From f2d79f6522810e1dde2285fc42acb568884c54db Mon Sep 17 00:00:00 2001 From: GeiserX <9169332+GeiserX@users.noreply.github.com> Date: Mon, 9 Nov 2026 10:57:23 +0100 Subject: [PATCH 1/4] fix(couple): say why CYP21A2 was not assessed, from the table's message The not-assessed list printed only the reason code (low_mapq0_share). It now prints step 35's message row, which says the BAM lacks multi-mapping reads and how to realign; a table without that row keeps the reason code. Bead: pgp-pfw6 --- bin/couple_report.py | 29 +++++++++++++++++++++++------ docs/39-couple.md | 2 +- tests/test_couple_report.py | 14 ++++++++++++++ 3 files changed, 38 insertions(+), 7 deletions(-) diff --git a/bin/couple_report.py b/bin/couple_report.py index 1096de13..9cd5d3c4 100755 --- a/bin/couple_report.py +++ b/bin/couple_report.py @@ -413,17 +413,34 @@ def smn_finding(path, genes): return [finding("SMN1", text, 1 if p["cn"] == 1 else 2)], "SMN1 %d cop%s" % (p["cn"], "y" if p["cn"] == 1 else "ies") -def cyp21a2_finding(path, genes): - """CYP21A2 from depth and PSV sites (step 35's _cyp21a2_psv.tsv): - ([findings], text of what was read). A deletion or a possible - conversion is a finding on one copy, on two when a site has no CYP21A2 - copy left.""" +def cyp21a2_table(path): + """Step 35's CYP21A2 table (metric, value) as a dict.""" t = {} with open(path, encoding="utf-8", errors="replace") as f: for line in f: c = line.rstrip("\n").split("\t", 1) if len(c) == 2 and c[0] != "metric": t[c[0]] = c[1] + return t + + +def cyp21a2_gap(path, txt): + """Why step 35 did not assess CYP21A2, for the not-assessed list: the + table's message (it says, for a BAM without multi-mapping reads, that the + aligner and not the genome stopped the call), or the short text with the + reason code for a table from before the message row.""" + msg = cyp21a2_table(path).get("message", ".") + if msg.startswith("not assessed: "): + return "CYP21A2 " + msg + return txt + + +def cyp21a2_finding(path, genes): + """CYP21A2 from depth and PSV sites (step 35's _cyp21a2_psv.tsv): + ([findings], text of what was read). A deletion or a possible + conversion is a finding on one copy, on two when a site has no CYP21A2 + copy left.""" + t = cyp21a2_table(path) if t.get("status") not in ("called", "not assessed"): die(["%s: not step 35's CYP21A2 table (bin/copy_number.py call --locus CYP21A2)" % path]) if t["status"] != "called": @@ -835,7 +852,7 @@ def cmd_screen(a): m, txt = cyp21a2_finding(cyp[s], genes) f += m if txt.startswith("CYP21A2 not assessed"): - gaps.append("CYP21A2 deletion and conversions of %s: %s." % (s, txt)) + gaps.append("CYP21A2 deletion and conversions of %s: %s." % (s, cyp21a2_gap(cyp[s], txt))) else: gaps.append("CYP21A2 deletion and conversions of %s: step 35's CYP21A2 table was not passed " "to the couple screen (--cyp21a2)." % s) diff --git a/docs/39-couple.md b/docs/39-couple.md index 5644ef26..dbc549f4 100644 --- a/docs/39-couple.md +++ b/docs/39-couple.md @@ -25,7 +25,7 @@ Before this step a couple had to compare two ClinVar tables by hand ([Multi-Samp | ClinVar pathogenic or likely pathogenic hit | step 06, `clinvar/_clinvar_hits.vcf` (required) | the genotype carries the alternate allele and ClinVar's `GENEINFO` names a gene of the carrier list | | Deletion | step 19 (Delly), `delly/_sv.vcf.gz` | `SVTYPE=DEL`, `FILTER` PASS and a per-sample `FT` that is not a failed filter, the genotype carries it, it is 50 bp or longer, it removes at least one exon of a listed gene (GENCODE exons), when it is longer than 1,000 bp read depth shows the loss, and it does not match a common deletion (see below) | | SMN1 copy number | step 35 (Parascopy), `paralogs/_smn_copy_number.tsv` | SMN1 exon 7 at 1 copy (a carrier) or 0, with filter PASS and quality 20 or more, by step 35's rule | -| CYP21A2 deletion or conversion | step 35 (depth and six PSV sites), `paralogs/_cyp21a2_psv.tsv` | the table's `finding` is `deletion` or `conversion` (on both copies when a site has no CYP21A2 copy left); unconfirmed, short reads. Step 39 and the Nextflow couple screen (`COUPLE_CARRIER`) both pass it | +| CYP21A2 deletion or conversion | step 35 (depth and six PSV sites), `paralogs/_cyp21a2_psv.tsv` | the table's `finding` is `deletion` or `conversion` (on both copies when a site has no CYP21A2 copy left); unconfirmed, short reads. A table whose `status` is `not assessed` gives no finding, and the list of what was not assessed prints its `message` (why, such as a BAM without multi-mapping reads), or its `reason` for a table without that row. Step 39 and the Nextflow couple screen (`COUPLE_CARRIER`) both pass it | | FMR1 and FXN repeats | step 09 (ExpansionHunter), `expansion_hunter/_eh.vcf` | an FMR1 allele of 55 CGG or more (a premutation; more than 200 is a full mutation), an FXN allele of 66 GAA or more | Short-read Delly can mark PASS a long deletion, even one of many megabases, that read depth contradicts, and such a call removes an exon of hundreds of listed genes at once. So a deletion longer than 1,000 bp counts only when Delly's own read-depth copy number (`FORMAT/RDCN`, the depth inside the deletion against its flanks) is below a normal region's copies: 1 on a male's chrX or chrY outside the pseudoautosomal regions, 2 everywhere else. When the pedigree gives no sex, every region is judged against 2. Delly infers the sex itself and scales RDCN to it, so a long artefact on an unsexed male's chrX or chrY reads 1 and still counts: give the sex in the pedigree and in the samplesheet. A heterozygous loss reads 1, a homozygous or hemizygous loss 0. A long deletion with RDCN at the normal count or more, or with no estimate (`.` or a negative value, no reads in the flanks), is set aside, and the table of what was assessed gives the count. 1,000 bp is Delly's own line between small and large SVs in its read counts (`indelsize` in Delly's source); a deletion that size or smaller rests on its split reads and read pairs alone. A deletion VCF without the RDCN field (not written by Delly 2.x) is read as before, without the depth check. diff --git a/tests/test_couple_report.py b/tests/test_couple_report.py index 60bc5b4b..10f469ed 100644 --- a/tests/test_couple_report.py +++ b/tests/test_couple_report.py @@ -257,6 +257,20 @@ def main(): [r["findings_a"] for r in rows(f"{t}/smnn/couple_A_B.tsv") if r["gene"] == "SMN1"] == ["."] and "SMN1 copy number of A: SMN1 not assessed: no read over chr5:70951946-70951946; copy number not resolved." in md6n, md6n) + # 6b. CYP21A2 not assessed: the table's message, the reason code for an older table + why = ("not assessed: the BAM has few or no multi-mapping reads here (reads of mapping quality 0 make up " + "0.0% of the depth over CYP21A2 and CYP21A1P, under 2%), the sign of an aligner that leaves out the " + "reads that fit both copies") + na = "metric\tvalue\nstatus\tnot assessed\ncyp21a2_copies\t.\nfinding\t.\nreason\tlow_mapq0_share\n" + ca, cb = put(f"{t}/A_cyp.tsv", na + f"message\t{why}\n"), put(f"{t}/B_cyp.tsv", na) + run("screen", "--pedigree", ped, "--genes", GENES, "--clinvar", f"A={a_none}", "--clinvar", f"B={a_none}", + "--cyp21a2", f"A={ca}", "--cyp21a2", f"B={cb}", "--out-dir", f"{t}/cyp") + md6c = open(f"{t}/cyp/couple_A_B.md").read() if os.path.exists(f"{t}/cyp/couple_A_B.md") else "" + check("CYP21A2 not assessed: the not-assessed list prints the table's message (the aligner stopped the call)", + f"CYP21A2 deletion and conversions of A: CYP21A2 {why}." in md6c, md6c) + check("CYP21A2 not assessed in a table without the message row: the reason code", + "CYP21A2 deletion and conversions of B: CYP21A2 not assessed (low_mapq0_share)." in md6c, md6c) + # 3b. read depth: a long Delly deletion counts only when RDCN shows the loss genes_mid = {g: mid(g) for g in ("GBA1", "PAH", "CFTR", "HBB", "DMD", "OTC")} dexons = put(f"{t}/depth_exons.bed", "".join( From e43820153503134a86c939751f6d5339ce165a22 Mon Sep 17 00:00:00 2001 From: GeiserX <9169332+GeiserX@users.noreply.github.com> Date: Mon, 9 Nov 2026 10:57:27 +0100 Subject: [PATCH 2/4] test(e2e): check the Nextflow Lp(a) card prints the KIV-2 4925G>A line Bead: pgp-pfw6 --- tests/e2e/lpa-1.sh | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/tests/e2e/lpa-1.sh b/tests/e2e/lpa-1.sh index 3089c320..e8124874 100755 --- a/tests/e2e/lpa-1.sh +++ b/tests/e2e/lpa-1.sh @@ -139,6 +139,15 @@ check "control: the comparison sees a difference" bash -c '! cmp -s "$1" "$2"' _ HTML=$(find "$NF_OUT" -name "${H}_report.html" | head -n 1) check "the HTML report has the Lp(a) card with the count" has "

Lp\(a\): LPA KIV-2 Repeat Count

" "$(cat "$HTML" 2>/dev/null)" check "and the card shows the count" has "KIV-2 repeats \(both chromosomes\): ${N} " "$(cat "$HTML" 2>/dev/null)" +# The 4925G>A line beside the count: HTML_REPORT got the LPA task's +# _lpa_kiv2_4925.tsv and its reader ran (no "wrote no", no failed check). +NULL_LINE=$(grep -o 'KIV-2 4925G>A null allele (rs1484919544): [^<]*' "$HTML" 2>/dev/null | head -n 1) +check "the card prints the KIV-2 4925G>A null-allele line" has '^KIV-2 4925G>A null allele \(rs1484919544\): ' "$NULL_LINE" +check "and the line is a reading of the LPA task's table" lacks 'wrote no|the check failed' \ + "$(grep -A1 -F "$NULL_LINE" "$HTML" 2>/dev/null)" +check "control: a card without the line fails the check" lacks 'KIV-2 4925G>A null allele \(rs1484919544\): ' \ + "$(sed 's/KIV-2 4925G>A null allele//' "$HTML" 2>/dev/null)" +echo "lpa: the Nextflow card's 4925G>A line: ${NULL_LINE}" >> "$E2E_NOTES" rm -rf "${G:?}/${V}" "${G:?}/${L}" "${T:?}"/*.bam "${T:?}"/*.bai "${T:?}/lpa.sam" finish From 21b90514c3aeccb2b0199e97d09001221ac0c6f5 Mon Sep 17 00:00:00 2001 From: GeiserX <9169332+GeiserX@users.noreply.github.com> Date: Mon, 9 Nov 2026 10:57:30 +0100 Subject: [PATCH 3/4] ci(e2e): run the step 35 and 46 cases when bin/traits_report.py changes Bead: pgp-pfw6 --- scripts/ci/e2e-case-paths.tsv | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/scripts/ci/e2e-case-paths.tsv b/scripts/ci/e2e-case-paths.tsv index 59ebfe45..6ae6b653 100644 --- a/scripts/ci/e2e-case-paths.tsv +++ b/scripts/ci/e2e-case-paths.tsv @@ -72,19 +72,19 @@ clinical-filter-mane-and-quality-3-modules assets/construct_variants.tsv assets/ clinvar-clip-check-1 assets/construct_variants.tsv assets/deep_intronic_sites.tsv bin/cdna_scan.py bin/clinvar_hits.awk bin/clinvar_join_adjacent.awk bin/clip_check.py bin/render_report.py scripts/06-clinvar-screen.sh scripts/ci/fake-docker/lib.sh clinvar-combined-allele-1 assets/construct_variants.tsv assets/deep_intronic_sites.tsv assets/stub/sample.bam assets/stub/sample.bam.bai bin/cdna_scan.py bin/clinvar_hits.awk bin/clinvar_join_adjacent.awk bin/clip_check.py modules/local/clinvar_screen/* modules/local/vcf_precheck/* scripts/06-clinvar-screen.sh scripts/24-html-report.sh scripts/ci/fake-docker/lib.sh scripts/generate-report.sh scripts/validate-setup.sh tests/fixtures/vcf/combined_allele_clinvar.vcf tests/fixtures/vcf/combined_allele_sample.vcf clinvar-cpsr-quality-1 assets/construct_variants.tsv assets/deep_intronic_sites.tsv bin/cdna_scan.py bin/clinvar_hits.awk bin/clinvar_join_adjacent.awk bin/clip_check.py bin/render_report.py scripts/06-clinvar-screen.sh scripts/ci/fake-docker/lib.sh -cn-engine-1-parity assets/bloodtype_markers.tsv bin/bloodtype_report.py bin/cn_loci.tsv bin/copy_number.py bin/hba_copy_number.py bin/lpa_kiv2.py scripts/41-bloodtype.sh scripts/46-lpa.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh -cn-guard-1-mapq0 bin/cn_loci.tsv bin/copy_number.py modules/local/parascopy/* scripts/35-paralogs.sh +cn-engine-1-parity assets/bloodtype_markers.tsv bin/bloodtype_report.py bin/cn_loci.tsv bin/copy_number.py bin/hba_copy_number.py bin/lpa_kiv2.py bin/traits_report.py scripts/41-bloodtype.sh scripts/46-lpa.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh +cn-guard-1-mapq0 bin/cn_loci.tsv bin/copy_number.py bin/traits_report.py modules/local/parascopy/* scripts/35-paralogs.sh cn-intervals-1-catalog bin/cn_loci.tsv scripts/ci/build-cn-intervals.py scripts/ci/fake-docker/lib.sh -cn-intervals-2-hg002 assets/par_grch38.bed assets/paralog_loci.tsv bin/cn_loci.tsv bin/copy_number.py bin/hba_copy_number.py bin/lpa_kiv2.py modules/local/deepvariant/* modules/local/parascopy/* modules/local/vcf_precheck/* scripts/35-paralogs.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh +cn-intervals-2-hg002 assets/par_grch38.bed assets/paralog_loci.tsv bin/cn_loci.tsv bin/copy_number.py bin/hba_copy_number.py bin/lpa_kiv2.py bin/traits_report.py modules/local/deepvariant/* modules/local/parascopy/* modules/local/vcf_precheck/* scripts/35-paralogs.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh cn-report-1-tables assets/carrier_genes.tsv assets/par_grch38.bed bin/collect_summary.py bin/couple_report.py bin/family_report.py bin/paraphase_report.py bin/render_report.py bin/results_index.py scripts/24-html-report.sh scripts/39-couple.sh scripts/ci/fake-docker/lib.sh scripts/generate-report.sh comphet-phasing-1-reads assets/construct_variants.tsv assets/stub/sample.bam assets/stub/sample.bam.bai bin/clip_check.py bin/comphet_phase.py bin/constraint_join.awk bin/csq_rank.awk modules/local/slivar/* modules/local/vcf_precheck/* modules/local/vep/* scripts/13-vep-annotation.sh scripts/31-slivar.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh tests/fixtures/comphet/make_fixture.py construct-scan-1-both assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/construct_variants.tsv assets/deep_intronic_sites.tsv assets/mito_confirmed.tsv assets/stub/sample.bam assets/stub/sample.bam.bai assets/stub/sample.vcf.gz bin/cdna_scan.py bin/clinvar_hits.awk bin/clinvar_join_adjacent.awk bin/clip_check.py bin/collect_summary.py bin/render_report.py bin/results_index.py modules/local/clinvar_screen/* modules/local/html_report/* modules/local/vcf_precheck/* scripts/06-clinvar-screen.sh scripts/24-html-report.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh consumer-export-1 assets/chip_genes.tsv assets/par_grch38.bed bin/chip_report.py bin/export_consumer.py modules/local/chip/* modules/local/export_consumer/* modules/local/vcf_precheck/* scripts/40-export-consumer.sh scripts/49-chip.sh scripts/chip-to-vcf.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh tests/fixtures/consumer_export/sites.tsv.gz containers-software-versions scripts/ci/fake-docker/lib.sh scripts/ci/gen-containers-config.sh -couple-carrier-1 assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/construct_variants.tsv assets/deep_intronic_sites.tsv assets/families.example.tsv assets/mito_confirmed.tsv assets/par_grch38.bed assets/paralog_loci.tsv assets/pedigree.example.tsv assets/pgx_genes.tsv assets/str_extra_loci.json assets/stub/db/catalog.json assets/stub/db/hla.dat assets/stub/db/kir.dat assets/stub/pedigree.tsv assets/stub/sample.bam assets/stub/sample.bam.bai assets/stub/sample.vcf.gz bin/cdna_scan.py bin/clinvar_hits.awk bin/clinvar_join_adjacent.awk bin/clip_check.py bin/cn_loci.tsv bin/collect_summary.py bin/copy_number.py bin/couple_report.py bin/cyp2d6_depth_check.py bin/family_report.py bin/family_segments.py bin/hba_copy_number.py bin/ibd_report.py bin/lpa_kiv2.py bin/mosaic_sex_loss.py bin/pgx_outside_calls.py bin/render_report.py bin/results_index.py bin/rfc1_motif.py bin/strchive_convert.py modules/local/clinvar_screen/* modules/local/couple/* modules/local/delly/* modules/local/expansion_hunter/* modules/local/hla_typing/* modules/local/html_report/* modules/local/parascopy/* modules/local/somalier/* modules/local/t1k_build/* modules/local/vcf_precheck/* scripts/06-clinvar-screen.sh scripts/08-hla-typing.sh scripts/09-expansion-hunter.sh scripts/19-delly.sh scripts/24-html-report.sh scripts/32-pypgx.sh scripts/33-sample-qc.sh scripts/35-paralogs.sh scripts/36-pgx-consensus.sh scripts/38-family.sh scripts/39-couple.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh +couple-carrier-1 assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/construct_variants.tsv assets/deep_intronic_sites.tsv assets/families.example.tsv assets/mito_confirmed.tsv assets/par_grch38.bed assets/paralog_loci.tsv assets/pedigree.example.tsv assets/pgx_genes.tsv assets/str_extra_loci.json assets/stub/db/catalog.json assets/stub/db/hla.dat assets/stub/db/kir.dat assets/stub/pedigree.tsv assets/stub/sample.bam assets/stub/sample.bam.bai assets/stub/sample.vcf.gz bin/cdna_scan.py bin/clinvar_hits.awk bin/clinvar_join_adjacent.awk bin/clip_check.py bin/cn_loci.tsv bin/collect_summary.py bin/copy_number.py bin/couple_report.py bin/cyp2d6_depth_check.py bin/family_report.py bin/family_segments.py bin/hba_copy_number.py bin/ibd_report.py bin/lpa_kiv2.py bin/mosaic_sex_loss.py bin/pgx_outside_calls.py bin/render_report.py bin/results_index.py bin/rfc1_motif.py bin/strchive_convert.py bin/traits_report.py modules/local/clinvar_screen/* modules/local/couple/* modules/local/delly/* modules/local/expansion_hunter/* modules/local/hla_typing/* modules/local/html_report/* modules/local/parascopy/* modules/local/somalier/* modules/local/t1k_build/* modules/local/vcf_precheck/* scripts/06-clinvar-screen.sh scripts/08-hla-typing.sh scripts/09-expansion-hunter.sh scripts/19-delly.sh scripts/24-html-report.sh scripts/32-pypgx.sh scripts/33-sample-qc.sh scripts/35-paralogs.sh scripts/36-pgx-consensus.sh scripts/38-family.sh scripts/39-couple.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh couple-common-sv-1 assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/construct_variants.tsv assets/deep_intronic_sites.tsv assets/families.example.tsv assets/mito_confirmed.tsv assets/par_grch38.bed assets/pedigree.example.tsv assets/stub/pedigree.tsv assets/stub/sample.bam assets/stub/sample.bam.bai assets/stub/sample.vcf.gz bin/cdna_scan.py bin/clinvar_hits.awk bin/clinvar_join_adjacent.awk bin/clip_check.py bin/cn_loci.tsv bin/collect_summary.py bin/copy_number.py bin/couple_report.py bin/family_report.py bin/family_segments.py bin/hba_copy_number.py bin/ibd_report.py bin/lpa_kiv2.py bin/render_report.py bin/results_index.py modules/local/clinvar_screen/* modules/local/couple/* modules/local/delly/* modules/local/html_report/* modules/local/vcf_precheck/* scripts/06-clinvar-screen.sh scripts/19-delly.sh scripts/24-html-report.sh scripts/38-family.sh scripts/39-couple.sh scripts/ci/fake-docker/lib.sh scripts/setup.sh scripts/validate-setup.sh cpic-phenoconversion-1-medications assets/pgx_contraindications.tsv assets/pgx_genes.tsv assets/pgx_inhibitors.tsv bin/cn_loci.tsv bin/collect_summary.py bin/copy_number.py bin/cyp2d6_depth_check.py bin/hba_copy_number.py bin/lpa_kiv2.py bin/pgx_mito_merge.py bin/pgx_outside_calls.py bin/pgx_parse.py bin/pgx_refblock_fill.py modules/local/cpic_lookup/* modules/local/pharmcat/* modules/local/vcf_precheck/* scripts/07-pharmacogenomics.sh scripts/27-cpic-lookup.sh scripts/32-pypgx.sh scripts/36-pgx-consensus.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh -cyp21a2-short-reads-1-hg002 bin/cn_loci.tsv bin/copy_number.py modules/local/parascopy/* scripts/35-paralogs.sh +cyp21a2-short-reads-1-hg002 bin/cn_loci.tsv bin/copy_number.py bin/traits_report.py modules/local/parascopy/* scripts/35-paralogs.sh exomiser-1 assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/families.example.tsv assets/mito_confirmed.tsv assets/par_grch38.bed assets/pedigree.example.tsv assets/pgx_genes.tsv assets/stub/db/hla.dat assets/stub/db/kir.dat assets/stub/pedigree.tsv assets/stub/sample.bam assets/stub/sample.bam.bai assets/stub/sample.vcf.gz assets/stub/sample.vcf.gz.tbi bin/cn_loci.tsv bin/collect_summary.py bin/copy_number.py bin/cyp2d6_depth_check.py bin/exomiser_report.py bin/family_report.py bin/family_segments.py bin/hba_copy_number.py bin/ibd_report.py bin/lpa_kiv2.py bin/pgx_outside_calls.py bin/render_report.py bin/results_index.py modules/local/exomiser/* modules/local/hla_typing/* modules/local/html_report/* modules/local/t1k_build/* modules/local/vcf_precheck/* scripts/08-hla-typing.sh scripts/24-html-report.sh scripts/32-pypgx.sh scripts/36-pgx-consensus.sh scripts/38-family.sh scripts/48-exomiser.sh scripts/ci/fake-docker/lib.sh scripts/setup.sh scripts/validate-setup.sh expansions-and-rfc1-1-motif assets/str_extra_loci.json assets/stub/db/catalog.json bin/rfc1_motif.py bin/strchive_convert.py scripts/09-expansion-hunter.sh scripts/09b-stranger.sh scripts/ci/fake-docker/lib.sh scripts/generate-report.sh families-file-1 assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/construct_variants.tsv assets/deep_intronic_sites.tsv assets/families.example.tsv assets/mito_confirmed.tsv assets/par_grch38.bed assets/pedigree.example.tsv assets/pgx_genes.tsv assets/stub/db/hla.dat assets/stub/db/kir.dat assets/stub/pedigree.tsv assets/stub/sample.bam assets/stub/sample.bam.bai assets/stub/sample.vcf.gz bin/cdna_scan.py bin/clinvar_hits.awk bin/clinvar_join_adjacent.awk bin/clip_check.py bin/cn_loci.tsv bin/collect_summary.py bin/copy_number.py bin/couple_report.py bin/cyp2d6_depth_check.py bin/family_report.py bin/family_segments.py bin/hba_copy_number.py bin/ibd_report.py bin/lpa_kiv2.py bin/pgx_outside_calls.py bin/render_report.py bin/results_index.py modules/local/align_minimap2/* modules/local/clinvar_screen/* modules/local/couple/* modules/local/deepvariant/* modules/local/fastp/* modules/local/hla_typing/* modules/local/html_report/* modules/local/t1k_build/* modules/local/vcf_precheck/* scripts/01b-fastp-qc.sh scripts/06-clinvar-screen.sh scripts/08-hla-typing.sh scripts/24-html-report.sh scripts/32-pypgx.sh scripts/36-pgx-consensus.sh scripts/38-family.sh scripts/39-couple.sh scripts/ci/check-images.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh tests/fixtures/families/stub_families.tsv @@ -93,7 +93,7 @@ fixitfelix-chr21-1 assets/callability_genes.tsv scripts/16b-mosdepth.sh scripts/ followups-ci-3-sv-rule-regions assets/sv_rule_regions.tsv scripts/ci/build-sv-rule-regions.sh scripts/ci/fake-docker/lib.sh followups-clinvar-traits-1-rules-html assets/genotype_rules.tsv assets/traits.tsv bin/render_report.py bin/traits_report.py scripts/42-traits.sh scripts/ci/check-rule-alleles.sh followups-cn-1-couple-report assets/carrier_genes.tsv assets/par_grch38.bed assets/stub/pedigree.tsv bin/collect_summary.py bin/couple_report.py bin/family_report.py bin/render_report.py bin/results_index.py modules/local/couple/* modules/local/html_report/* scripts/39-couple.sh scripts/ci/fake-docker/lib.sh -followups-nf-1-nf-wiring assets/stub/* assets/test_samplesheet.csv assets/steps.tsv bin/collect_summary.py bin/render_report.py bin/results_index.py bin/run_state.py conf/test.config conf/test_all.config conf/containers.config modules/local/html_report/* modules/local/couple/* modules/local/parascopy/* modules/local/deepvariant/* modules/local/cpsr/* modules/local/clinvar_screen/* modules/local/locityper/* workflows/* tests/fixtures/consumer_export/sites.tsv.gz +followups-nf-1-nf-wiring assets/stub/* assets/test_samplesheet.csv assets/steps.tsv bin/collect_summary.py bin/render_report.py bin/results_index.py bin/run_state.py bin/traits_report.py conf/test.config conf/test_all.config conf/containers.config modules/local/html_report/* modules/local/couple/* modules/local/parascopy/* modules/local/deepvariant/* modules/local/cpsr/* modules/local/clinvar_screen/* modules/local/locityper/* workflows/* tests/fixtures/consumer_export/sites.tsv.gz genome-lookup-1 scripts/ci/fake-docker/lib.sh scripts/owngenome-lookup.sh genotype-rule-rows-1-str-extra assets/str_extra_loci.json assets/stub/db/catalog.json scripts/09-expansion-hunter.sh scripts/ci/fake-docker/lib.sh scripts/setup.sh genotype-rules-1-phase assets/genotype_rules.tsv assets/traits.tsv bin/traits_report.py modules/local/traits/* modules/local/vcf_precheck/* scripts/42-traits.sh scripts/ci/check-rule-alleles.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh @@ -106,7 +106,7 @@ hla-second-caller-1-bash assets/pgx_genes.tsv assets/stub/db/hla.dat assets/stub hla-second-caller-2-nextflow assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/mito_confirmed.tsv assets/pgx_genes.tsv assets/stub/db/hla.dat assets/stub/db/kir.dat assets/stub/sample.vcf.gz bin/cn_loci.tsv bin/collect_summary.py bin/copy_number.py bin/cyp2d6_depth_check.py bin/hba_copy_number.py bin/lpa_kiv2.py bin/pgx_mito_merge.py bin/pgx_outside_calls.py bin/pgx_refblock_fill.py bin/render_report.py bin/results_index.py modules/local/hla_typing/* modules/local/html_report/* modules/local/pgx_consensus/* modules/local/pharmcat/* modules/local/t1k_build/* modules/local/vcf_precheck/* scripts/07-pharmacogenomics.sh scripts/08-hla-typing.sh scripts/21-cyrius.sh scripts/24-html-report.sh scripts/32-pypgx.sh scripts/36-pgx-consensus.sh scripts/ci/fake-docker/lib.sh scripts/cyrius-constraints.txt scripts/setup.sh scripts/validate-setup.sh ibd-segments-1 assets/families.example.tsv assets/par_grch38.bed assets/pedigree.example.tsv assets/stub/pedigree.tsv bin/family_report.py bin/family_segments.py bin/ibd_report.py scripts/38-family.sh scripts/ci/fake-docker/lib.sh scripts/setup.sh live-server-1-weblog assets/live/* assets/viewer/index.html bin/live_results.py bin/owngenome_live.py bin/owngenome_live_results.py bin/render_report.py bin/run_state.py modules/local/roh/* modules/local/vcf_precheck/* scripts/11-roh-analysis.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh -lpa-1 assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/mito_confirmed.tsv assets/par_grch38.bed assets/stub/sample.vcf.gz bin/cn_loci.tsv bin/collect_summary.py bin/copy_number.py bin/hba_copy_number.py bin/lpa_kiv2.py bin/render_report.py bin/results_index.py modules/local/deepvariant/* modules/local/html_report/* modules/local/lpa/* modules/local/vcf_precheck/* scripts/24-html-report.sh scripts/46-lpa.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh +lpa-1 assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/mito_confirmed.tsv assets/par_grch38.bed assets/stub/sample.vcf.gz bin/cn_loci.tsv bin/collect_summary.py bin/copy_number.py bin/hba_copy_number.py bin/lpa_kiv2.py bin/render_report.py bin/results_index.py bin/traits_report.py modules/local/deepvariant/* modules/local/html_report/* modules/local/lpa/* modules/local/vcf_precheck/* scripts/24-html-report.sh scripts/46-lpa.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh mei-1 assets/mei_sites.tsv assets/par_grch38.bed assets/sv_rule_regions.tsv bin/annotsv_postfilter.py bin/cnvpytor_to_vcf.py bin/collect_summary.py bin/family_report.py bin/mei_report.py bin/sv_svlen_fix.py modules/local/align_minimap2/* modules/local/annotsv/* modules/local/deepvariant/* modules/local/fastp/* modules/local/mei/* modules/local/vcf_precheck/* scripts/01b-fastp-qc.sh scripts/05-annotsv.sh scripts/15-duphold.sh scripts/18-cnvpytor.sh scripts/19-delly.sh scripts/50-mei.sh scripts/ci/check-images.sh scripts/ci/fake-docker/lib.sh scripts/setup.sh scripts/validate-setup.sh tests/fixtures/annotsv/class45.sh mito-extended-1-deletions assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/construct_variants.tsv assets/deep_intronic_sites.tsv assets/mito_confirmed.tsv assets/stub/db/clinvar.vcf.gz assets/stub/db/clinvar.vcf.gz.tbi assets/stub/sample.bam assets/stub/sample.bam.bai assets/stub/sample.vcf.gz bin/cdna_scan.py bin/clinvar_hits.awk bin/clinvar_join_adjacent.awk bin/clip_check.py bin/collect_summary.py bin/render_report.py bin/results_index.py modules/local/clinvar_screen/* modules/local/html_report/* modules/local/mito_variants/* modules/local/vcf_precheck/* scripts/06-clinvar-screen.sh scripts/16b-mosdepth.sh scripts/20-mtoolbox.sh scripts/24-html-report.sh scripts/ci/build-mito-confirmed.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh mocha-1 assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/mito_confirmed.tsv assets/stub/sample.vcf.gz bin/collect_summary.py bin/mocha_report.py bin/render_report.py bin/results_index.py modules/local/html_report/* modules/local/mocha/* modules/local/vcf_precheck/* scripts/24-html-report.sh scripts/51-mocha.sh scripts/ci/fake-docker/lib.sh scripts/setup.sh scripts/validate-setup.sh @@ -120,14 +120,14 @@ nextflow-report-parity-1-sections assets/acmg_sf.tsv assets/callability_genes.ts nf-wiring-1-report-tables assets/acmg_sf.tsv assets/test_samplesheet.csv assets/stub/* bin/clip_check.py bin/collect_summary.py bin/cpsr_sample_id bin/render_report.py bin/results_index.py conf/test_all.config conf/test.config modules/local/align_minimap2/* modules/local/clinical_filter/* modules/local/clinvar_screen/* modules/local/cpsr/* modules/local/html_report/* modules/local/slivar/* modules/local/vep/* scripts/24-html-report.sh tests/fixtures/consumer_export/sites.tsv.gz nf-wiring-2-sv-str-tools bin/cnvpytor_to_vcf.py bin/family_report.py bin/manta_inv_filter.py bin/strchive_convert.py bin/sv_svlen_fix.py modules/local/cnvpytor/* modules/local/duphold/* modules/local/expansion_hunter/* modules/local/indexcov/* modules/local/manta/* modules/local/vcf_precheck/* output-contract-1-hg002 assets/* bin/* modules/* scripts/* -paralog-catalog-1-gba assets/paralog_loci.tsv assets/parascopy_models_v1.7.txt bin/cn_loci.tsv bin/copy_number.py bin/hba_copy_number.py bin/lpa_kiv2.py modules/local/parascopy/* modules/local/vcf_precheck/* scripts/35-paralogs.sh scripts/ci/fake-docker/lib.sh scripts/setup.sh scripts/validate-setup.sh -paralog-checks-and-doc-fixes-1-hba assets/par_grch38.bed assets/paralog_loci.tsv bin/cn_loci.tsv bin/collect_summary.py bin/copy_number.py bin/hba_copy_number.py bin/lpa_kiv2.py bin/paraphase_report.py modules/local/align_minimap2/* modules/local/deepvariant/* modules/local/fastp/* modules/local/paraphase/* modules/local/parascopy/* modules/local/vcf_precheck/* scripts/01b-fastp-qc.sh scripts/35-paralogs.sh scripts/35b-paraphase.sh scripts/ci/check-images.sh scripts/ci/fake-docker/lib.sh scripts/setup.sh scripts/validate-setup.sh -paralog-rows-1 assets/paralog_loci.tsv assets/parascopy_models_v1.7.txt bin/cn_loci.tsv bin/collect_summary.py bin/copy_number.py bin/hba_copy_number.py bin/lpa_kiv2.py bin/paraphase_report.py bin/render_report.py scripts/35-paralogs.sh scripts/ci/fake-docker/lib.sh scripts/setup.sh scripts/validate-setup.sh +paralog-catalog-1-gba assets/paralog_loci.tsv assets/parascopy_models_v1.7.txt bin/cn_loci.tsv bin/copy_number.py bin/hba_copy_number.py bin/lpa_kiv2.py bin/traits_report.py modules/local/parascopy/* modules/local/vcf_precheck/* scripts/35-paralogs.sh scripts/ci/fake-docker/lib.sh scripts/setup.sh scripts/validate-setup.sh +paralog-checks-and-doc-fixes-1-hba assets/par_grch38.bed assets/paralog_loci.tsv bin/cn_loci.tsv bin/collect_summary.py bin/copy_number.py bin/hba_copy_number.py bin/lpa_kiv2.py bin/paraphase_report.py bin/traits_report.py modules/local/align_minimap2/* modules/local/deepvariant/* modules/local/fastp/* modules/local/paraphase/* modules/local/parascopy/* modules/local/vcf_precheck/* scripts/01b-fastp-qc.sh scripts/35-paralogs.sh scripts/35b-paraphase.sh scripts/ci/check-images.sh scripts/ci/fake-docker/lib.sh scripts/setup.sh scripts/validate-setup.sh +paralog-rows-1 assets/paralog_loci.tsv assets/parascopy_models_v1.7.txt bin/cn_loci.tsv bin/collect_summary.py bin/copy_number.py bin/hba_copy_number.py bin/lpa_kiv2.py bin/paraphase_report.py bin/render_report.py bin/traits_report.py scripts/35-paralogs.sh scripts/ci/fake-docker/lib.sh scripts/setup.sh scripts/validate-setup.sh paralogs-paraphase-1 assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/mito_confirmed.tsv assets/par_grch38.bed assets/stub/sample.vcf.gz bin/collect_summary.py bin/paraphase_report.py bin/render_report.py bin/results_index.py modules/local/align_minimap2/* modules/local/deepvariant/* modules/local/fastp/* modules/local/html_report/* modules/local/paraphase/* modules/local/vcf_precheck/* scripts/01b-fastp-qc.sh scripts/24-html-report.sh scripts/35b-paraphase.sh scripts/ci/check-images.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh paralogs-report-section-1-nf-report-tables assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/construct_variants.tsv assets/deep_intronic_sites.tsv assets/mito_confirmed.tsv assets/par_grch38.bed assets/pgx_genes.tsv assets/stub/sample.bam assets/stub/sample.bam.bai assets/stub/sample.vcf.gz bin/cdna_scan.py bin/clinvar_hits.awk bin/clinvar_join_adjacent.awk bin/clip_check.py bin/cn_loci.tsv bin/collect_summary.py bin/comphet_phase.py bin/constraint_join.awk bin/copy_number.py bin/csq_rank.awk bin/cyp2d6_depth_check.py bin/export_consumer.py bin/hba_copy_number.py bin/lpa_kiv2.py bin/pgx_outside_calls.py bin/render_report.py bin/results_index.py modules/local/clinvar_screen/* modules/local/export_consumer/* modules/local/html_report/* modules/local/pypgx/* modules/local/slivar/* modules/local/vcf_precheck/* scripts/06-clinvar-screen.sh scripts/24-html-report.sh scripts/31-slivar.sh scripts/32-pypgx.sh scripts/36-pgx-consensus.sh scripts/40-export-consumer.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh tests/fixtures/consumer_export/sites.tsv.gz pgx-1-depth-check bin/cyp2d6_depth_check.py scripts/21-cyrius.sh scripts/32-pypgx.sh scripts/ci/alt-depth-ab.sh scripts/ci/fake-docker/lib.sh pgx-2-outside-calls assets/pgx_contraindications.tsv assets/pgx_genes.tsv assets/pgx_inhibitors.tsv bin/cn_loci.tsv bin/collect_summary.py bin/copy_number.py bin/cyp2d6_depth_check.py bin/hba_copy_number.py bin/lpa_kiv2.py bin/pgx_mito_merge.py bin/pgx_outside_calls.py bin/pgx_parse.py bin/pgx_refblock_fill.py scripts/07-pharmacogenomics.sh scripts/27-cpic-lookup.sh scripts/32-pypgx.sh scripts/36-pgx-consensus.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh -pgx-4-parascopy assets/paralog_loci.tsv bin/cn_loci.tsv bin/copy_number.py bin/hba_copy_number.py bin/lpa_kiv2.py scripts/35-paralogs.sh scripts/ci/fake-docker/lib.sh scripts/setup.sh scripts/validate-setup.sh +pgx-4-parascopy assets/paralog_loci.tsv bin/cn_loci.tsv bin/copy_number.py bin/hba_copy_number.py bin/lpa_kiv2.py bin/traits_report.py scripts/35-paralogs.sh scripts/ci/fake-docker/lib.sh scripts/setup.sh scripts/validate-setup.sh pgx-5-kir assets/pgx_genes.tsv assets/stub/db/hla.dat assets/stub/db/kir.dat bin/cn_loci.tsv bin/copy_number.py bin/cyp2d6_depth_check.py bin/hba_copy_number.py bin/lpa_kiv2.py bin/pgx_outside_calls.py bin/render_report.py scripts/08-hla-typing.sh scripts/24-html-report.sh scripts/32-pypgx.sh scripts/36-pgx-consensus.sh scripts/ci/fake-docker/lib.sh scripts/setup.sh scripts/validate-setup.sh pgx-6-gvcf-column assets/live/index.html assets/par_grch38.bed assets/pgs_scores.tsv assets/viewer/index.html bin/collect_summary.py bin/pgx_mito_merge.py bin/pgx_refblock_fill.py modules/local/align_minimap2/* modules/local/deepvariant/* modules/local/fastp/* modules/local/indexcov/* modules/local/pharmcat/* modules/local/prs/* modules/local/vcf_precheck/* scripts/01b-fastp-qc.sh scripts/07-pharmacogenomics.sh scripts/16-indexcov.sh scripts/25-prs.sh scripts/26-ancestry.sh scripts/ci/check-images.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh pgx-inhibitor-rows-1-contraindication assets/construct_variants.tsv assets/deep_intronic_sites.tsv assets/pgx_contraindications.tsv assets/pgx_genes.tsv assets/pgx_inhibitors.tsv assets/stub/sample.bam assets/stub/sample.bam.bai bin/cdna_scan.py bin/clinvar_hits.awk bin/clinvar_join_adjacent.awk bin/clip_check.py bin/cn_loci.tsv bin/collect_summary.py bin/copy_number.py bin/cyp2d6_depth_check.py bin/hba_copy_number.py bin/lpa_kiv2.py bin/pgx_mito_merge.py bin/pgx_outside_calls.py bin/pgx_parse.py bin/pgx_refblock_fill.py modules/local/clinvar_screen/* modules/local/cpic_lookup/* modules/local/pharmcat/* modules/local/vcf_precheck/* scripts/06-clinvar-screen.sh scripts/07-pharmacogenomics.sh scripts/27-cpic-lookup.sh scripts/32-pypgx.sh scripts/36-pgx-consensus.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh From fbdd58499fa019690d2eeee0bc27fafb3aec6cb9 Mon Sep 17 00:00:00 2001 From: GeiserX <9169332+GeiserX@users.noreply.github.com> Date: Mon, 9 Nov 2026 12:37:18 +0100 Subject: [PATCH 4/4] test(e2e): show the Lp(a) reading check red, and run report cases when traits_report.py changes lpa-1 gains a control: a copy of the HTML whose reading says step 46 wrote no table must fail the check. Every case row that runs collect_summary.py now lists bin/traits_report.py, which it imports for the marker table. --- scripts/ci/e2e-case-paths.tsv | 122 +++++++++++++++++----------------- tests/e2e/lpa-1.sh | 3 + 2 files changed, 64 insertions(+), 61 deletions(-) diff --git a/scripts/ci/e2e-case-paths.tsv b/scripts/ci/e2e-case-paths.tsv index 6ae6b653..4db632ea 100644 --- a/scripts/ci/e2e-case-paths.tsv +++ b/scripts/ci/e2e-case-paths.tsv @@ -40,30 +40,30 @@ 51-text-report - 60-nextflow - 90-report-assets - -acmg-sf-rules-1-reports assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/construct_variants.tsv assets/deep_intronic_sites.tsv assets/mito_confirmed.tsv assets/stub/sample.bam assets/stub/sample.bam.bai assets/stub/sample.vcf.gz bin/cdna_scan.py bin/clinvar_hits.awk bin/clinvar_join_adjacent.awk bin/clip_check.py bin/collect_summary.py bin/render_report.py bin/results_index.py modules/local/clinvar_screen/* modules/local/html_report/* modules/local/vcf_precheck/* scripts/06-clinvar-screen.sh scripts/24-html-report.sh scripts/ci/fake-docker/lib.sh scripts/generate-report.sh scripts/validate-setup.sh -align-read-count-gate-1 assets/callability_genes.tsv assets/par_grch38.bed bin/collect_summary.py bin/render_report.py modules/local/align_minimap2/* modules/local/deepvariant/* modules/local/fastp/* modules/local/mosdepth/* modules/local/vcf_precheck/* scripts/01b-fastp-qc.sh scripts/16b-mosdepth.sh scripts/ci/check-images.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh +acmg-sf-rules-1-reports assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/construct_variants.tsv assets/deep_intronic_sites.tsv assets/mito_confirmed.tsv assets/stub/sample.bam assets/stub/sample.bam.bai assets/stub/sample.vcf.gz bin/cdna_scan.py bin/clinvar_hits.awk bin/clinvar_join_adjacent.awk bin/clip_check.py bin/collect_summary.py bin/render_report.py bin/results_index.py bin/traits_report.py modules/local/clinvar_screen/* modules/local/html_report/* modules/local/vcf_precheck/* scripts/06-clinvar-screen.sh scripts/24-html-report.sh scripts/ci/fake-docker/lib.sh scripts/generate-report.sh scripts/validate-setup.sh +align-read-count-gate-1 assets/callability_genes.tsv assets/par_grch38.bed bin/collect_summary.py bin/render_report.py bin/traits_report.py modules/local/align_minimap2/* modules/local/deepvariant/* modules/local/fastp/* modules/local/mosdepth/* modules/local/vcf_precheck/* scripts/01b-fastp-qc.sh scripts/16b-mosdepth.sh scripts/ci/check-images.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh alignment-markdup-gvcf-sex-1-align scripts/ci/fake-docker/lib.sh alignment-markdup-gvcf-sex-2-ploidy scripts/ci/fake-docker/lib.sh -alignment-markdup-gvcf-sex-3-homref assets/pgs_scores.tsv bin/collect_summary.py scripts/14-imputation-prep.sh scripts/25-prs.sh scripts/ci/fake-docker/lib.sh +alignment-markdup-gvcf-sex-3-homref assets/pgs_scores.tsv bin/collect_summary.py bin/traits_report.py scripts/14-imputation-prep.sh scripts/25-prs.sh scripts/ci/fake-docker/lib.sh alignment-markdup-gvcf-sex-4-bwamem2 scripts/02a-alignment-bwamem2.sh scripts/ci/fake-docker/lib.sh -ancestry-fine-grained-1 assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/mito_confirmed.tsv assets/pgs_scores.tsv assets/stub/sample.vcf.gz bin/ancestry_fine_report.py bin/collect_summary.py bin/render_report.py bin/results_index.py modules/local/ancestry_fine/* modules/local/html_report/* modules/local/prs/* modules/local/vcf_precheck/* scripts/24-html-report.sh scripts/25-prs.sh scripts/26-ancestry.sh scripts/26b-ancestry-fine.sh scripts/chip-to-vcf.sh scripts/ci/fake-docker/lib.sh scripts/setup.sh scripts/validate-setup.sh -ancient-similarity-1 assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/mito_confirmed.tsv assets/stub/sample.vcf.gz bin/ancient_report.py bin/collect_summary.py bin/render_report.py bin/results_index.py modules/local/ancient/* modules/local/html_report/* modules/local/vcf_precheck/* scripts/24-html-report.sh scripts/44-ancient.sh scripts/ci/fake-docker/lib.sh scripts/setup.sh scripts/validate-setup.sh -annotsv-delly-depth-1-chain assets/par_grch38.bed assets/sv_rule_regions.tsv bin/annotsv_postfilter.py bin/cnvpytor_to_vcf.py bin/collect_summary.py bin/family_report.py bin/sv_svlen_fix.py scripts/05-annotsv.sh scripts/15-duphold.sh scripts/18-cnvpytor.sh scripts/19-delly.sh scripts/ci/fake-docker/lib.sh tests/fixtures/annotsv/class45.sh -annotsv-report-section-1-chain assets/par_grch38.bed assets/sv_rule_regions.tsv bin/annotsv_postfilter.py bin/cnvpytor_to_vcf.py bin/collect_summary.py bin/family_report.py bin/sv_svlen_fix.py scripts/05-annotsv.sh scripts/15-duphold.sh scripts/18-cnvpytor.sh scripts/19-delly.sh scripts/22-survivor-merge.sh scripts/24-html-report.sh scripts/ci/fake-docker/lib.sh scripts/generate-report.sh tests/fixtures/annotsv/class45.sh -annotsv-sv-inputs-1-manta assets/par_grch38.bed assets/sv_rule_regions.tsv bin/annotsv_postfilter.py bin/cnvpytor_to_vcf.py bin/collect_summary.py bin/family_report.py bin/manta_inv_filter.py bin/sv_svlen_fix.py scripts/04-manta.sh scripts/05-annotsv.sh scripts/15-duphold.sh scripts/18-cnvpytor.sh scripts/19-delly.sh scripts/ci/fake-docker/lib.sh -archaic-ancestry-1 assets/pgs_scores.tsv bin/archaic_report.py bin/collect_summary.py modules/local/archaic/* modules/local/prs/* modules/local/vcf_precheck/* scripts/25-prs.sh scripts/26-ancestry.sh scripts/43-archaic.sh scripts/ci/fake-docker/lib.sh scripts/generate-report.sh scripts/setup.sh scripts/validate-setup.sh +ancestry-fine-grained-1 assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/mito_confirmed.tsv assets/pgs_scores.tsv assets/stub/sample.vcf.gz bin/ancestry_fine_report.py bin/collect_summary.py bin/render_report.py bin/results_index.py bin/traits_report.py modules/local/ancestry_fine/* modules/local/html_report/* modules/local/prs/* modules/local/vcf_precheck/* scripts/24-html-report.sh scripts/25-prs.sh scripts/26-ancestry.sh scripts/26b-ancestry-fine.sh scripts/chip-to-vcf.sh scripts/ci/fake-docker/lib.sh scripts/setup.sh scripts/validate-setup.sh +ancient-similarity-1 assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/mito_confirmed.tsv assets/stub/sample.vcf.gz bin/ancient_report.py bin/collect_summary.py bin/render_report.py bin/results_index.py bin/traits_report.py modules/local/ancient/* modules/local/html_report/* modules/local/vcf_precheck/* scripts/24-html-report.sh scripts/44-ancient.sh scripts/ci/fake-docker/lib.sh scripts/setup.sh scripts/validate-setup.sh +annotsv-delly-depth-1-chain assets/par_grch38.bed assets/sv_rule_regions.tsv bin/annotsv_postfilter.py bin/cnvpytor_to_vcf.py bin/collect_summary.py bin/family_report.py bin/sv_svlen_fix.py bin/traits_report.py scripts/05-annotsv.sh scripts/15-duphold.sh scripts/18-cnvpytor.sh scripts/19-delly.sh scripts/ci/fake-docker/lib.sh tests/fixtures/annotsv/class45.sh +annotsv-report-section-1-chain assets/par_grch38.bed assets/sv_rule_regions.tsv bin/annotsv_postfilter.py bin/cnvpytor_to_vcf.py bin/collect_summary.py bin/family_report.py bin/sv_svlen_fix.py bin/traits_report.py scripts/05-annotsv.sh scripts/15-duphold.sh scripts/18-cnvpytor.sh scripts/19-delly.sh scripts/22-survivor-merge.sh scripts/24-html-report.sh scripts/ci/fake-docker/lib.sh scripts/generate-report.sh tests/fixtures/annotsv/class45.sh +annotsv-sv-inputs-1-manta assets/par_grch38.bed assets/sv_rule_regions.tsv bin/annotsv_postfilter.py bin/cnvpytor_to_vcf.py bin/collect_summary.py bin/family_report.py bin/manta_inv_filter.py bin/sv_svlen_fix.py bin/traits_report.py scripts/04-manta.sh scripts/05-annotsv.sh scripts/15-duphold.sh scripts/18-cnvpytor.sh scripts/19-delly.sh scripts/ci/fake-docker/lib.sh +archaic-ancestry-1 assets/pgs_scores.tsv bin/archaic_report.py bin/collect_summary.py bin/traits_report.py modules/local/archaic/* modules/local/prs/* modules/local/vcf_precheck/* scripts/25-prs.sh scripts/26-ancestry.sh scripts/43-archaic.sh scripts/ci/fake-docker/lib.sh scripts/generate-report.sh scripts/setup.sh scripts/validate-setup.sh bash-step-08-hla - bash-step-09-str assets/str_extra_loci.json assets/stub/db/catalog.json bin/rfc1_motif.py bin/strchive_convert.py scripts/09-expansion-hunter.sh scripts/09b-stranger.sh scripts/ci/fake-docker/lib.sh bash-step-10-telomere scripts/10-telomere-hunter.sh scripts/ci/fake-docker/lib.sh scripts/setup.sh bash-step-11-roh scripts/11-roh-analysis.sh scripts/ci/fake-docker/lib.sh bash-step-14-imputation scripts/14-imputation-prep.sh scripts/ci/fake-docker/lib.sh bash-step-19-delly scripts/19-delly.sh scripts/ci/fake-docker/lib.sh scripts/setup.sh -bash-step-20-numt assets/callability_genes.tsv bin/collect_summary.py scripts/16b-mosdepth.sh scripts/20-mtoolbox.sh scripts/ci/fake-docker/lib.sh +bash-step-20-numt assets/callability_genes.tsv bin/collect_summary.py bin/traits_report.py scripts/16b-mosdepth.sh scripts/20-mtoolbox.sh scripts/ci/fake-docker/lib.sh bash-step-bash42 assets/construct_variants.tsv bin/clip_check.py bin/cpsr_sample_id scripts/03d-octopus.sh scripts/04a-tiddit.sh scripts/10-telomere-hunter.sh scripts/17-cpsr.sh scripts/19-delly.sh scripts/ci/fake-docker/lib.sh bloodtype-1 assets/bloodtype_markers.tsv bin/bloodtype_report.py bin/cn_loci.tsv bin/copy_number.py bin/hba_copy_number.py bin/lpa_kiv2.py modules/local/bloodtype/* modules/local/vcf_precheck/* scripts/41-bloodtype.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh bumps-drop-in-baseline scripts/ci/fake-docker/lib.sh callability-1-catalog assets/callability_genes.tsv assets/paralog_loci.tsv assets/pgx_genes.tsv bin/cn_loci.tsv scripts/ci/build-callability.sh scripts/ci/fake-docker/lib.sh -callability-2-genes assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/mito_confirmed.tsv assets/stub/sample.vcf.gz bin/collect_summary.py bin/render_report.py bin/results_index.py modules/local/html_report/* modules/local/mosdepth/* modules/local/vcf_precheck/* scripts/16b-mosdepth.sh scripts/24-html-report.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh +callability-2-genes assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/mito_confirmed.tsv assets/stub/sample.vcf.gz bin/collect_summary.py bin/render_report.py bin/results_index.py bin/traits_report.py modules/local/html_report/* modules/local/mosdepth/* modules/local/vcf_precheck/* scripts/16b-mosdepth.sh scripts/24-html-report.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh chip-clonal-1 assets/chip_genes.tsv bin/chip_report.py bin/render_report.py modules/local/chip/* modules/local/vcf_precheck/* scripts/49-chip.sh scripts/ci/fake-docker/lib.sh scripts/setup.sh scripts/validate-setup.sh ci-e2e-2-locityper assets/locityper_loci.bed bin/locityper_report.py scripts/53-locityper.sh scripts/setup.sh clinical-filter-mane-and-quality-1-tiers assets/construct_variants.tsv bin/clip_check.py bin/comphet_phase.py bin/constraint_join.awk bin/csq_rank.awk scripts/23-clinical-filter.sh scripts/31-slivar.sh scripts/ci/fake-docker/lib.sh @@ -76,23 +76,23 @@ cn-engine-1-parity assets/bloodtype_markers.tsv bin/bloodtype_report.py bin/cn_l cn-guard-1-mapq0 bin/cn_loci.tsv bin/copy_number.py bin/traits_report.py modules/local/parascopy/* scripts/35-paralogs.sh cn-intervals-1-catalog bin/cn_loci.tsv scripts/ci/build-cn-intervals.py scripts/ci/fake-docker/lib.sh cn-intervals-2-hg002 assets/par_grch38.bed assets/paralog_loci.tsv bin/cn_loci.tsv bin/copy_number.py bin/hba_copy_number.py bin/lpa_kiv2.py bin/traits_report.py modules/local/deepvariant/* modules/local/parascopy/* modules/local/vcf_precheck/* scripts/35-paralogs.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh -cn-report-1-tables assets/carrier_genes.tsv assets/par_grch38.bed bin/collect_summary.py bin/couple_report.py bin/family_report.py bin/paraphase_report.py bin/render_report.py bin/results_index.py scripts/24-html-report.sh scripts/39-couple.sh scripts/ci/fake-docker/lib.sh scripts/generate-report.sh +cn-report-1-tables assets/carrier_genes.tsv assets/par_grch38.bed bin/collect_summary.py bin/couple_report.py bin/family_report.py bin/paraphase_report.py bin/render_report.py bin/results_index.py bin/traits_report.py scripts/24-html-report.sh scripts/39-couple.sh scripts/ci/fake-docker/lib.sh scripts/generate-report.sh comphet-phasing-1-reads assets/construct_variants.tsv assets/stub/sample.bam assets/stub/sample.bam.bai bin/clip_check.py bin/comphet_phase.py bin/constraint_join.awk bin/csq_rank.awk modules/local/slivar/* modules/local/vcf_precheck/* modules/local/vep/* scripts/13-vep-annotation.sh scripts/31-slivar.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh tests/fixtures/comphet/make_fixture.py -construct-scan-1-both assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/construct_variants.tsv assets/deep_intronic_sites.tsv assets/mito_confirmed.tsv assets/stub/sample.bam assets/stub/sample.bam.bai assets/stub/sample.vcf.gz bin/cdna_scan.py bin/clinvar_hits.awk bin/clinvar_join_adjacent.awk bin/clip_check.py bin/collect_summary.py bin/render_report.py bin/results_index.py modules/local/clinvar_screen/* modules/local/html_report/* modules/local/vcf_precheck/* scripts/06-clinvar-screen.sh scripts/24-html-report.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh +construct-scan-1-both assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/construct_variants.tsv assets/deep_intronic_sites.tsv assets/mito_confirmed.tsv assets/stub/sample.bam assets/stub/sample.bam.bai assets/stub/sample.vcf.gz bin/cdna_scan.py bin/clinvar_hits.awk bin/clinvar_join_adjacent.awk bin/clip_check.py bin/collect_summary.py bin/render_report.py bin/results_index.py bin/traits_report.py modules/local/clinvar_screen/* modules/local/html_report/* modules/local/vcf_precheck/* scripts/06-clinvar-screen.sh scripts/24-html-report.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh consumer-export-1 assets/chip_genes.tsv assets/par_grch38.bed bin/chip_report.py bin/export_consumer.py modules/local/chip/* modules/local/export_consumer/* modules/local/vcf_precheck/* scripts/40-export-consumer.sh scripts/49-chip.sh scripts/chip-to-vcf.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh tests/fixtures/consumer_export/sites.tsv.gz containers-software-versions scripts/ci/fake-docker/lib.sh scripts/ci/gen-containers-config.sh couple-carrier-1 assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/construct_variants.tsv assets/deep_intronic_sites.tsv assets/families.example.tsv assets/mito_confirmed.tsv assets/par_grch38.bed assets/paralog_loci.tsv assets/pedigree.example.tsv assets/pgx_genes.tsv assets/str_extra_loci.json assets/stub/db/catalog.json assets/stub/db/hla.dat assets/stub/db/kir.dat assets/stub/pedigree.tsv assets/stub/sample.bam assets/stub/sample.bam.bai assets/stub/sample.vcf.gz bin/cdna_scan.py bin/clinvar_hits.awk bin/clinvar_join_adjacent.awk bin/clip_check.py bin/cn_loci.tsv bin/collect_summary.py bin/copy_number.py bin/couple_report.py bin/cyp2d6_depth_check.py bin/family_report.py bin/family_segments.py bin/hba_copy_number.py bin/ibd_report.py bin/lpa_kiv2.py bin/mosaic_sex_loss.py bin/pgx_outside_calls.py bin/render_report.py bin/results_index.py bin/rfc1_motif.py bin/strchive_convert.py bin/traits_report.py modules/local/clinvar_screen/* modules/local/couple/* modules/local/delly/* modules/local/expansion_hunter/* modules/local/hla_typing/* modules/local/html_report/* modules/local/parascopy/* modules/local/somalier/* modules/local/t1k_build/* modules/local/vcf_precheck/* scripts/06-clinvar-screen.sh scripts/08-hla-typing.sh scripts/09-expansion-hunter.sh scripts/19-delly.sh scripts/24-html-report.sh scripts/32-pypgx.sh scripts/33-sample-qc.sh scripts/35-paralogs.sh scripts/36-pgx-consensus.sh scripts/38-family.sh scripts/39-couple.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh -couple-common-sv-1 assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/construct_variants.tsv assets/deep_intronic_sites.tsv assets/families.example.tsv assets/mito_confirmed.tsv assets/par_grch38.bed assets/pedigree.example.tsv assets/stub/pedigree.tsv assets/stub/sample.bam assets/stub/sample.bam.bai assets/stub/sample.vcf.gz bin/cdna_scan.py bin/clinvar_hits.awk bin/clinvar_join_adjacent.awk bin/clip_check.py bin/cn_loci.tsv bin/collect_summary.py bin/copy_number.py bin/couple_report.py bin/family_report.py bin/family_segments.py bin/hba_copy_number.py bin/ibd_report.py bin/lpa_kiv2.py bin/render_report.py bin/results_index.py modules/local/clinvar_screen/* modules/local/couple/* modules/local/delly/* modules/local/html_report/* modules/local/vcf_precheck/* scripts/06-clinvar-screen.sh scripts/19-delly.sh scripts/24-html-report.sh scripts/38-family.sh scripts/39-couple.sh scripts/ci/fake-docker/lib.sh scripts/setup.sh scripts/validate-setup.sh -cpic-phenoconversion-1-medications assets/pgx_contraindications.tsv assets/pgx_genes.tsv assets/pgx_inhibitors.tsv bin/cn_loci.tsv bin/collect_summary.py bin/copy_number.py bin/cyp2d6_depth_check.py bin/hba_copy_number.py bin/lpa_kiv2.py bin/pgx_mito_merge.py bin/pgx_outside_calls.py bin/pgx_parse.py bin/pgx_refblock_fill.py modules/local/cpic_lookup/* modules/local/pharmcat/* modules/local/vcf_precheck/* scripts/07-pharmacogenomics.sh scripts/27-cpic-lookup.sh scripts/32-pypgx.sh scripts/36-pgx-consensus.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh +couple-common-sv-1 assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/construct_variants.tsv assets/deep_intronic_sites.tsv assets/families.example.tsv assets/mito_confirmed.tsv assets/par_grch38.bed assets/pedigree.example.tsv assets/stub/pedigree.tsv assets/stub/sample.bam assets/stub/sample.bam.bai assets/stub/sample.vcf.gz bin/cdna_scan.py bin/clinvar_hits.awk bin/clinvar_join_adjacent.awk bin/clip_check.py bin/cn_loci.tsv bin/collect_summary.py bin/copy_number.py bin/couple_report.py bin/family_report.py bin/family_segments.py bin/hba_copy_number.py bin/ibd_report.py bin/lpa_kiv2.py bin/render_report.py bin/results_index.py bin/traits_report.py modules/local/clinvar_screen/* modules/local/couple/* modules/local/delly/* modules/local/html_report/* modules/local/vcf_precheck/* scripts/06-clinvar-screen.sh scripts/19-delly.sh scripts/24-html-report.sh scripts/38-family.sh scripts/39-couple.sh scripts/ci/fake-docker/lib.sh scripts/setup.sh scripts/validate-setup.sh +cpic-phenoconversion-1-medications assets/pgx_contraindications.tsv assets/pgx_genes.tsv assets/pgx_inhibitors.tsv bin/cn_loci.tsv bin/collect_summary.py bin/copy_number.py bin/cyp2d6_depth_check.py bin/hba_copy_number.py bin/lpa_kiv2.py bin/pgx_mito_merge.py bin/pgx_outside_calls.py bin/pgx_parse.py bin/pgx_refblock_fill.py bin/traits_report.py modules/local/cpic_lookup/* modules/local/pharmcat/* modules/local/vcf_precheck/* scripts/07-pharmacogenomics.sh scripts/27-cpic-lookup.sh scripts/32-pypgx.sh scripts/36-pgx-consensus.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh cyp21a2-short-reads-1-hg002 bin/cn_loci.tsv bin/copy_number.py bin/traits_report.py modules/local/parascopy/* scripts/35-paralogs.sh -exomiser-1 assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/families.example.tsv assets/mito_confirmed.tsv assets/par_grch38.bed assets/pedigree.example.tsv assets/pgx_genes.tsv assets/stub/db/hla.dat assets/stub/db/kir.dat assets/stub/pedigree.tsv assets/stub/sample.bam assets/stub/sample.bam.bai assets/stub/sample.vcf.gz assets/stub/sample.vcf.gz.tbi bin/cn_loci.tsv bin/collect_summary.py bin/copy_number.py bin/cyp2d6_depth_check.py bin/exomiser_report.py bin/family_report.py bin/family_segments.py bin/hba_copy_number.py bin/ibd_report.py bin/lpa_kiv2.py bin/pgx_outside_calls.py bin/render_report.py bin/results_index.py modules/local/exomiser/* modules/local/hla_typing/* modules/local/html_report/* modules/local/t1k_build/* modules/local/vcf_precheck/* scripts/08-hla-typing.sh scripts/24-html-report.sh scripts/32-pypgx.sh scripts/36-pgx-consensus.sh scripts/38-family.sh scripts/48-exomiser.sh scripts/ci/fake-docker/lib.sh scripts/setup.sh scripts/validate-setup.sh +exomiser-1 assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/families.example.tsv assets/mito_confirmed.tsv assets/par_grch38.bed assets/pedigree.example.tsv assets/pgx_genes.tsv assets/stub/db/hla.dat assets/stub/db/kir.dat assets/stub/pedigree.tsv assets/stub/sample.bam assets/stub/sample.bam.bai assets/stub/sample.vcf.gz assets/stub/sample.vcf.gz.tbi bin/cn_loci.tsv bin/collect_summary.py bin/copy_number.py bin/cyp2d6_depth_check.py bin/exomiser_report.py bin/family_report.py bin/family_segments.py bin/hba_copy_number.py bin/ibd_report.py bin/lpa_kiv2.py bin/pgx_outside_calls.py bin/render_report.py bin/results_index.py bin/traits_report.py modules/local/exomiser/* modules/local/hla_typing/* modules/local/html_report/* modules/local/t1k_build/* modules/local/vcf_precheck/* scripts/08-hla-typing.sh scripts/24-html-report.sh scripts/32-pypgx.sh scripts/36-pgx-consensus.sh scripts/38-family.sh scripts/48-exomiser.sh scripts/ci/fake-docker/lib.sh scripts/setup.sh scripts/validate-setup.sh expansions-and-rfc1-1-motif assets/str_extra_loci.json assets/stub/db/catalog.json bin/rfc1_motif.py bin/strchive_convert.py scripts/09-expansion-hunter.sh scripts/09b-stranger.sh scripts/ci/fake-docker/lib.sh scripts/generate-report.sh -families-file-1 assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/construct_variants.tsv assets/deep_intronic_sites.tsv assets/families.example.tsv assets/mito_confirmed.tsv assets/par_grch38.bed assets/pedigree.example.tsv assets/pgx_genes.tsv assets/stub/db/hla.dat assets/stub/db/kir.dat assets/stub/pedigree.tsv assets/stub/sample.bam assets/stub/sample.bam.bai assets/stub/sample.vcf.gz bin/cdna_scan.py bin/clinvar_hits.awk bin/clinvar_join_adjacent.awk bin/clip_check.py bin/cn_loci.tsv bin/collect_summary.py bin/copy_number.py bin/couple_report.py bin/cyp2d6_depth_check.py bin/family_report.py bin/family_segments.py bin/hba_copy_number.py bin/ibd_report.py bin/lpa_kiv2.py bin/pgx_outside_calls.py bin/render_report.py bin/results_index.py modules/local/align_minimap2/* modules/local/clinvar_screen/* modules/local/couple/* modules/local/deepvariant/* modules/local/fastp/* modules/local/hla_typing/* modules/local/html_report/* modules/local/t1k_build/* modules/local/vcf_precheck/* scripts/01b-fastp-qc.sh scripts/06-clinvar-screen.sh scripts/08-hla-typing.sh scripts/24-html-report.sh scripts/32-pypgx.sh scripts/36-pgx-consensus.sh scripts/38-family.sh scripts/39-couple.sh scripts/ci/check-images.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh tests/fixtures/families/stub_families.tsv -family-joint-1 assets/construct_variants.tsv assets/deep_intronic_sites.tsv assets/families.example.tsv assets/par_grch38.bed assets/pedigree.example.tsv assets/stub/pedigree.tsv assets/stub/sample.bam assets/stub/sample.bam.bai bin/cdna_scan.py bin/clinvar_hits.awk bin/clinvar_join_adjacent.awk bin/clip_check.py bin/collect_summary.py bin/family_report.py bin/family_segments.py bin/ibd_report.py bin/mosaic_sex_loss.py modules/local/align_minimap2/* modules/local/clinvar_screen/* modules/local/deepvariant/* modules/local/fastp/* modules/local/roh/* modules/local/somalier/* modules/local/vcf_precheck/* scripts/01b-fastp-qc.sh scripts/06-clinvar-screen.sh scripts/11-roh-analysis.sh scripts/33-sample-qc.sh scripts/38-family.sh scripts/ci/check-images.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh +families-file-1 assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/construct_variants.tsv assets/deep_intronic_sites.tsv assets/families.example.tsv assets/mito_confirmed.tsv assets/par_grch38.bed assets/pedigree.example.tsv assets/pgx_genes.tsv assets/stub/db/hla.dat assets/stub/db/kir.dat assets/stub/pedigree.tsv assets/stub/sample.bam assets/stub/sample.bam.bai assets/stub/sample.vcf.gz bin/cdna_scan.py bin/clinvar_hits.awk bin/clinvar_join_adjacent.awk bin/clip_check.py bin/cn_loci.tsv bin/collect_summary.py bin/copy_number.py bin/couple_report.py bin/cyp2d6_depth_check.py bin/family_report.py bin/family_segments.py bin/hba_copy_number.py bin/ibd_report.py bin/lpa_kiv2.py bin/pgx_outside_calls.py bin/render_report.py bin/results_index.py bin/traits_report.py modules/local/align_minimap2/* modules/local/clinvar_screen/* modules/local/couple/* modules/local/deepvariant/* modules/local/fastp/* modules/local/hla_typing/* modules/local/html_report/* modules/local/t1k_build/* modules/local/vcf_precheck/* scripts/01b-fastp-qc.sh scripts/06-clinvar-screen.sh scripts/08-hla-typing.sh scripts/24-html-report.sh scripts/32-pypgx.sh scripts/36-pgx-consensus.sh scripts/38-family.sh scripts/39-couple.sh scripts/ci/check-images.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh tests/fixtures/families/stub_families.tsv +family-joint-1 assets/construct_variants.tsv assets/deep_intronic_sites.tsv assets/families.example.tsv assets/par_grch38.bed assets/pedigree.example.tsv assets/stub/pedigree.tsv assets/stub/sample.bam assets/stub/sample.bam.bai bin/cdna_scan.py bin/clinvar_hits.awk bin/clinvar_join_adjacent.awk bin/clip_check.py bin/collect_summary.py bin/family_report.py bin/family_segments.py bin/ibd_report.py bin/mosaic_sex_loss.py bin/traits_report.py modules/local/align_minimap2/* modules/local/clinvar_screen/* modules/local/deepvariant/* modules/local/fastp/* modules/local/roh/* modules/local/somalier/* modules/local/vcf_precheck/* scripts/01b-fastp-qc.sh scripts/06-clinvar-screen.sh scripts/11-roh-analysis.sh scripts/33-sample-qc.sh scripts/38-family.sh scripts/ci/check-images.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh fixitfelix-chr21-1 assets/callability_genes.tsv scripts/16b-mosdepth.sh scripts/ci/fake-docker/lib.sh scripts/setup.sh followups-ci-3-sv-rule-regions assets/sv_rule_regions.tsv scripts/ci/build-sv-rule-regions.sh scripts/ci/fake-docker/lib.sh followups-clinvar-traits-1-rules-html assets/genotype_rules.tsv assets/traits.tsv bin/render_report.py bin/traits_report.py scripts/42-traits.sh scripts/ci/check-rule-alleles.sh -followups-cn-1-couple-report assets/carrier_genes.tsv assets/par_grch38.bed assets/stub/pedigree.tsv bin/collect_summary.py bin/couple_report.py bin/family_report.py bin/render_report.py bin/results_index.py modules/local/couple/* modules/local/html_report/* scripts/39-couple.sh scripts/ci/fake-docker/lib.sh +followups-cn-1-couple-report assets/carrier_genes.tsv assets/par_grch38.bed assets/stub/pedigree.tsv bin/collect_summary.py bin/couple_report.py bin/family_report.py bin/render_report.py bin/results_index.py bin/traits_report.py modules/local/couple/* modules/local/html_report/* scripts/39-couple.sh scripts/ci/fake-docker/lib.sh followups-nf-1-nf-wiring assets/stub/* assets/test_samplesheet.csv assets/steps.tsv bin/collect_summary.py bin/render_report.py bin/results_index.py bin/run_state.py bin/traits_report.py conf/test.config conf/test_all.config conf/containers.config modules/local/html_report/* modules/local/couple/* modules/local/parascopy/* modules/local/deepvariant/* modules/local/cpsr/* modules/local/clinvar_screen/* modules/local/locityper/* workflows/* tests/fixtures/consumer_export/sites.tsv.gz genome-lookup-1 scripts/ci/fake-docker/lib.sh scripts/owngenome-lookup.sh genotype-rule-rows-1-str-extra assets/str_extra_loci.json assets/stub/db/catalog.json scripts/09-expansion-hunter.sh scripts/ci/fake-docker/lib.sh scripts/setup.sh @@ -100,67 +100,67 @@ genotype-rules-1-phase assets/genotype_rules.tsv assets/traits.tsv bin/traits_re genotype-rules-2-g2 assets/genotype_rules.tsv bin/collect_summary.py bin/genotype_rules_indels.py bin/traits_report.py genotype-rules-2-lpa-null bin/cn_loci.tsv bin/collect_summary.py bin/copy_number.py bin/lpa_kiv2.py bin/render_report.py bin/traits_report.py modules/local/lpa/* scripts/24-html-report.sh scripts/46-lpa.sh scripts/generate-report.sh genotype-rules-2-smn1-marker bin/collect_summary.py bin/copy_number.py bin/render_report.py bin/traits_report.py modules/local/parascopy/* scripts/24-html-report.sh scripts/35-paralogs.sh scripts/generate-report.sh -haplogroup-explore-1-files assets/callability_genes.tsv assets/live/index.html assets/mito_confirmed.tsv assets/viewer/index.html bin/collect_summary.py bin/y_tree_place.py bin/yleaf_run.py modules/local/indexcov/* modules/local/mito_haplogroup/* modules/local/mito_variants/* modules/local/vcf_precheck/* modules/local/y_haplogroup/* scripts/12-mito-haplogroup.sh scripts/16-indexcov.sh scripts/16b-mosdepth.sh scripts/20-mtoolbox.sh scripts/37-y-haplogroup.sh scripts/ci/fake-docker/lib.sh scripts/generate-report.sh scripts/setup.sh scripts/validate-setup.sh -hba-short-read-accuracy-1-nf-report assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/mito_confirmed.tsv assets/par_grch38.bed assets/stub/sample.vcf.gz bin/cn_loci.tsv bin/collect_summary.py bin/copy_number.py bin/export_consumer.py bin/hba_copy_number.py bin/lpa_kiv2.py bin/render_report.py bin/results_index.py modules/local/export_consumer/* modules/local/html_report/* modules/local/vcf_precheck/* scripts/24-html-report.sh scripts/40-export-consumer.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh tests/fixtures/consumer_export/sites.tsv.gz +haplogroup-explore-1-files assets/callability_genes.tsv assets/live/index.html assets/mito_confirmed.tsv assets/viewer/index.html bin/collect_summary.py bin/traits_report.py bin/y_tree_place.py bin/yleaf_run.py modules/local/indexcov/* modules/local/mito_haplogroup/* modules/local/mito_variants/* modules/local/vcf_precheck/* modules/local/y_haplogroup/* scripts/12-mito-haplogroup.sh scripts/16-indexcov.sh scripts/16b-mosdepth.sh scripts/20-mtoolbox.sh scripts/37-y-haplogroup.sh scripts/ci/fake-docker/lib.sh scripts/generate-report.sh scripts/setup.sh scripts/validate-setup.sh +hba-short-read-accuracy-1-nf-report assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/mito_confirmed.tsv assets/par_grch38.bed assets/stub/sample.vcf.gz bin/cn_loci.tsv bin/collect_summary.py bin/copy_number.py bin/export_consumer.py bin/hba_copy_number.py bin/lpa_kiv2.py bin/render_report.py bin/results_index.py bin/traits_report.py modules/local/export_consumer/* modules/local/html_report/* modules/local/vcf_precheck/* scripts/24-html-report.sh scripts/40-export-consumer.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh tests/fixtures/consumer_export/sites.tsv.gz hla-second-caller-1-bash assets/pgx_genes.tsv assets/stub/db/hla.dat assets/stub/db/kir.dat bin/cn_loci.tsv bin/copy_number.py bin/cyp2d6_depth_check.py bin/hba_copy_number.py bin/lpa_kiv2.py bin/pgx_outside_calls.py bin/render_report.py scripts/08-hla-typing.sh scripts/24-html-report.sh scripts/32-pypgx.sh scripts/36-pgx-consensus.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh -hla-second-caller-2-nextflow assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/mito_confirmed.tsv assets/pgx_genes.tsv assets/stub/db/hla.dat assets/stub/db/kir.dat assets/stub/sample.vcf.gz bin/cn_loci.tsv bin/collect_summary.py bin/copy_number.py bin/cyp2d6_depth_check.py bin/hba_copy_number.py bin/lpa_kiv2.py bin/pgx_mito_merge.py bin/pgx_outside_calls.py bin/pgx_refblock_fill.py bin/render_report.py bin/results_index.py modules/local/hla_typing/* modules/local/html_report/* modules/local/pgx_consensus/* modules/local/pharmcat/* modules/local/t1k_build/* modules/local/vcf_precheck/* scripts/07-pharmacogenomics.sh scripts/08-hla-typing.sh scripts/21-cyrius.sh scripts/24-html-report.sh scripts/32-pypgx.sh scripts/36-pgx-consensus.sh scripts/ci/fake-docker/lib.sh scripts/cyrius-constraints.txt scripts/setup.sh scripts/validate-setup.sh +hla-second-caller-2-nextflow assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/mito_confirmed.tsv assets/pgx_genes.tsv assets/stub/db/hla.dat assets/stub/db/kir.dat assets/stub/sample.vcf.gz bin/cn_loci.tsv bin/collect_summary.py bin/copy_number.py bin/cyp2d6_depth_check.py bin/hba_copy_number.py bin/lpa_kiv2.py bin/pgx_mito_merge.py bin/pgx_outside_calls.py bin/pgx_refblock_fill.py bin/render_report.py bin/results_index.py bin/traits_report.py modules/local/hla_typing/* modules/local/html_report/* modules/local/pgx_consensus/* modules/local/pharmcat/* modules/local/t1k_build/* modules/local/vcf_precheck/* scripts/07-pharmacogenomics.sh scripts/08-hla-typing.sh scripts/21-cyrius.sh scripts/24-html-report.sh scripts/32-pypgx.sh scripts/36-pgx-consensus.sh scripts/ci/fake-docker/lib.sh scripts/cyrius-constraints.txt scripts/setup.sh scripts/validate-setup.sh ibd-segments-1 assets/families.example.tsv assets/par_grch38.bed assets/pedigree.example.tsv assets/stub/pedigree.tsv bin/family_report.py bin/family_segments.py bin/ibd_report.py scripts/38-family.sh scripts/ci/fake-docker/lib.sh scripts/setup.sh live-server-1-weblog assets/live/* assets/viewer/index.html bin/live_results.py bin/owngenome_live.py bin/owngenome_live_results.py bin/render_report.py bin/run_state.py modules/local/roh/* modules/local/vcf_precheck/* scripts/11-roh-analysis.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh lpa-1 assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/mito_confirmed.tsv assets/par_grch38.bed assets/stub/sample.vcf.gz bin/cn_loci.tsv bin/collect_summary.py bin/copy_number.py bin/hba_copy_number.py bin/lpa_kiv2.py bin/render_report.py bin/results_index.py bin/traits_report.py modules/local/deepvariant/* modules/local/html_report/* modules/local/lpa/* modules/local/vcf_precheck/* scripts/24-html-report.sh scripts/46-lpa.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh -mei-1 assets/mei_sites.tsv assets/par_grch38.bed assets/sv_rule_regions.tsv bin/annotsv_postfilter.py bin/cnvpytor_to_vcf.py bin/collect_summary.py bin/family_report.py bin/mei_report.py bin/sv_svlen_fix.py modules/local/align_minimap2/* modules/local/annotsv/* modules/local/deepvariant/* modules/local/fastp/* modules/local/mei/* modules/local/vcf_precheck/* scripts/01b-fastp-qc.sh scripts/05-annotsv.sh scripts/15-duphold.sh scripts/18-cnvpytor.sh scripts/19-delly.sh scripts/50-mei.sh scripts/ci/check-images.sh scripts/ci/fake-docker/lib.sh scripts/setup.sh scripts/validate-setup.sh tests/fixtures/annotsv/class45.sh -mito-extended-1-deletions assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/construct_variants.tsv assets/deep_intronic_sites.tsv assets/mito_confirmed.tsv assets/stub/db/clinvar.vcf.gz assets/stub/db/clinvar.vcf.gz.tbi assets/stub/sample.bam assets/stub/sample.bam.bai assets/stub/sample.vcf.gz bin/cdna_scan.py bin/clinvar_hits.awk bin/clinvar_join_adjacent.awk bin/clip_check.py bin/collect_summary.py bin/render_report.py bin/results_index.py modules/local/clinvar_screen/* modules/local/html_report/* modules/local/mito_variants/* modules/local/vcf_precheck/* scripts/06-clinvar-screen.sh scripts/16b-mosdepth.sh scripts/20-mtoolbox.sh scripts/24-html-report.sh scripts/ci/build-mito-confirmed.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh -mocha-1 assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/mito_confirmed.tsv assets/stub/sample.vcf.gz 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scripts/06-clinvar-screen.sh scripts/07-pharmacogenomics.sh scripts/08-hla-typing.sh scripts/11-roh-analysis.sh scripts/16b-mosdepth.sh scripts/20-mtoolbox.sh scripts/25-prs.sh scripts/32-pypgx.sh scripts/36-pgx-consensus.sh scripts/ci/fake-docker/lib.sh scripts/ci/parity-diff.sh scripts/validate-setup.sh -nextflow-from-fastq-2-nextflow assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/construct_variants.tsv assets/deep_intronic_sites.tsv assets/live/index.html assets/mito_confirmed.tsv assets/par_grch38.bed assets/pgs_scores.tsv assets/pgx_contraindications.tsv assets/pgx_genes.tsv assets/pgx_inhibitors.tsv assets/stub/db/hla.dat assets/stub/db/kir.dat assets/stub/sample.bam assets/stub/sample.bam.bai assets/stub/sample.vcf.gz assets/viewer/index.html bin/cdna_scan.py bin/clinvar_hits.awk bin/clinvar_join_adjacent.awk bin/clip_check.py bin/cn_loci.tsv bin/collect_summary.py bin/copy_number.py bin/cyp2d6_depth_check.py bin/hba_copy_number.py bin/lpa_kiv2.py bin/pgx_mito_merge.py bin/pgx_outside_calls.py bin/pgx_parse.py bin/pgx_refblock_fill.py bin/render_report.py bin/results_index.py modules/local/align_minimap2/* modules/local/clinvar_screen/* modules/local/cpic_lookup/* modules/local/cyrius/* modules/local/deepvariant/* modules/local/fastp/* modules/local/hla_typing/* modules/local/html_report/* modules/local/indexcov/* modules/local/mito_haplogroup/* modules/local/mito_variants/* modules/local/mosdepth/* modules/local/multiqc/* modules/local/pharmcat/* modules/local/prs/* modules/local/roh/* modules/local/t1k_build/* modules/local/telomere_hunter/* modules/local/vcf_precheck/* modules/local/vcfanno/* scripts/01b-fastp-qc.sh scripts/06-clinvar-screen.sh scripts/07-pharmacogenomics.sh scripts/08-hla-typing.sh scripts/10-telomere-hunter.sh scripts/11-roh-analysis.sh scripts/12-mito-haplogroup.sh scripts/16-indexcov.sh scripts/16b-mosdepth.sh scripts/20-mtoolbox.sh scripts/21-cyrius.sh scripts/24-html-report.sh scripts/25-prs.sh scripts/26-ancestry.sh scripts/27-cpic-lookup.sh scripts/28-multiqc.sh scripts/30-vcfanno.sh scripts/32-pypgx.sh scripts/36-pgx-consensus.sh scripts/ci/check-images.sh scripts/ci/fake-docker/lib.sh scripts/cyrius-constraints.txt scripts/validate-setup.sh -nextflow-from-fastq-3-sexcheck assets/callability_genes.tsv assets/live/index.html assets/viewer/index.html bin/collect_summary.py modules/local/indexcov/* modules/local/mosdepth/* modules/local/vcf_precheck/* scripts/16-indexcov.sh scripts/16b-mosdepth.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh -nextflow-hardening-1-manta assets/par_grch38.bed assets/sv_rule_regions.tsv bin/annotsv_postfilter.py bin/cnvpytor_to_vcf.py bin/collect_summary.py bin/family_report.py bin/manta_inv_filter.py bin/sv_svlen_fix.py scripts/04-manta.sh scripts/05-annotsv.sh scripts/15-duphold.sh scripts/18-cnvpytor.sh scripts/19-delly.sh scripts/ci/fake-docker/lib.sh -nextflow-hardening-2-nf assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/construct_variants.tsv assets/deep_intronic_sites.tsv assets/live/index.html assets/mito_confirmed.tsv assets/par_grch38.bed assets/pgx_genes.tsv assets/stub/sample.bam assets/stub/sample.bam.bai assets/stub/sample.vcf.gz assets/sv_rule_regions.tsv assets/viewer/index.html bin/annotsv_postfilter.py bin/cdna_scan.py bin/clinvar_hits.awk bin/clinvar_join_adjacent.awk bin/clip_check.py bin/cn_loci.tsv bin/cnvpytor_to_vcf.py bin/collect_summary.py bin/copy_number.py bin/cyp2d6_depth_check.py bin/family_report.py bin/hba_copy_number.py bin/lpa_kiv2.py bin/manta_inv_filter.py bin/pgx_mito_merge.py bin/pgx_outside_calls.py bin/pgx_refblock_fill.py bin/render_report.py bin/results_index.py bin/sv_svlen_fix.py bin/y_tree_place.py bin/yleaf_run.py modules/local/clinvar_screen/* modules/local/delly/* modules/local/html_report/* modules/local/indexcov/* modules/local/manta/* modules/local/mito_haplogroup/* modules/local/mosdepth/* 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assets/mei_sites.tsv assets/par_grch38.bed assets/sv_rule_regions.tsv bin/annotsv_postfilter.py bin/cnvpytor_to_vcf.py bin/collect_summary.py bin/family_report.py bin/mei_report.py bin/sv_svlen_fix.py bin/traits_report.py modules/local/align_minimap2/* modules/local/annotsv/* modules/local/deepvariant/* modules/local/fastp/* modules/local/mei/* modules/local/vcf_precheck/* scripts/01b-fastp-qc.sh scripts/05-annotsv.sh scripts/15-duphold.sh scripts/18-cnvpytor.sh scripts/19-delly.sh scripts/50-mei.sh scripts/ci/check-images.sh scripts/ci/fake-docker/lib.sh scripts/setup.sh scripts/validate-setup.sh tests/fixtures/annotsv/class45.sh +mito-extended-1-deletions assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/construct_variants.tsv assets/deep_intronic_sites.tsv assets/mito_confirmed.tsv assets/stub/db/clinvar.vcf.gz assets/stub/db/clinvar.vcf.gz.tbi assets/stub/sample.bam assets/stub/sample.bam.bai assets/stub/sample.vcf.gz bin/cdna_scan.py bin/clinvar_hits.awk bin/clinvar_join_adjacent.awk bin/clip_check.py bin/collect_summary.py bin/render_report.py bin/results_index.py bin/traits_report.py modules/local/clinvar_screen/* modules/local/html_report/* modules/local/mito_variants/* modules/local/vcf_precheck/* scripts/06-clinvar-screen.sh scripts/16b-mosdepth.sh scripts/20-mtoolbox.sh scripts/24-html-report.sh scripts/ci/build-mito-confirmed.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh +mocha-1 assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/mito_confirmed.tsv assets/stub/sample.vcf.gz bin/collect_summary.py bin/mocha_report.py bin/render_report.py bin/results_index.py bin/traits_report.py modules/local/html_report/* modules/local/mocha/* modules/local/vcf_precheck/* scripts/24-html-report.sh scripts/51-mocha.sh scripts/ci/fake-docker/lib.sh scripts/setup.sh scripts/validate-setup.sh +mosaic-loy-lox-1 assets/callability_genes.tsv bin/collect_summary.py bin/mosaic_sex_loss.py 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assets/callability_genes.tsv assets/live/index.html assets/viewer/index.html bin/collect_summary.py bin/traits_report.py modules/local/indexcov/* modules/local/mosdepth/* modules/local/vcf_precheck/* scripts/16-indexcov.sh scripts/16b-mosdepth.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh +nextflow-hardening-1-manta assets/par_grch38.bed assets/sv_rule_regions.tsv bin/annotsv_postfilter.py bin/cnvpytor_to_vcf.py bin/collect_summary.py bin/family_report.py bin/manta_inv_filter.py bin/sv_svlen_fix.py bin/traits_report.py scripts/04-manta.sh scripts/05-annotsv.sh scripts/15-duphold.sh scripts/18-cnvpytor.sh scripts/19-delly.sh scripts/ci/fake-docker/lib.sh +nextflow-hardening-2-nf assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/construct_variants.tsv assets/deep_intronic_sites.tsv assets/live/index.html assets/mito_confirmed.tsv assets/par_grch38.bed assets/pgx_genes.tsv assets/stub/sample.bam assets/stub/sample.bam.bai assets/stub/sample.vcf.gz assets/sv_rule_regions.tsv assets/viewer/index.html bin/annotsv_postfilter.py bin/cdna_scan.py bin/clinvar_hits.awk bin/clinvar_join_adjacent.awk bin/clip_check.py bin/cn_loci.tsv bin/cnvpytor_to_vcf.py bin/collect_summary.py bin/copy_number.py bin/cyp2d6_depth_check.py bin/family_report.py bin/hba_copy_number.py bin/lpa_kiv2.py bin/manta_inv_filter.py bin/pgx_mito_merge.py bin/pgx_outside_calls.py bin/pgx_refblock_fill.py bin/render_report.py bin/results_index.py bin/sv_svlen_fix.py bin/traits_report.py bin/y_tree_place.py bin/yleaf_run.py modules/local/clinvar_screen/* modules/local/delly/* modules/local/html_report/* modules/local/indexcov/* modules/local/manta/* modules/local/mito_haplogroup/* modules/local/mosdepth/* modules/local/pgx_consensus/* modules/local/pharmcat/* modules/local/pypgx/* modules/local/survivor_merge/* modules/local/telomere_hunter/* modules/local/vcf_precheck/* modules/local/vcfanno/* modules/local/y_haplogroup/* scripts/04-manta.sh 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bin/annotsv_postfilter.py bin/cdna_scan.py bin/clinvar_hits.awk bin/clinvar_join_adjacent.awk bin/clip_check.py bin/cn_loci.tsv bin/cnvpytor_to_vcf.py bin/collect_summary.py bin/comphet_phase.py bin/constraint_join.awk bin/copy_number.py bin/csq_rank.awk bin/cyp2d6_depth_check.py bin/export_consumer.py bin/family_report.py bin/hba_copy_number.py bin/lpa_kiv2.py bin/pgx_outside_calls.py bin/render_report.py bin/results_index.py bin/rfc1_motif.py bin/strchive_convert.py bin/sv_svlen_fix.py bin/traits_report.py modules/local/annotsv/* modules/local/clinvar_screen/* modules/local/expansion_hunter/* modules/local/export_consumer/* modules/local/html_report/* modules/local/mito_variants/* modules/local/pypgx/* modules/local/slivar/* modules/local/stranger/* modules/local/vcf_precheck/* modules/local/vep/* scripts/05-annotsv.sh scripts/06-clinvar-screen.sh scripts/09-expansion-hunter.sh scripts/09b-stranger.sh scripts/13-vep-annotation.sh scripts/15-duphold.sh scripts/16b-mosdepth.sh scripts/18-cnvpytor.sh scripts/19-delly.sh scripts/20-mtoolbox.sh scripts/24-html-report.sh scripts/31-slivar.sh scripts/32-pypgx.sh scripts/36-pgx-consensus.sh scripts/40-export-consumer.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh tests/fixtures/consumer_export/sites.tsv.gz +nf-wiring-1-report-tables assets/acmg_sf.tsv assets/test_samplesheet.csv assets/stub/* bin/clip_check.py bin/collect_summary.py bin/cpsr_sample_id bin/render_report.py bin/results_index.py bin/traits_report.py conf/test_all.config conf/test.config modules/local/align_minimap2/* modules/local/clinical_filter/* modules/local/clinvar_screen/* modules/local/cpsr/* modules/local/html_report/* modules/local/slivar/* modules/local/vep/* scripts/24-html-report.sh tests/fixtures/consumer_export/sites.tsv.gz nf-wiring-2-sv-str-tools bin/cnvpytor_to_vcf.py bin/family_report.py bin/manta_inv_filter.py bin/strchive_convert.py bin/sv_svlen_fix.py modules/local/cnvpytor/* modules/local/duphold/* modules/local/expansion_hunter/* modules/local/indexcov/* modules/local/manta/* modules/local/vcf_precheck/* output-contract-1-hg002 assets/* bin/* modules/* scripts/* paralog-catalog-1-gba assets/paralog_loci.tsv assets/parascopy_models_v1.7.txt bin/cn_loci.tsv bin/copy_number.py bin/hba_copy_number.py bin/lpa_kiv2.py bin/traits_report.py modules/local/parascopy/* modules/local/vcf_precheck/* scripts/35-paralogs.sh scripts/ci/fake-docker/lib.sh scripts/setup.sh scripts/validate-setup.sh paralog-checks-and-doc-fixes-1-hba assets/par_grch38.bed assets/paralog_loci.tsv bin/cn_loci.tsv bin/collect_summary.py bin/copy_number.py bin/hba_copy_number.py bin/lpa_kiv2.py bin/paraphase_report.py bin/traits_report.py modules/local/align_minimap2/* modules/local/deepvariant/* modules/local/fastp/* modules/local/paraphase/* modules/local/parascopy/* modules/local/vcf_precheck/* scripts/01b-fastp-qc.sh scripts/35-paralogs.sh scripts/35b-paraphase.sh scripts/ci/check-images.sh scripts/ci/fake-docker/lib.sh scripts/setup.sh scripts/validate-setup.sh paralog-rows-1 assets/paralog_loci.tsv assets/parascopy_models_v1.7.txt bin/cn_loci.tsv bin/collect_summary.py bin/copy_number.py bin/hba_copy_number.py bin/lpa_kiv2.py bin/paraphase_report.py bin/render_report.py bin/traits_report.py scripts/35-paralogs.sh scripts/ci/fake-docker/lib.sh scripts/setup.sh scripts/validate-setup.sh -paralogs-paraphase-1 assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/mito_confirmed.tsv assets/par_grch38.bed assets/stub/sample.vcf.gz bin/collect_summary.py bin/paraphase_report.py bin/render_report.py bin/results_index.py modules/local/align_minimap2/* modules/local/deepvariant/* modules/local/fastp/* modules/local/html_report/* modules/local/paraphase/* modules/local/vcf_precheck/* scripts/01b-fastp-qc.sh scripts/24-html-report.sh scripts/35b-paraphase.sh scripts/ci/check-images.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh 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scripts/40-export-consumer.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh tests/fixtures/consumer_export/sites.tsv.gz +paralogs-paraphase-1 assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/mito_confirmed.tsv assets/par_grch38.bed assets/stub/sample.vcf.gz bin/collect_summary.py bin/paraphase_report.py bin/render_report.py bin/results_index.py bin/traits_report.py modules/local/align_minimap2/* modules/local/deepvariant/* modules/local/fastp/* modules/local/html_report/* modules/local/paraphase/* modules/local/vcf_precheck/* scripts/01b-fastp-qc.sh scripts/24-html-report.sh scripts/35b-paraphase.sh scripts/ci/check-images.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh +paralogs-report-section-1-nf-report-tables assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/construct_variants.tsv assets/deep_intronic_sites.tsv assets/mito_confirmed.tsv assets/par_grch38.bed assets/pgx_genes.tsv assets/stub/sample.bam 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assets/paralog_loci.tsv bin/cn_loci.tsv bin/copy_number.py bin/hba_copy_number.py bin/lpa_kiv2.py bin/traits_report.py scripts/35-paralogs.sh scripts/ci/fake-docker/lib.sh scripts/setup.sh scripts/validate-setup.sh pgx-5-kir assets/pgx_genes.tsv assets/stub/db/hla.dat assets/stub/db/kir.dat bin/cn_loci.tsv bin/copy_number.py bin/cyp2d6_depth_check.py bin/hba_copy_number.py bin/lpa_kiv2.py bin/pgx_outside_calls.py bin/render_report.py scripts/08-hla-typing.sh scripts/24-html-report.sh scripts/32-pypgx.sh scripts/36-pgx-consensus.sh scripts/ci/fake-docker/lib.sh scripts/setup.sh scripts/validate-setup.sh -pgx-6-gvcf-column assets/live/index.html assets/par_grch38.bed assets/pgs_scores.tsv assets/viewer/index.html bin/collect_summary.py bin/pgx_mito_merge.py bin/pgx_refblock_fill.py modules/local/align_minimap2/* modules/local/deepvariant/* modules/local/fastp/* modules/local/indexcov/* modules/local/pharmcat/* modules/local/prs/* modules/local/vcf_precheck/* scripts/01b-fastp-qc.sh scripts/07-pharmacogenomics.sh scripts/16-indexcov.sh scripts/25-prs.sh scripts/26-ancestry.sh scripts/ci/check-images.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh -pgx-inhibitor-rows-1-contraindication assets/construct_variants.tsv assets/deep_intronic_sites.tsv assets/pgx_contraindications.tsv assets/pgx_genes.tsv assets/pgx_inhibitors.tsv assets/stub/sample.bam assets/stub/sample.bam.bai bin/cdna_scan.py bin/clinvar_hits.awk bin/clinvar_join_adjacent.awk bin/clip_check.py bin/cn_loci.tsv bin/collect_summary.py bin/copy_number.py bin/cyp2d6_depth_check.py bin/hba_copy_number.py bin/lpa_kiv2.py bin/pgx_mito_merge.py bin/pgx_outside_calls.py bin/pgx_parse.py bin/pgx_refblock_fill.py modules/local/clinvar_screen/* modules/local/cpic_lookup/* modules/local/pharmcat/* modules/local/vcf_precheck/* scripts/06-clinvar-screen.sh scripts/07-pharmacogenomics.sh scripts/27-cpic-lookup.sh scripts/32-pypgx.sh scripts/36-pgx-consensus.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh -pgx-parse-fixes-1-labels assets/pgx_contraindications.tsv assets/pgx_genes.tsv assets/pgx_inhibitors.tsv bin/cn_loci.tsv bin/collect_summary.py bin/copy_number.py bin/cyp2d6_depth_check.py bin/hba_copy_number.py bin/lpa_kiv2.py bin/pgx_outside_calls.py bin/pgx_parse.py scripts/27-cpic-lookup.sh scripts/32-pypgx.sh scripts/36-pgx-consensus.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh +pgx-6-gvcf-column assets/live/index.html assets/par_grch38.bed assets/pgs_scores.tsv assets/viewer/index.html bin/collect_summary.py bin/pgx_mito_merge.py bin/pgx_refblock_fill.py bin/traits_report.py modules/local/align_minimap2/* modules/local/deepvariant/* modules/local/fastp/* modules/local/indexcov/* modules/local/pharmcat/* modules/local/prs/* modules/local/vcf_precheck/* scripts/01b-fastp-qc.sh scripts/07-pharmacogenomics.sh scripts/16-indexcov.sh scripts/25-prs.sh scripts/26-ancestry.sh scripts/ci/check-images.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh +pgx-inhibitor-rows-1-contraindication assets/construct_variants.tsv assets/deep_intronic_sites.tsv assets/pgx_contraindications.tsv assets/pgx_genes.tsv assets/pgx_inhibitors.tsv assets/stub/sample.bam assets/stub/sample.bam.bai bin/cdna_scan.py bin/clinvar_hits.awk bin/clinvar_join_adjacent.awk bin/clip_check.py bin/cn_loci.tsv bin/collect_summary.py bin/copy_number.py bin/cyp2d6_depth_check.py bin/hba_copy_number.py bin/lpa_kiv2.py bin/pgx_mito_merge.py bin/pgx_outside_calls.py bin/pgx_parse.py bin/pgx_refblock_fill.py bin/traits_report.py modules/local/clinvar_screen/* modules/local/cpic_lookup/* modules/local/pharmcat/* modules/local/vcf_precheck/* scripts/06-clinvar-screen.sh scripts/07-pharmacogenomics.sh scripts/27-cpic-lookup.sh scripts/32-pypgx.sh scripts/36-pgx-consensus.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh +pgx-parse-fixes-1-labels assets/pgx_contraindications.tsv assets/pgx_genes.tsv assets/pgx_inhibitors.tsv bin/cn_loci.tsv 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modules/local/vcf_precheck/* scripts/07-pharmacogenomics.sh scripts/08-hla-typing.sh scripts/10-telomere-hunter.sh scripts/17-cpsr.sh scripts/24-html-report.sh scripts/27-cpic-lookup.sh scripts/32-pypgx.sh scripts/36-pgx-consensus.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh +short-sample-id-stub assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/construct_variants.tsv assets/mito_confirmed.tsv assets/pgx_contraindications.tsv assets/pgx_genes.tsv assets/pgx_inhibitors.tsv assets/stub/db/hla.dat assets/stub/db/kir.dat assets/stub/sample.bam assets/stub/sample.bam.bai assets/stub/sample.vcf.gz assets/stub/sample.vcf.gz.tbi bin/clip_check.py bin/cn_loci.tsv bin/collect_summary.py bin/copy_number.py bin/cpsr_sample_id bin/cyp2d6_depth_check.py bin/hba_copy_number.py bin/lpa_kiv2.py bin/pgx_mito_merge.py bin/pgx_outside_calls.py bin/pgx_parse.py bin/pgx_refblock_fill.py bin/render_report.py bin/results_index.py bin/traits_report.py modules/local/cpic_lookup/* modules/local/cpsr/* modules/local/hla_typing/* modules/local/html_report/* modules/local/pharmcat/* modules/local/t1k_build/* modules/local/telomere_hunter/* modules/local/vcf_precheck/* scripts/07-pharmacogenomics.sh scripts/08-hla-typing.sh scripts/10-telomere-hunter.sh scripts/17-cpsr.sh scripts/24-html-report.sh scripts/27-cpic-lookup.sh scripts/32-pypgx.sh scripts/36-pgx-consensus.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh single-source-lib-ownership scripts/11-roh-analysis.sh scripts/ci/fake-docker/lib.sh str-catalog-1-strchive assets/str_extra_loci.json assets/stub/db/catalog.json assets/stub/sample.bam assets/stub/sample.bam.bai bin/rfc1_motif.py bin/strchive_convert.py modules/local/expansion_hunter/* modules/local/stranger/* modules/local/vcf_precheck/* scripts/09-expansion-hunter.sh scripts/09b-stranger.sh scripts/ci/fake-docker/lib.sh scripts/setup.sh scripts/validate-setup.sh -str-extra-repeats-1-readings assets/str_extra_loci.json bin/collect_summary.py bin/render_report.py bin/results_index.py bin/run_delta.py bin/strchive_convert.py modules/local/expansion_hunter/* modules/local/html_report/* scripts/09-expansion-hunter.sh scripts/24-html-report.sh scripts/generate-report.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh +str-extra-repeats-1-readings assets/str_extra_loci.json bin/collect_summary.py bin/render_report.py bin/results_index.py bin/run_delta.py bin/strchive_convert.py bin/traits_report.py modules/local/expansion_hunter/* modules/local/html_report/* scripts/09-expansion-hunter.sh scripts/24-html-report.sh scripts/generate-report.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh sv-mito-telomere-steps-1-sv-merge scripts/22-survivor-merge.sh scripts/ci/fake-docker/lib.sh tests/fixtures/sv/cnvpytor.vcf.in tests/fixtures/sv/delly.vcf.in tests/fixtures/sv/manta.vcf.in -sv-mito-telomere-steps-2-mito assets/callability_genes.tsv bin/collect_summary.py scripts/12-mito-haplogroup.sh scripts/16b-mosdepth.sh scripts/20-mtoolbox.sh scripts/ci/fake-docker/lib.sh scripts/generate-report.sh +sv-mito-telomere-steps-2-mito assets/callability_genes.tsv bin/collect_summary.py bin/traits_report.py scripts/12-mito-haplogroup.sh scripts/16b-mosdepth.sh scripts/20-mtoolbox.sh scripts/ci/fake-docker/lib.sh scripts/generate-report.sh sv-mito-telomere-steps-3-y-haplogroup assets/live/index.html assets/viewer/index.html bin/y_tree_place.py bin/yleaf_run.py scripts/16-indexcov.sh scripts/37-y-haplogroup.sh scripts/ci/fake-docker/lib.sh scripts/setup.sh sv-mito-telomere-steps-4-clinvar-tier bin/constraint_join.awk bin/csq_rank.awk scripts/23-clinical-filter.sh scripts/ci/fake-docker/lib.sh sv-mito-telomere-steps-5-giab scripts/benchmark-variants.sh scripts/ci/fake-docker/lib.sh @@ -168,12 +168,12 @@ sv-mito-telomere-steps-6-scatter scripts/03a-gatk-haplotypecaller.sh scripts/03b traits-panel-1 assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/genotype_rules.tsv assets/mito_confirmed.tsv assets/stub/sample.vcf.gz assets/traits.tsv bin/collect_summary.py bin/render_report.py bin/results_index.py bin/traits_report.py modules/local/html_report/* modules/local/traits/* modules/local/vcf_precheck/* scripts/24-html-report.sh scripts/42-traits.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh vcf-precheck-ref-spotcheck-1 assets/par_grch38.bed modules/local/align_minimap2/* modules/local/deepvariant/* modules/local/fastp/* modules/local/roh/* modules/local/vcf_precheck/* scripts/01b-fastp-qc.sh scripts/11-roh-analysis.sh scripts/ci/check-images.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh tests/fixtures/vcf/grch37_no_contigs.vcf vendor-vcf-intake-1-bash bin/pgx_mito_merge.py bin/pgx_refblock_fill.py scripts/07-pharmacogenomics.sh scripts/ci/fake-docker/lib.sh -vendor-vcf-intake-2-nf-report assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/construct_variants.tsv assets/deep_intronic_sites.tsv assets/mito_confirmed.tsv assets/pgx_contraindications.tsv assets/pgx_genes.tsv assets/pgx_inhibitors.tsv assets/stub/sample.bam assets/stub/sample.bam.bai assets/stub/sample.vcf.gz bin/cdna_scan.py bin/clinvar_hits.awk bin/clinvar_join_adjacent.awk bin/clip_check.py bin/cn_loci.tsv bin/collect_summary.py bin/copy_number.py bin/cyp2d6_depth_check.py bin/hba_copy_number.py bin/lpa_kiv2.py bin/pgx_mito_merge.py bin/pgx_outside_calls.py bin/pgx_parse.py bin/pgx_refblock_fill.py bin/render_report.py bin/results_index.py modules/local/clinvar_screen/* modules/local/cpic_lookup/* modules/local/html_report/* modules/local/mito_haplogroup/* modules/local/mosdepth/* modules/local/multiqc/* modules/local/pharmcat/* modules/local/roh/* modules/local/vcf_precheck/* scripts/06-clinvar-screen.sh scripts/07-pharmacogenomics.sh scripts/11-roh-analysis.sh scripts/12-mito-haplogroup.sh scripts/16b-mosdepth.sh scripts/20-mtoolbox.sh scripts/24-html-report.sh scripts/27-cpic-lookup.sh scripts/28-multiqc.sh scripts/32-pypgx.sh scripts/36-pgx-consensus.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh -vendor-vcf-intake-3-nf-stops assets/callability_genes.tsv assets/construct_variants.tsv assets/deep_intronic_sites.tsv assets/stub/sample.bam assets/stub/sample.bam.bai bin/cdna_scan.py bin/clinvar_hits.awk bin/clinvar_join_adjacent.awk bin/clip_check.py bin/collect_summary.py bin/pgx_mito_merge.py bin/pgx_refblock_fill.py modules/local/clinvar_screen/* modules/local/mito_haplogroup/* modules/local/pharmcat/* modules/local/roh/* modules/local/vcf_precheck/* scripts/06-clinvar-screen.sh scripts/07-pharmacogenomics.sh scripts/11-roh-analysis.sh scripts/12-mito-haplogroup.sh scripts/16b-mosdepth.sh scripts/20-mtoolbox.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh -vendor-vcf-intake-4-nf-header-clinvar assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/construct_variants.tsv assets/deep_intronic_sites.tsv assets/mito_confirmed.tsv assets/pgx_contraindications.tsv assets/pgx_genes.tsv assets/pgx_inhibitors.tsv assets/stub/sample.bam assets/stub/sample.bam.bai assets/stub/sample.vcf.gz bin/cdna_scan.py bin/clinvar_hits.awk bin/clinvar_join_adjacent.awk bin/clip_check.py bin/cn_loci.tsv bin/collect_summary.py bin/copy_number.py bin/cyp2d6_depth_check.py bin/hba_copy_number.py bin/lpa_kiv2.py bin/pgx_mito_merge.py bin/pgx_outside_calls.py bin/pgx_parse.py bin/pgx_refblock_fill.py bin/render_report.py bin/results_index.py modules/local/clinvar_screen/* modules/local/cpic_lookup/* modules/local/html_report/* modules/local/mito_haplogroup/* modules/local/pharmcat/* modules/local/roh/* modules/local/vcf_precheck/* scripts/06-clinvar-screen.sh scripts/07-pharmacogenomics.sh scripts/11-roh-analysis.sh scripts/12-mito-haplogroup.sh scripts/16b-mosdepth.sh scripts/20-mtoolbox.sh scripts/24-html-report.sh scripts/27-cpic-lookup.sh scripts/32-pypgx.sh scripts/36-pgx-consensus.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh +vendor-vcf-intake-2-nf-report assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/construct_variants.tsv assets/deep_intronic_sites.tsv assets/mito_confirmed.tsv assets/pgx_contraindications.tsv assets/pgx_genes.tsv assets/pgx_inhibitors.tsv assets/stub/sample.bam assets/stub/sample.bam.bai assets/stub/sample.vcf.gz bin/cdna_scan.py bin/clinvar_hits.awk bin/clinvar_join_adjacent.awk bin/clip_check.py bin/cn_loci.tsv bin/collect_summary.py bin/copy_number.py bin/cyp2d6_depth_check.py bin/hba_copy_number.py bin/lpa_kiv2.py bin/pgx_mito_merge.py bin/pgx_outside_calls.py bin/pgx_parse.py bin/pgx_refblock_fill.py bin/render_report.py bin/results_index.py bin/traits_report.py modules/local/clinvar_screen/* modules/local/cpic_lookup/* modules/local/html_report/* modules/local/mito_haplogroup/* modules/local/mosdepth/* modules/local/multiqc/* modules/local/pharmcat/* modules/local/roh/* modules/local/vcf_precheck/* scripts/06-clinvar-screen.sh scripts/07-pharmacogenomics.sh scripts/11-roh-analysis.sh scripts/12-mito-haplogroup.sh scripts/16b-mosdepth.sh scripts/20-mtoolbox.sh scripts/24-html-report.sh scripts/27-cpic-lookup.sh scripts/28-multiqc.sh scripts/32-pypgx.sh scripts/36-pgx-consensus.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh +vendor-vcf-intake-3-nf-stops assets/callability_genes.tsv assets/construct_variants.tsv assets/deep_intronic_sites.tsv assets/stub/sample.bam assets/stub/sample.bam.bai bin/cdna_scan.py bin/clinvar_hits.awk bin/clinvar_join_adjacent.awk bin/clip_check.py bin/collect_summary.py bin/pgx_mito_merge.py bin/pgx_refblock_fill.py bin/traits_report.py modules/local/clinvar_screen/* modules/local/mito_haplogroup/* modules/local/pharmcat/* modules/local/roh/* modules/local/vcf_precheck/* scripts/06-clinvar-screen.sh scripts/07-pharmacogenomics.sh scripts/11-roh-analysis.sh scripts/12-mito-haplogroup.sh scripts/16b-mosdepth.sh scripts/20-mtoolbox.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh +vendor-vcf-intake-4-nf-header-clinvar assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/construct_variants.tsv assets/deep_intronic_sites.tsv assets/mito_confirmed.tsv assets/pgx_contraindications.tsv assets/pgx_genes.tsv assets/pgx_inhibitors.tsv assets/stub/sample.bam assets/stub/sample.bam.bai assets/stub/sample.vcf.gz bin/cdna_scan.py bin/clinvar_hits.awk bin/clinvar_join_adjacent.awk bin/clip_check.py bin/cn_loci.tsv bin/collect_summary.py bin/copy_number.py bin/cyp2d6_depth_check.py bin/hba_copy_number.py bin/lpa_kiv2.py bin/pgx_mito_merge.py bin/pgx_outside_calls.py bin/pgx_parse.py bin/pgx_refblock_fill.py bin/render_report.py bin/results_index.py bin/traits_report.py modules/local/clinvar_screen/* modules/local/cpic_lookup/* modules/local/html_report/* modules/local/mito_haplogroup/* modules/local/pharmcat/* modules/local/roh/* modules/local/vcf_precheck/* scripts/06-clinvar-screen.sh scripts/07-pharmacogenomics.sh scripts/11-roh-analysis.sh scripts/12-mito-haplogroup.sh scripts/16b-mosdepth.sh scripts/20-mtoolbox.sh scripts/24-html-report.sh scripts/27-cpic-lookup.sh scripts/32-pypgx.sh scripts/36-pgx-consensus.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh vendor-vcf-intake-5-docs scripts/ci/fake-docker/lib.sh viral-reads-1 bin/viral_report.py modules/local/vcf_precheck/* modules/local/viral/* scripts/47-viral.sh scripts/ci/fake-docker/lib.sh scripts/generate-report.sh scripts/setup.sh scripts/validate-setup.sh -vntyper-1 assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/mito_confirmed.tsv assets/stub/sample.vcf.gz bin/collect_summary.py bin/render_report.py bin/results_index.py bin/vntyper_report.py modules/local/html_report/* modules/local/vcf_precheck/* modules/local/vntyper/* scripts/24-html-report.sh scripts/52-vntyper.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh -y-private-report-1-private-and-tree assets/live/index.html assets/viewer/index.html bin/collect_summary.py bin/render_report.py bin/results_index.py bin/run_delta.py bin/y_private_snps.py bin/y_tree_place.py bin/yleaf_run.py modules/local/html_report/* modules/local/y_haplogroup/* scripts/16-indexcov.sh scripts/24-html-report.sh scripts/37-y-haplogroup.sh scripts/generate-report.sh scripts/ci/fake-docker/lib.sh scripts/setup.sh -y-str-1 assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/live/index.html assets/mito_confirmed.tsv assets/stub/sample.vcf.gz assets/viewer/index.html assets/ystr_panel.tsv bin/collect_summary.py bin/render_report.py bin/results_index.py bin/ystr_report.py modules/local/html_report/* modules/local/indexcov/* modules/local/vcf_precheck/* modules/local/y_str/* scripts/16-indexcov.sh scripts/24-html-report.sh scripts/45-y-str.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh +vntyper-1 assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/mito_confirmed.tsv assets/stub/sample.vcf.gz bin/collect_summary.py bin/render_report.py bin/results_index.py bin/traits_report.py bin/vntyper_report.py modules/local/html_report/* modules/local/vcf_precheck/* modules/local/vntyper/* scripts/24-html-report.sh scripts/52-vntyper.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh +y-private-report-1-private-and-tree assets/live/index.html assets/viewer/index.html bin/collect_summary.py bin/render_report.py bin/results_index.py bin/run_delta.py bin/traits_report.py bin/y_private_snps.py bin/y_tree_place.py bin/yleaf_run.py modules/local/html_report/* modules/local/y_haplogroup/* scripts/16-indexcov.sh scripts/24-html-report.sh scripts/37-y-haplogroup.sh scripts/generate-report.sh scripts/ci/fake-docker/lib.sh scripts/setup.sh +y-str-1 assets/acmg_sf.tsv assets/callability_genes.tsv assets/carrier_genes.tsv assets/live/index.html assets/mito_confirmed.tsv assets/stub/sample.vcf.gz assets/viewer/index.html assets/ystr_panel.tsv bin/collect_summary.py bin/render_report.py bin/results_index.py bin/traits_report.py bin/ystr_report.py modules/local/html_report/* modules/local/indexcov/* modules/local/vcf_precheck/* modules/local/y_str/* scripts/16-indexcov.sh scripts/24-html-report.sh scripts/45-y-str.sh scripts/ci/fake-docker/lib.sh scripts/validate-setup.sh y-tree-current-1-placement assets/live/index.html assets/viewer/index.html bin/y_tree_place.py bin/yleaf_run.py scripts/16-indexcov.sh scripts/37-y-haplogroup.sh scripts/ci/fake-docker/lib.sh scripts/setup.sh diff --git a/tests/e2e/lpa-1.sh b/tests/e2e/lpa-1.sh index e8124874..2a01370d 100755 --- a/tests/e2e/lpa-1.sh +++ b/tests/e2e/lpa-1.sh @@ -145,6 +145,9 @@ NULL_LINE=$(grep -o 'KIV-2 4925G>A null allele (rs1484919544): [^<]*' "$HTML" check "the card prints the KIV-2 4925G>A null-allele line" has '^KIV-2 4925G>A null allele \(rs1484919544\): ' "$NULL_LINE" check "and the line is a reading of the LPA task's table" lacks 'wrote no|the check failed' \ "$(grep -A1 -F "$NULL_LINE" "$HTML" 2>/dev/null)" +check "control: a card whose reading says the table is missing fails the check" has 'wrote no|the check failed' \ + "$(awk -v l="$NULL_LINE" 'f { print "

step 46 wrote no x.tsv

"; f = 0; next } index($0, l) { f = 1 } 1' "$HTML" 2>/dev/null \ + | grep -A1 -F "$NULL_LINE")" check "control: a card without the line fails the check" lacks 'KIV-2 4925G>A null allele \(rs1484919544\): ' \ "$(sed 's/KIV-2 4925G>A null allele//' "$HTML" 2>/dev/null)" echo "lpa: the Nextflow card's 4925G>A line: ${NULL_LINE}" >> "$E2E_NOTES"