|
545 | 545 | tag: autozyg
|
546 | 546 | - format: png
|
547 | 547 | id: SAMPLEID
|
548 |
| - path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_regions/SAMPLEID_rhocall_filter_cadd_vep_upd_regions_1.png |
| 548 | + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_regions/SAMPLEID_upd_regions_1.png |
549 | 549 | step: chromograph_upd
|
550 | 550 | tag: regions
|
551 | 551 | - format: png
|
|
800 | 800 | tag: qc-metrics
|
801 | 801 | - format: yml
|
802 | 802 | id: CASEID
|
803 |
| - path: PATHTOCASE/pipeline_info/nf_core_pipeline_software_mqc_versions.yml |
| 803 | + path: PATHTOCASE/pipeline_info/nf_core_raredisease_software_mqc_versions.yml |
804 | 804 | step: software-versions
|
805 | 805 | tag: software-versions
|
806 | 806 | - format: meta
|
|
813 | 813 | path: PATHTOCASE/multiqc/multiqc_report.html
|
814 | 814 | step: multiqc
|
815 | 815 | tag: multiqc-html
|
816 |
| -- format: meta |
817 |
| - id: CASEID |
818 |
| - path: PATHTOCASE/multiqc/multiqc_data/mosdepth_cov_dist.json |
819 |
| - step: multiqc |
820 |
| - tag: multiqc-mosdepth-covdist |
821 |
| -- format: meta |
822 |
| - id: CASEID |
823 |
| - path: PATHTOCASE/multiqc/multiqc_data/mosdepth_cumcov_dist.json |
824 |
| - step: multiqc |
825 |
| - tag: multiqc-mosdepth-cumcov |
826 |
| -- format: meta |
827 |
| - id: CASEID |
828 |
| - path: PATHTOCASE/multiqc/multiqc_data/mosdepth_perchrom.json |
829 |
| - step: multiqc |
830 |
| - tag: multiqc-mosdepth-perchrom |
831 |
| -- format: meta |
832 |
| - id: CASEID |
833 |
| - path: PATHTOCASE/multiqc/multiqc_data/multiqc_general_stats.json |
834 |
| - step: multiqc |
835 |
| - tag: multiqc-general-stats |
836 |
| -- format: meta |
837 |
| - id: CASEID |
838 |
| - path: PATHTOCASE/multiqc/multiqc_data/multiqc_peddy.json |
839 |
| - step: multiqc |
840 |
| - tag: multiqc-peddy |
841 |
| -- format: meta |
842 |
| - id: CASEID |
843 |
| - path: PATHTOCASE/multiqc/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.json |
844 |
| - step: multiqc |
845 |
| - tag: multiqc-picard-alignment |
846 |
| -- format: meta |
847 |
| - id: CASEID |
848 |
| - path: PATHTOCASE/multiqc/multiqc_data/multiqc_picard_HsMetrics.json |
849 |
| - step: multiqc |
850 |
| - tag: multiqc-picard-hs |
851 |
| -- format: meta |
852 |
| - id: CASEID |
853 |
| - path: PATHTOCASE/multiqc/multiqc_data/multiqc_picard_insertSize.json |
854 |
| - step: multiqc |
855 |
| - tag: multiqc-picard-insertsize |
856 |
| -- format: meta |
857 |
| - id: CASEID |
858 |
| - path: PATHTOCASE/multiqc/multiqc_data/multiqc_picard_quality_by_cycle.json |
859 |
| - step: multiqc |
860 |
| - tag: multiqc-picard-qualitycycle |
861 |
| -- format: meta |
862 |
| - id: CASEID |
863 |
| - path: PATHTOCASE/multiqc/multiqc_data/multiqc_picard_quality_score_distribution.json |
864 |
| - step: multiqc |
865 |
| - tag: multiqc-picard-qualitydistr |
866 |
| -- format: meta |
867 |
| - id: CASEID |
868 |
| - path: PATHTOCASE/multiqc/multiqc_data/multiqc_picard_wgsmetrics.json |
869 |
| - step: multiqc |
870 |
| - tag: multiqc-picard-wgs |
871 |
| -- format: meta |
872 |
| - id: CASEID |
873 |
| - path: PATHTOCASE/multiqc/multiqc_data/multiqc_qualimap_bamqc_genome_results.json |
874 |
| - step: multiqc |
875 |
| - tag: multiqc-picard-bamqc |
876 |
| -- format: meta |
877 |
| - id: CASEID |
878 |
| - path: PATHTOCASE/multiqc/multiqc_data/picard_histogram_1.json |
879 |
| - step: multiqc |
880 |
| - tag: multiqc-picard-histogram1 |
881 |
| -- format: meta |
882 |
| - id: CASEID |
883 |
| - path: PATHTOCASE/multiqc/multiqc_data/picard_histogram_2.json |
884 |
| - step: multiqc |
885 |
| - tag: multiqc-picard-histogram2 |
886 |
| -- format: meta |
887 |
| - id: CASEID |
888 |
| - path: PATHTOCASE/multiqc/multiqc_data/picard_histogram_3.json |
889 |
| - step: multiqc |
890 |
| - tag: multiqc-picard-histogram3 |
891 | 816 | - format: csv
|
892 | 817 | id: CASEID
|
893 | 818 | path: PATHTOCASE/CASEID_samplesheet.csv
|
|
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