From 4b28d9b014bead1b8e44e38cfd1e3cd7e76c7177 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 22 Jan 2025 15:13:56 +0100 Subject: [PATCH] update raredisease filenames --- .../raredisease_bundle_filenames.yaml | 202 +++++++++--------- 1 file changed, 101 insertions(+), 101 deletions(-) diff --git a/cg/resources/raredisease_bundle_filenames.yaml b/cg/resources/raredisease_bundle_filenames.yaml index f09adeea2e..971d5f6d31 100644 --- a/cg/resources/raredisease_bundle_filenames.yaml +++ b/cg/resources/raredisease_bundle_filenames.yaml @@ -200,7 +200,7 @@ id: CASEID path: PATHTOCASE/repeat_expansions/CASEID_repeat_expansion_stranger.vcf.gz path_index: ~ - step: expansionhunter_stanger + step: expansionhunter_stranger tag: case_sv_str - format: vcf id: CASEID @@ -647,302 +647,302 @@ step: chromograph_rhoviz tag: autozyg - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_regions_chromograph/CASEID_rhocall_filter_cadd_vep_upd_regions_1.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_regions/SAMPLEID_rhocall_filter_cadd_vep_upd_regions_1.png path_index: ~ step: chromograph_upd tag: regions - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_regions_chromograph/CASEID_rhocall_filter_cadd_vep_upd_regions_2.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_regions/SAMPLEID_upd_regions_2.png path_index: ~ step: chromograph_upd tag: regions - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_regions_chromograph/CASEID_rhocall_filter_cadd_vep_upd_regions_3.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_regions/SAMPLEID_upd_regions_3.png path_index: ~ step: chromograph_upd tag: regions - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_regions_chromograph/CASEID_rhocall_filter_cadd_vep_upd_regions_4.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_regions/SAMPLEID_upd_regions_4.png path_index: ~ step: chromograph_upd tag: regions - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_regions_chromograph/CASEID_rhocall_filter_cadd_vep_upd_regions_5.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_regions/SAMPLEID_upd_regions_5.png path_index: ~ step: chromograph_upd tag: regions - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_regions_chromograph/CASEID_rhocall_filter_cadd_vep_upd_regions_6.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_regions/SAMPLEID_upd_regions_6.png path_index: ~ step: chromograph_upd tag: regions - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_regions_chromograph/CASEID_rhocall_filter_cadd_vep_upd_regions_7.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_regions/SAMPLEID_upd_regions_7.png path_index: ~ step: chromograph_upd tag: regions - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_regions_chromograph/CASEID_rhocall_filter_cadd_vep_upd_regions_8.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_regions/SAMPLEID_upd_regions_8.png path_index: ~ step: chromograph_upd tag: regions - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_regions_chromograph/CASEID_rhocall_filter_cadd_vep_upd_regions_9.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_regions/SAMPLEID_upd_regions_9.png path_index: ~ step: chromograph_upd tag: regions - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_regions_chromograph/CASEID_rhocall_filter_cadd_vep_upd_regions_10.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_regions/SAMPLEID_upd_regions_10.png path_index: ~ step: chromograph_upd tag: regions - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_regions_chromograph/CASEID_rhocall_filter_cadd_vep_upd_regions_11.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_regions/SAMPLEID_upd_regions_11.png path_index: ~ step: chromograph_upd tag: regions - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_regions_chromograph/CASEID_rhocall_filter_cadd_vep_upd_regions_12.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_regions/SAMPLEID_upd_regions_12.png path_index: ~ step: chromograph_upd tag: regions - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_regions_chromograph/CASEID_rhocall_filter_cadd_vep_upd_regions_13.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_regions/SAMPLEID_upd_regions_13.png path_index: ~ step: chromograph_upd tag: regions - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_regions_chromograph/CASEID_rhocall_filter_cadd_vep_upd_regions_14.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_regions/SAMPLEID_upd_regions_14.png path_index: ~ step: chromograph_upd tag: regions - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_regions_chromograph/CASEID_rhocall_filter_cadd_vep_upd_regions_15.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_regions/SAMPLEID_upd_regions_15.png path_index: ~ step: chromograph_upd tag: regions - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_regions_chromograph/CASEID_rhocall_filter_cadd_vep_upd_regions_16.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_regions/SAMPLEID_upd_regions_16.png path_index: ~ step: chromograph_upd tag: regions - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_regions_chromograph/CASEID_rhocall_filter_cadd_vep_upd_regions_17.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_regions/SAMPLEID_upd_regions_17.png path_index: ~ step: chromograph_upd tag: regions - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_regions_chromograph/CASEID_rhocall_filter_cadd_vep_upd_regions_18.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_regions/SAMPLEID_upd_regions_18.png path_index: ~ step: chromograph_upd tag: regions - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_regions_chromograph/CASEID_rhocall_filter_cadd_vep_upd_regions_19.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_regions/SAMPLEID_upd_regions_19.png path_index: ~ step: chromograph_upd tag: regions - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_regions_chromograph/CASEID_rhocall_filter_cadd_vep_upd_regions_20.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_regions/SAMPLEID_upd_regions_20.png path_index: ~ step: chromograph_upd tag: regions - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_regions_chromograph/CASEID_rhocall_filter_cadd_vep_upd_regions_21.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_regions/SAMPLEID_upd_regions_21.png path_index: ~ step: chromograph_upd tag: regions - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_regions_chromograph/CASEID_rhocall_filter_cadd_vep_upd_regions_22.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_regions/SAMPLEID_upd_regions_22.png path_index: ~ step: chromograph_upd tag: regions - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_regions_chromograph/CASEID_rhocall_filter_cadd_vep_upd_regions_X.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_regions/SAMPLEID_upd_regions_X.png path_index: ~ step: chromograph_upd tag: regions - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_regions_chromograph/CASEID_rhocall_filter_cadd_vep_upd_regions_Y.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_regions/SAMPLEID_upd_regions_Y.png path_index: ~ step: chromograph_upd tag: regions - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_regions_chromograph/CASEID_rhocall_filter_cadd_vep_upd_regions_M.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_regions/SAMPLEID_upd_regions_M.png path_index: ~ step: chromograph_upd tag: regions - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_sites_chromograph/CASEID_rhocall_filter_cadd_vep_upd_sites_1.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_1.png path_index: ~ step: chromograph_upd tag: sites - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_sites_chromograph/CASEID_rhocall_filter_cadd_vep_upd_sites_2.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_2.png path_index: ~ step: chromograph_upd tag: sites - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_sites_chromograph/CASEID_rhocall_filter_cadd_vep_upd_sites_3.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_3.png path_index: ~ step: chromograph_upd tag: sites - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_sites_chromograph/CASEID_rhocall_filter_cadd_vep_upd_sites_4.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_4.png path_index: ~ step: chromograph_upd tag: sites - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_sites_chromograph/CASEID_rhocall_filter_cadd_vep_upd_sites_5.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_5.png path_index: ~ step: chromograph_upd tag: sites - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_sites_chromograph/CASEID_rhocall_filter_cadd_vep_upd_sites_6.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_6.png path_index: ~ step: chromograph_upd tag: sites - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_sites_chromograph/CASEID_rhocall_filter_cadd_vep_upd_sites_7.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_7.png path_index: ~ step: chromograph_upd tag: sites - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_sites_chromograph/CASEID_rhocall_filter_cadd_vep_upd_sites_8.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_8.png path_index: ~ step: chromograph_upd tag: sites - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_sites_chromograph/CASEID_rhocall_filter_cadd_vep_upd_sites_9.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_9.png path_index: ~ step: chromograph_upd tag: sites - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_sites_chromograph/CASEID_rhocall_filter_cadd_vep_upd_sites_10.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_10.png path_index: ~ step: chromograph_upd tag: sites - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_sites_chromograph/CASEID_rhocall_filter_cadd_vep_upd_sites_11.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_11.png path_index: ~ step: chromograph_upd tag: sites - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_sites_chromograph/CASEID_rhocall_filter_cadd_vep_upd_sites_12.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_12.png path_index: ~ step: chromograph_upd tag: sites - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_sites_chromograph/CASEID_rhocall_filter_cadd_vep_upd_sites_13.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_13.png path_index: ~ step: chromograph_upd tag: sites - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_sites_chromograph/CASEID_rhocall_filter_cadd_vep_upd_sites_14.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_14.png path_index: ~ step: chromograph_upd tag: sites - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_sites_chromograph/CASEID_rhocall_filter_cadd_vep_upd_sites_15.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_15.png path_index: ~ step: chromograph_upd tag: sites - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_sites_chromograph/CASEID_rhocall_filter_cadd_vep_upd_sites_16.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_16.png path_index: ~ step: chromograph_upd tag: sites - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_sites_chromograph/CASEID_rhocall_filter_cadd_vep_upd_sites_17.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_17.png path_index: ~ step: chromograph_upd tag: sites - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_sites_chromograph/CASEID_rhocall_filter_cadd_vep_upd_sites_18.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_18.png path_index: ~ step: chromograph_upd tag: sites - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_sites_chromograph/CASEID_rhocall_filter_cadd_vep_upd_sites_19.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_19.png path_index: ~ step: chromograph_upd tag: sites - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_sites_chromograph/CASEID_rhocall_filter_cadd_vep_upd_sites_20.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_20.png path_index: ~ step: chromograph_upd tag: sites - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_sites_chromograph/CASEID_rhocall_filter_cadd_vep_upd_sites_21.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_21.png path_index: ~ step: chromograph_upd tag: sites - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_sites_chromograph/CASEID_rhocall_filter_cadd_vep_upd_sites_22.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_22.png path_index: ~ step: chromograph_upd tag: sites - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_sites_chromograph/CASEID_rhocall_filter_cadd_vep_upd_sites_X.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_X.png path_index: ~ step: chromograph_upd tag: sites - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_sites_chromograph/CASEID_rhocall_filter_cadd_vep_upd_sites_Y.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_Y.png path_index: ~ step: chromograph_upd tag: sites - format: png - id: CASEID - path: PATHTOCASE/annotate_snv/genome/CASEID_rhocall_filter_cadd_vep_upd_sites_chromograph/CASEID_rhocall_filter_cadd_vep_upd_sites_M.png + id: SAMPLEID + path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_M.png path_index: ~ step: chromograph_upd tag: sites