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Update nextflow.config to load custom pipeline configs #582

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Update nextflow.config to load custom pipeline configs

Update nextflow.config to load custom pipeline configs #582

Run time

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Job Run time
Run standard pipeline test (23.04.0)
5m 6s
Run standard pipeline test
4m 54s
Run standard pipeline test (edge version)
4m 53s
Run extended pipeline test (23.04.0)
11m 1s
Run extended pipeline test
10m 47s
23.04.0 test_genome_options
3m 18s
23.04.0 test_genome_options_spikein
4m 50s
23.04.0 test_samplesheet
9m 31s
23.04.0 test_samplesheet_2
2m 41s
23.04.0 test_samplesheet_3
51s
23.04.0 test_filtering_noqfilter
3m 13s
23.04.0 test_filtering_withqfilter
3m 25s
23.04.0 test_bam_scale_none
2m 23s
23.04.0 test_bam_scale_spikein
2m 40s
23.04.0 test_bam_scale_cpm
3m 6s
23.04.0 test_bam_scale_rpkm
2m 52s
23.04.0 test_bam_scale_bpm
2m 41s
23.04.0 test_bam_scale_cpm_iggscale
2m 49s
23.04.0 test_peak_callers_seacr
4m 31s
23.04.0 test_peak_callers_macs2
7m 5s
23.04.0 test_peak_callers_invalid
36s
23.04.0 test_peak_callers_seacr_macs2
2m 39s
23.04.0 test_peak_callers_macs2_seacr
2m 36s
23.04.0 test_peak_callers_seacr_macs2_noigg
2m 22s
23.04.0 test_peak_callers_ctrl_tests
5m 36s
23.04.0 test_consensus_peaks_group
4m 24s
23.04.0 test_consensus_peaks_all
4m 22s
23.04.0 test_consensus_peaks_invalid
31s
23.04.0 verify_output_only_input
59s
23.04.0 verify_output_save_merged
1m 46s
23.04.0 verify_output_save_trimmed
1m 53s
23.04.0 verify_output_skip_trimming
1m 32s
23.04.0 verify_output_skip_fastqc
1m 32s
23.04.0 verify_output_save_ref
1m 4s
23.04.0 verify_output_align_only_align
3m 11s
23.04.0 verify_output_align_only_align_end_to_end
2m 9s
23.04.0 verify_output_align_only_align_local
2m 9s
23.04.0 verify_output_align_intermed
3m 6s
23.04.0 verify_output_align_save_spikein_align
2m 0s
23.04.0 verify_output_align_save_unaligned
1m 59s
23.04.0 verify_output_align_duplicates_mark
2m 37s
23.04.0 verify_output_align_duplicates_remove
3m 4s
23.04.0 verify_output_align_duplicates_remove_target
3m 9s
23.04.0 verify_output_align_linear_duplicates_remove
3m 5s
23.04.0 verify_output_align_linear_duplicates_remove_target
3m 0s
23.04.0 verify_output_only_filtering
5m 3s
23.04.0 verify_output_only_filtering_with_mitochondrial_reads
2m 36s
23.04.0 verify_output_only_filtering_without_mitochondrial_reads
2m 26s
23.04.0 verify_output_only_filtering_without_mitochondrial_reads_mito_name_null
2m 38s
23.04.0 verify_output_peak_calling_only_peak_calling
4m 57s
23.04.0 verify_output_reporting_skip_preseq_false
3m 50s
23.04.0 verify_output_reporting_skip_preseq_true
4m 52s
23.04.0 verify_output_reporting_skip_dtqc_false
11m 17s
23.04.0 verify_output_reporting_skip_dtqc_true
9m 50s
23.04.0 verify_output_reporting_skip_heatmaps_false
4m 34s
23.04.0 verify_output_reporting_skip_heatmaps_true
3m 10s
23.04.0 verify_output_reporting_skip_heatmaps_grouped
4m 3s
23.04.0 verify_output_reporting_skip_igv_false
4m 26s
23.04.0 verify_output_reporting_skip_igv_true
4m 13s
23.04.0 verify_output_reporting_skip_multiqc_false
4m 38s
23.04.0 verify_output_reporting_skip_multiqc_true
4m 13s
23.04.0 verify_output_reporting_skip_peak_qc_false
4m 44s
23.04.0 verify_output_reporting_skip_peak_qc_true
4m 42s
23.04.0 verify_output_reporting_skip_reporting
2m 44s
test_genome_options
3m 23s
test_genome_options_spikein
5m 19s
test_samplesheet
9m 24s
test_samplesheet_2
2m 27s
test_samplesheet_3
47s
test_filtering_noqfilter
3m 34s
test_filtering_withqfilter
3m 8s
test_bam_scale_none
2m 41s
test_bam_scale_spikein
2m 34s
test_bam_scale_cpm
2m 55s
test_bam_scale_rpkm
2m 36s
test_bam_scale_bpm
2m 48s
test_bam_scale_cpm_iggscale
4m 29s
test_peak_callers_seacr
4m 9s
test_peak_callers_macs2
13m 30s
test_peak_callers_invalid
43s
test_peak_callers_seacr_macs2
2m 42s
test_peak_callers_macs2_seacr
2m 41s
test_peak_callers_seacr_macs2_noigg
2m 19s
test_peak_callers_ctrl_tests
6m 4s
test_consensus_peaks_group
5m 10s
test_consensus_peaks_all
4m 25s
test_consensus_peaks_invalid
35s
verify_output_only_input
56s
verify_output_save_merged
1m 40s
verify_output_save_trimmed
2m 31s
verify_output_skip_trimming
1m 27s
verify_output_skip_fastqc
1m 34s
verify_output_save_ref
1m 27s
verify_output_align_only_align
2m 59s
verify_output_align_only_align_end_to_end
1m 58s
verify_output_align_only_align_local
3m 15s
verify_output_align_intermed
10m 30s
verify_output_align_save_spikein_align
2m 20s
verify_output_align_save_unaligned
2m 11s
verify_output_align_duplicates_mark
3m 10s
verify_output_align_duplicates_remove
3m 40s
verify_output_align_duplicates_remove_target
2m 59s
verify_output_align_linear_duplicates_remove
3m 1s
verify_output_align_linear_duplicates_remove_target
2m 51s
verify_output_only_filtering
4m 45s
verify_output_only_filtering_with_mitochondrial_reads
2m 51s
verify_output_only_filtering_without_mitochondrial_reads
2m 31s
verify_output_only_filtering_without_mitochondrial_reads_mito_name_null
3m 19s
verify_output_peak_calling_only_peak_calling
4m 56s
verify_output_reporting_skip_preseq_false
3m 34s
verify_output_reporting_skip_preseq_true
4m 8s
verify_output_reporting_skip_dtqc_false
10m 22s
verify_output_reporting_skip_dtqc_true
10m 2s
verify_output_reporting_skip_heatmaps_false
4m 15s
verify_output_reporting_skip_heatmaps_true
3m 12s
verify_output_reporting_skip_heatmaps_grouped
3m 39s
verify_output_reporting_skip_igv_false
4m 14s
verify_output_reporting_skip_igv_true
15m 36s
verify_output_reporting_skip_multiqc_false
4m 44s
verify_output_reporting_skip_multiqc_true
4m 26s
verify_output_reporting_skip_peak_qc_false
4m 42s
verify_output_reporting_skip_peak_qc_true
4m 27s
verify_output_reporting_skip_reporting
2m 47s
7h 58m 16s