From 1aa5c6007e18047b6af25fb24821edfe51d5145b Mon Sep 17 00:00:00 2001 From: Ksenia Krasheninnikova Date: Wed, 6 Dec 2023 16:17:07 +0000 Subject: [PATCH 1/3] Update paths for full test --- assets/test_gsMetZobe1.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/assets/test_gsMetZobe1.yaml b/assets/test_gsMetZobe1.yaml index c2bd4ab7..a1ffcd27 100644 --- a/assets/test_gsMetZobe1.yaml +++ b/assets/test_gsMetZobe1.yaml @@ -1,16 +1,16 @@ dataset: id: gsMetZobe1 illumina_10X: - reads: /lustre/scratch124/tol/projects/darwin/users/kk16/development/nextflow/gsMetZobe1/10x/ + reads: /lustre/scratch123/tol/resources/genomeassembly/testdata/gsMetZobe1/10x/ pacbio: reads: - - reads: /lustre/scratch124/tol/projects/darwin/users/kk16/development/nextflow/gsMetZobe1/pacbio/m64125_200823_145825.ccs.bc1019_BAK8B_OA--bc1019_BAK8B_OA.filtered.fasta.gz + - reads: /lustre/scratch123/tol/resources/genomeassembly/testdata/gsMetZobe1/pacbio/m64125_200823_145825.ccs.bc1019_BAK8B_OA--bc1019_BAK8B_OA.filtered.fasta.gz HiC: reads: - - reads: /lustre/scratch124/tol/projects/darwin/users/kk16/development/nextflow/gsMetZobe1/hic-arima/35528_4#7.cram + - reads: /lustre/scratch123/tol/resources/genomeassembly/testdata/gsMetZobe1/hic-arima/35528_4#7.cram hic_motif: GATC,GANTC,CTNAG,TTAA busco: - lineages_path: /lustre/scratch123/tol/resources/busco/v5/ + lineage_path: /lustre/scratch123/tol/resources/busco/v5/ lineage: fungi_odb10 mito: species: Metschnikowia zobellii From 3285eaf51f3b6db913f9dd9ece0631fc99ea95cd Mon Sep 17 00:00:00 2001 From: Ksenia Krasheninnikova Date: Thu, 7 Dec 2023 10:19:18 +0000 Subject: [PATCH 2/3] Add extra dataset for testing --- assets/test_gsMetZobe1.yaml | 2 +- assets/test_iyVesGerm1.yaml | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/assets/test_gsMetZobe1.yaml b/assets/test_gsMetZobe1.yaml index a1ffcd27..0f709eff 100644 --- a/assets/test_gsMetZobe1.yaml +++ b/assets/test_gsMetZobe1.yaml @@ -7,7 +7,7 @@ dataset: - reads: /lustre/scratch123/tol/resources/genomeassembly/testdata/gsMetZobe1/pacbio/m64125_200823_145825.ccs.bc1019_BAK8B_OA--bc1019_BAK8B_OA.filtered.fasta.gz HiC: reads: - - reads: /lustre/scratch123/tol/resources/genomeassembly/testdata/gsMetZobe1/hic-arima/35528_4#7.cram + - reads: /lustre/scratch123/tol/resources/genomeassembly/testdata/gsMetZobe1/hic-arima2/35528_4#7.cram hic_motif: GATC,GANTC,CTNAG,TTAA busco: lineage_path: /lustre/scratch123/tol/resources/busco/v5/ diff --git a/assets/test_iyVesGerm1.yaml b/assets/test_iyVesGerm1.yaml index a7b967b4..40548051 100644 --- a/assets/test_iyVesGerm1.yaml +++ b/assets/test_iyVesGerm1.yaml @@ -1,16 +1,16 @@ dataset: id: iyVesGerm1 illumina_10X: - reads: /lustre/scratch124/tol/projects/darwin/users/kk16/development/nextflow/sanger-tol-genomeassembly/test/10X_iyVesGerm1 + reads: /lustre/scratch123/tol/resources/genomeassembly/testdata/iyVesGerm1/10x pacbio: reads: - - reads: /lustre/scratch124/tol/projects/darwin/data/insects/Vespula_germanica/genomic_data/iyVesGerm1/pacbio/fasta/m64094_200217_145414.ccs.bc1011_BAK8A_OA--bc1011_BAK8A_OA.filtered.fasta.gz + - reads: /lustre/scratch123/tol/resources/genomeassembly/testdata/iyVesGerm1/pacbio/m64094_200217_145414.ccs.bc1011_BAK8A_OA--bc1011_BAK8A_OA.filtered.fasta.gz HiC: reads: - - reads: /lustre/scratch124/tol/projects/darwin/data/insects/Vespula_germanica/genomic_data/iyVesGerm1/hic-arima2/34957_3#2.cram + - reads: /lustre/scratch123/tol/resources/genomeassembly/testdata/iyVesGerm1/hic-arima2/34957_3#2.cram hic_motif: GATC,GANTC,CTNAG,TTAA busco: - lineages_path: /lustre/scratch123/tol/resources/busco/v5/ + lineage_path: /lustre/scratch123/tol/resources/busco/v5/ lineage: insecta_odb10 mito: species: Vespula germanica From 84bd8627fd8ac626f31e03c983eb2101655c8e6a Mon Sep 17 00:00:00 2001 From: sanger-tolsoft <105875386+sanger-tolsoft@users.noreply.github.com> Date: Thu, 7 Dec 2023 10:32:03 +0000 Subject: [PATCH 3/3] [automated] Fix linting with Prettier --- assets/test_iyVesGerm1.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/assets/test_iyVesGerm1.yaml b/assets/test_iyVesGerm1.yaml index 40548051..596508c3 100644 --- a/assets/test_iyVesGerm1.yaml +++ b/assets/test_iyVesGerm1.yaml @@ -1,13 +1,13 @@ dataset: id: iyVesGerm1 illumina_10X: - reads: /lustre/scratch123/tol/resources/genomeassembly/testdata/iyVesGerm1/10x + reads: /lustre/scratch123/tol/resources/genomeassembly/testdata/iyVesGerm1/10x pacbio: reads: - reads: /lustre/scratch123/tol/resources/genomeassembly/testdata/iyVesGerm1/pacbio/m64094_200217_145414.ccs.bc1011_BAK8A_OA--bc1011_BAK8A_OA.filtered.fasta.gz HiC: reads: - - reads: /lustre/scratch123/tol/resources/genomeassembly/testdata/iyVesGerm1/hic-arima2/34957_3#2.cram + - reads: /lustre/scratch123/tol/resources/genomeassembly/testdata/iyVesGerm1/hic-arima2/34957_3#2.cram hic_motif: GATC,GANTC,CTNAG,TTAA busco: lineage_path: /lustre/scratch123/tol/resources/busco/v5/