From ecd7bce3b95351169d339c4933a1e790635e7261 Mon Sep 17 00:00:00 2001 From: Ksenia Krasheninnikova Date: Thu, 7 Dec 2023 10:34:42 +0000 Subject: [PATCH 1/3] Updated test for gfLaeSulp1, and removed redundant test --- assets/test_gfLaeSulp1.yaml | 30 ++++++++++++++---------------- assets/test_gfTriCing1.yaml | 18 ------------------ 2 files changed, 14 insertions(+), 34 deletions(-) delete mode 100644 assets/test_gfTriCing1.yaml diff --git a/assets/test_gfLaeSulp1.yaml b/assets/test_gfLaeSulp1.yaml index b392e000..f810b4ff 100644 --- a/assets/test_gfLaeSulp1.yaml +++ b/assets/test_gfLaeSulp1.yaml @@ -1,18 +1,16 @@ -samples: - - id: gfLaeSulp1 - assembly: - primary: /lustre/scratch124/tol/projects/darwin/data/fungi/Laetiporus_sulphureus/working/gfLaeSulp1.hifiasm.20210610/gfLaeSulp1.p_ctg.fa.gz - haplotigs: /lustre/scratch124/tol/projects/darwin/data/fungi/Laetiporus_sulphureus/working/gfLaeSulp1.hifiasm.20210610/gfLaeSulp1.a_ctg.fa.gz - illumina_10X: - reads: /lustre/scratch124/tol/projects/darwin/data/fungi/Laetiporus_sulphureus/genomic_data/gfLaeSulp1/10x/ - pacbio: - reads: - - reads: /lustre/scratch124/tol/projects/darwin/data/fungi/Laetiporus_sulphureus/genomic_data/gfLaeSulp1/pacbio/fasta/m64229e_210602_121910.ccs.bc1020_BAK8B_OA--bc1020_BAK8B_OA.filtered.fasta.gz - kmer_pref: /lustre/scratch124/tol/projects/darwin/data/fungi/Laetiporus_sulphureus/genomic_data/gfLaeSulp1/pacbio/kmer/k31/gfLaeSulp1.k31 +dataset: + id: gfLaeSulp1 + pacbio: + reads: + - reads: /lustre/scratch123/tol/resources/genomeassembly/testdata/gfLaeSulp1/pacbio/m64229e_210602_121910.ccs.bc1020_BAK8B_OA--bc1020_BAK8B_OA.filtered.fasta.gz HiC: reads: - - reads: /lustre/scratch124/tol/projects/darwin/data/fungi/Laetiporus_sulphureus/genomic_data/gfLaeSulp1/hic-arima2/40063_3#5.cram - arima_motif: GATC,GANTC,CTNAG,TTAA - busco: - lineages_path: /lustre/scratch123/tol/resources/busco/v5/ - lineage: fungi_odb10 + - reads: /lustre/scratch123/tol/resources/genomeassembly/testdata/gfLaeSulp1/hic-arima2/40063_3#5.cram +hic_motif: GATC,GANTC,CTNAG,TTAA +busco: + lineages_path: /lustre/scratch123/tol/resources/busco/v5/ + lineage: fungi_odb10 +mito: + species: Laetiporus sulphureus + min_length: 15000 + code: 4 diff --git a/assets/test_gfTriCing1.yaml b/assets/test_gfTriCing1.yaml deleted file mode 100644 index 21cc029f..00000000 --- a/assets/test_gfTriCing1.yaml +++ /dev/null @@ -1,18 +0,0 @@ -samples: - - id: gfTriCing1 - assembly: - primary: /lustre/scratch124/tol/projects/darwin/data/fungi/Tricholoma_cingulatum/working/gfTriCing1.hifiasm.20221205/gfTriCing1.p_ctg.fa.gz - haplotigs: /lustre/scratch124/tol/projects/darwin/data/fungi/Tricholoma_cingulatum/working/gfTriCing1.hifiasm.20221205/gfTriCing1.a_ctg.fa.gz - illumina_10X: - reads: /lustre/scratch124/tol/projects/darwin/data/fungi/Laetiporus_sulphureus/genomic_data/gfLaeSulp1/10x/ - pacbio: - reads: - - reads: /lustre/scratch124/tol/projects/darwin/data/fungi/Tricholoma_cingulatum/working/gfTriCing1.hicanu.20221205/gfTriCing1.trimmedReads.fasta.gz - kmer_pref: /lustre/scratch124/tol/projects/darwin/data/fungi/Tricholoma_cingulatum/genomic_data/gfTriCing1/pacbio/kmer/k31/gfTriCing1.k31 - HiC: - reads: - - reads: /lustre/scratch124/tol/projects/darwin/data/fungi/Tricholoma_cingulatum/genomic_data/gfTriCing1/hic-arima2/46142_2#8.cram - arima_motif: GATC,GANTC,CTNAG,TTAA - busco: - lineages_path: /lustre/scratch123/tol/resources/busco/v5/ - lineage: fungi_odb10 From 0b5d535370a35875b1211c3cad9ac7b52939e78b Mon Sep 17 00:00:00 2001 From: Ksenia Krasheninnikova Date: Thu, 7 Dec 2023 11:18:30 +0000 Subject: [PATCH 2/3] Fix prettier for test_gfLaeSulp1 --- assets/test_gfLaeSulp1.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/assets/test_gfLaeSulp1.yaml b/assets/test_gfLaeSulp1.yaml index f810b4ff..309e310c 100644 --- a/assets/test_gfLaeSulp1.yaml +++ b/assets/test_gfLaeSulp1.yaml @@ -2,14 +2,14 @@ dataset: id: gfLaeSulp1 pacbio: reads: - - reads: /lustre/scratch123/tol/resources/genomeassembly/testdata/gfLaeSulp1/pacbio/m64229e_210602_121910.ccs.bc1020_BAK8B_OA--bc1020_BAK8B_OA.filtered.fasta.gz + - reads: /lustre/scratch123/tol/resources/genomeassembly/testdata/gfLaeSulp1/pacbio/m64229e_210602_121910.ccs.bc1020_BAK8B_OA--bc1020_BAK8B_OA.filtered.fasta.gz HiC: reads: - reads: /lustre/scratch123/tol/resources/genomeassembly/testdata/gfLaeSulp1/hic-arima2/40063_3#5.cram hic_motif: GATC,GANTC,CTNAG,TTAA busco: - lineages_path: /lustre/scratch123/tol/resources/busco/v5/ - lineage: fungi_odb10 + lineages_path: /lustre/scratch123/tol/resources/busco/v5/ + lineage: fungi_odb10 mito: species: Laetiporus sulphureus min_length: 15000 From b3eab6e34d369a6da8624d7597cd8157f3800306 Mon Sep 17 00:00:00 2001 From: Ksenia Krasheninnikova Date: Thu, 7 Dec 2023 14:00:07 +0000 Subject: [PATCH 3/3] Set back paths for gfLaeSulp1 --- assets/test_gfLaeSulp1.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/assets/test_gfLaeSulp1.yaml b/assets/test_gfLaeSulp1.yaml index 309e310c..976a0a84 100644 --- a/assets/test_gfLaeSulp1.yaml +++ b/assets/test_gfLaeSulp1.yaml @@ -2,10 +2,10 @@ dataset: id: gfLaeSulp1 pacbio: reads: - - reads: /lustre/scratch123/tol/resources/genomeassembly/testdata/gfLaeSulp1/pacbio/m64229e_210602_121910.ccs.bc1020_BAK8B_OA--bc1020_BAK8B_OA.filtered.fasta.gz + - reads: /lustre/scratch124/tol/projects/darwin/data/fungi/Laetiporus_sulphureus/genomic_data/gfLaeSulp1/pacbio/fasta/m64229e_210602_121910.ccs.bc1020_BAK8B_OA--bc1020_BAK8B_OA.filtered.fasta.gz HiC: reads: - - reads: /lustre/scratch123/tol/resources/genomeassembly/testdata/gfLaeSulp1/hic-arima2/40063_3#5.cram + - reads: /lustre/scratch124/tol/projects/darwin/data/fungi/Laetiporus_sulphureus/genomic_data/gfLaeSulp1/hic-arima2/40063_3#5.cram hic_motif: GATC,GANTC,CTNAG,TTAA busco: lineages_path: /lustre/scratch123/tol/resources/busco/v5/