolder: - analysis_server: - host: b5.biotech.kth.se - port: - user: sara.sjunnebo - destination: test - mfs_path: - hiseq: data/ - miseq: data/ - hiseqx: data/ - novaseq: data/ - HiSeqX: - QC: - max_percentage_undetermined_indexes_pooled_lane: 5 - max_percentage_undetermined_indexes_unpooled_lane: 20 - minimum_percentage_Q30_bases_per_lane: 75 - minimum_yield_per_lane: 305000000 - max_frequency_most_represented_und_index_pooled_lane: 5 - max_frequency_most_represented_und_index_unpooled_lane: 40 - bcl2fastq: - bin: path_to_bcl_to_fastq - tenX_index_path: "data/test_10X_indexes" - smartseq_index_path: "data/test_smartseq_indexes" - options_10X: a - options_SMARTSEQ: d - options_10X_ST: e - options: - - output-dir: Demultiplexing - - opt: b - - c - options_10X_SINGLE: - - minimum-trimmed-read-length: 8 - - mask-short-adapter-reads: 8 - - ignore-missing-positions - - ignore-missing-controls - - ignore-missing-filter - - ignore-missing-bcls - - create-fastq-for-index-reads - options_10X_DUAL: - - minimum-trimmed-read-length: 8 - - mask-short-adapter-reads: 8 - - ignore-missing-positions - - ignore-missing-controls - - ignore-missing-filter - - ignore-missing-bcls - options_IDT_UMI: - - minimum-trimmed-read-length: 0 - - mask-short-adapter-reads: 0 - options_SMARTSEQ: - - create-fastq-for-index-reads - - no-lane-splitting - options_NOINDEX: - - create-fastq-for-index-reads - - barcode-mismatches: 0 - options_short_single_index: - - barcode-mismatches: 0 - samplesheets_dir: "data" - analysis_server: - host: - port: - user: - sync: - data_archive: - include: - - "*.file" - HiSeq: - QC: - max_number_undetermined_reads_simple_lane: 5000000 - max_percentage_undetermined_indexes_simple_lane: 5 - max_percentage_undetermined_indexes_NoIndex_lane: 30 - max_frequency_most_represented_und_index_NoIndex_lane: 40 - bcl2fastq: - bin: path_to_bcl_to_fastq - options: - - output-dir: Demultiplexing - - some-opt: some_val - - other-opt - samplesheets_dir: "data" - analysis_server: - host: - port: - user: - sync: - data_archive: - include: - - "*.file" - MiSeq: - QC: - max_number_undetermined_reads_simple_lane: 5000000 - max_percentage_undetermined_indexes_simple_lane: 5 - max_percentage_undetermined_indexes_NoIndex_lane: 30 - max_frequency_most_represented_und_index_NoIndex_lane: 40 - bcl2fastq: - bin: path_to_bcl_to_fastq - options: - - output-dir: Demultiplexing - samplesheets_dir: "data" - analysis_server: - host: - port: - user: - sync: - data_archive: - include: - - "*.file" - NextSeq: - samplesheets_dir: "data" - bcl2fastq: - bin: path_to_bcl_to_fastq - tenX_index_path: "data/test_10X_indexes" - smartseq_index_path: "data/test_smartseq_indexes" - options: - - output-dir: Demultiplexing - analysis_server: - host: - port: - user: - sync: - data_archive: - include: - - "*.file" - NovaSeq: - samplesheets_dir: "data" - bcl2fastq: - bin: path_to_bcl_to_fastq - tenX_index_path: "data/test_10X_indexes" - smartseq_index_path: "data/test_smartseq_indexes" - options: - - output-dir: Demultiplexing - analysis_server: - host: - port: - user: - sync: - data_archive: - include: - - "*.file" - DummySeq: - samplesheets_dir: "data" + status_dir: data/ + data_dir: data/test_data/ + deliver_runfolder: + analysis_server: + host: b5.biotech.kth.se + port: + user: sara.sjunnebo + destination: test + mfs_path: + hiseq: data/ + miseq: data/ + hiseqx: data/ + novaseq: data/ + HiSeqX: + QC: + max_percentage_undetermined_indexes_pooled_lane: 5 + max_percentage_undetermined_indexes_unpooled_lane: 20 + minimum_percentage_Q30_bases_per_lane: 75 + minimum_yield_per_lane: 305000000 + max_frequency_most_represented_und_index_pooled_lane: 5 + max_frequency_most_represented_und_index_unpooled_lane: 40 + bcl2fastq: + bin: path_to_bcl_to_fastq + tenX_index_path: "data/test_10X_indexes" + smartseq_index_path: "data/test_smartseq_indexes" + options_10X: a + options_10X_ST: e + options: + - output-dir: Demultiplexing + - opt: b + - c + options_10X_SINGLE: + - minimum-trimmed-read-length: 8 + - mask-short-adapter-reads: 8 + - ignore-missing-positions + - ignore-missing-controls + - ignore-missing-filter + - ignore-missing-bcls + - create-fastq-for-index-reads + options_10X_DUAL: + - minimum-trimmed-read-length: 8 + - mask-short-adapter-reads: 8 + - ignore-missing-positions + - ignore-missing-controls + - ignore-missing-filter + - ignore-missing-bcls + options_IDT_UMI: + - minimum-trimmed-read-length: 0 + - mask-short-adapter-reads: 0 + options_SMARTSEQ: + - create-fastq-for-index-reads + - no-lane-splitting + options_NOINDEX: + - create-fastq-for-index-reads + - barcode-mismatches: 0 + options_short_single_index: + - barcode-mismatches: 0 + samplesheets_dir: "data" + analysis_server: + host: + port: + user: + sync: + data_archive: + include: + - "*.file" + HiSeq: + QC: + max_number_undetermined_reads_simple_lane: 5000000 + max_percentage_undetermined_indexes_simple_lane: 5 + max_percentage_undetermined_indexes_NoIndex_lane: 30 + max_frequency_most_represented_und_index_NoIndex_lane: 40 + bcl2fastq: + bin: path_to_bcl_to_fastq + options: + - output-dir: Demultiplexing + - some-opt: some_val + - other-opt + samplesheets_dir: "data" + analysis_server: + host: + port: + user: + sync: + data_archive: + include: + - "*.file" + MiSeq: + QC: + max_number_undetermined_reads_simple_lane: 5000000 + max_percentage_undetermined_indexes_simple_lane: 5 + max_percentage_undetermined_indexes_NoIndex_lane: 30 + max_frequency_most_represented_und_index_NoIndex_lane: 40 + bcl2fastq: + bin: path_to_bcl_to_fastq + options: + - output-dir: Demultiplexing + samplesheets_dir: "data" + analysis_server: + host: + port: + user: + sync: + data_archive: + include: + - "*.file" + NextSeq: + samplesheets_dir: "data" + bcl2fastq: + bin: path_to_bcl_to_fastq + tenX_index_path: "data/test_10X_indexes" + smartseq_index_path: "data/test_smartseq_indexes" + options: + - output-dir: Demultiplexing + analysis_server: + host: + port: + user: + sync: + data_archive: + include: + - "*.file" + NovaSeq: + samplesheets_dir: "data" + bcl2fastq: + bin: path_to_bcl_to_fastq + tenX_index_path: "data/test_10X_indexes" + smartseq_index_path: "data/test_smartseq_indexes" + options: + - output-dir: Demultiplexing + analysis_server: + host: + port: + user: + sync: + data_archive: + include: + - "*.file" + DummySeq: + samplesheets_dir: "data" bioinfo_tab: data_dirs: