From e63f2a796a0736d227176a048306b4e979953973 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A9=20F=2E=20Rendeiro?= Date: Fri, 19 Oct 2018 11:59:44 +0200 Subject: [PATCH 1/5] Update atacseq.yaml --- pipelines/atacseq.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/pipelines/atacseq.yaml b/pipelines/atacseq.yaml index 1d5406e..a8b5f11 100755 --- a/pipelines/atacseq.yaml +++ b/pipelines/atacseq.yaml @@ -7,11 +7,13 @@ resources: mm10: /data/groups/lab_bock/shared/resources/genomes/mm10/indexed_bowtie2/mm10 mm9: /data/prod/ngs_resources/genomes/mm9/forBowtie2/mm9 ercc: /data/groups/lab_bock/shared/resources/genomes/ERCC92/indexed_bowtie2/ERCC92 + Calbicans_SC5314_A22: /data/groups/lab_bock/shared/resources/genomes/Calbicans_SC5314_A22/indexed_bowtie2/Calbicans_SC5314_A22 chromosome_sizes: hg38: /data/groups/lab_bock/shared/resources/genomes/hg38/hg38.chromSizes hg19: /data/groups/lab_bock/shared/resources/genomes/hg19/hg19.chromSizes mm10: /data/groups/lab_bock/shared/resources/genomes/mm10/mm10.chromSizes mm9: /data/prod/ngs_resources/genomes/mm9/mm9_chromlength.txt + Calbicans_SC5314_A22: /data/groups/lab_bock/shared/resources/genomes/Calbicans_SC5314_A22/Calbicans_SC5314_A22.chromSizes genome_windows: hg38: /data/groups/lab_bock/shared/resources/genomes/hg38/hg38.genomeWindows_1kb.bed hg19: /data/groups/lab_bock/shared/resources/genomes/hg19/hg19.genomeWindows_1kb.bed @@ -40,6 +42,7 @@ resources: hg38: /data/groups/lab_bock/shared/resources/genomes/hg38/hg38.fa hg19: /data/groups/lab_bock/shared/resources/genomes/hg19/hg19.fa mm10: /data/groups/lab_bock/shared/resources/genomes/mm10/mm10.fa + Calbicans_SC5314_A22: /data/groups/lab_bock/shared/resources/genomes/Calbicans_SC5314_A22/Calbicans_SC5314_A22.fa # The following section contains command-line tools used by the pipeline From 40aa427cfd14bf07e6880a0f4a2f56e4fcf5845e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A9=20F=2E=20Rendeiro?= Date: Fri, 19 Oct 2018 12:08:28 +0200 Subject: [PATCH 2/5] Add candida genome file paths --- pipelines/chipseq.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/pipelines/chipseq.yaml b/pipelines/chipseq.yaml index 9a977b1..bffed52 100644 --- a/pipelines/chipseq.yaml +++ b/pipelines/chipseq.yaml @@ -7,15 +7,18 @@ resources: mm10: /data/groups/lab_bock/shared/resources/genomes/mm10/indexed_bowtie2/mm10 sacCer3: /data/groups/lab_bock/shared/resources/genomes/sacCer3/indexed_bowtie2/sacCer3 ercc: /data/groups/lab_bock/shared/resources/genomes/ERCC92/indexed_bowtie2/ERCC92 + Calbicans_SC5314_A22: /data/groups/lab_bock/shared/resources/genomes/Calbicans_SC5314_A22/indexed_bowtie2/Calbicans_SC5314_A22 chromosome_sizes: hg38: /data/groups/lab_bock/shared/resources/genomes/hg38/hg38.chromSizes hg19: /data/groups/lab_bock/shared/resources/genomes/hg19/hg19.chromSizes mm10: /data/groups/lab_bock/shared/resources/genomes/mm10/mm10.chromSizes sacCer3: /data/groups/lab_bock/shared/resources/genomes/sacCer3/sacCer3.chrom.sizes + Calbicans_SC5314_A22: /data/groups/lab_bock/shared/resources/genomes/Calbicans_SC5314_A22/Calbicans_SC5314_A22.chromSizes genome_windows: hg38: /data/groups/lab_bock/shared/resources/genomes/hg38/hg38.genomeWindows_1kb.bed hg19: /data/groups/lab_bock/shared/resources/genomes/hg19/hg19.genomeWindows_1kb.bed mm10: /data/groups/lab_bock/shared/resources/genomes/mm10/mm10.genomeWindows_1kb.bed + Calbicans_SC5314_A22: /data/groups/lab_bock/shared/resources/genomes/Calbicans_SC5314_A22/Calbicans_SC5314_A22_genomeWindows_1kb.bed # tss: # hg38: /data/groups/lab_bock/shared/resources/genomes/hg38/hg38.genomeWindows_1kb.bed # hg19: /data/groups/lab_bock/shared/resources/genomes/hg19/hg19.genomeWindows_1kb.bed From a1f6ea6a31aa8a9645ff9269ae03cb4015ab49b2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A9=20F=2E=20Rendeiro?= Date: Fri, 19 Oct 2018 12:08:56 +0200 Subject: [PATCH 3/5] Add Candida genomewindows --- pipelines/atacseq.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/pipelines/atacseq.yaml b/pipelines/atacseq.yaml index a8b5f11..7951844 100755 --- a/pipelines/atacseq.yaml +++ b/pipelines/atacseq.yaml @@ -19,6 +19,7 @@ resources: hg19: /data/groups/lab_bock/shared/resources/genomes/hg19/hg19.genomeWindows_1kb.bed mm10: /data/groups/lab_bock/shared/resources/genomes/mm10/mm10.genomeWindows_1kb.bed mm9: /data/groups/lab_bock/shared/resources/genomes/mm9/mm9_genomeWindows_1kb.bed + Calbicans_SC5314_A22: /data/groups/lab_bock/shared/resources/genomes/Calbicans_SC5314_A22/Calbicans_SC5314_A22_genomeWindows_1kb.bed tss: hg38: /data/groups/lab_bock/shared/resources/genomes/hg38/hg38.genomeWindows_1kb.bed hg19: /data/groups/lab_bock/shared/resources/genomes/hg19/hg19.genomeWindows_1kb.bed From 90f7c92b0178600834d04efc2264767578aa4330 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A9=20F=2E=20Rendeiro?= Date: Fri, 19 Oct 2018 12:29:45 +0200 Subject: [PATCH 4/5] Add Candida to shift_reads.py --- pipelines/tools/shift_reads.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/pipelines/tools/shift_reads.py b/pipelines/tools/shift_reads.py index 7be5a26..a2227d3 100755 --- a/pipelines/tools/shift_reads.py +++ b/pipelines/tools/shift_reads.py @@ -19,7 +19,8 @@ def getChrSizes(chrmFile): "hg38": "/data/groups/lab_bock/shared/resources/genomes/hg38/hg38.chromSizes", "hg19": "/data/groups/lab_bock/shared/resources/genomes/hg19/hg19.chromSizes", "mm10": "/data/groups/lab_bock/shared/resources/genomes/mm10/mm10.chromSizes", - "dr7": "/data/groups/lab_bock/shared/resources/genomes/dr7/dr7.chromSizes" + "dr7": "/data/groups/lab_bock/shared/resources/genomes/dr7/dr7.chromSizes", + "Calbicans_SC5314_A22": "/data/groups/lab_bock/shared/resources/genomes/Calbicans_SC5314_A22/Calbicans_SC5314_A22.chromSizes" } From 298e5f97207d46894558a516e9a8508b656d5d2a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A9=20F=2E=20Rendeiro?= Date: Fri, 19 Oct 2018 12:30:13 +0200 Subject: [PATCH 5/5] Add Candida to fix_bedfile_genome_boundaries --- pipelines/tools/fix_bedfile_genome_boundaries.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/pipelines/tools/fix_bedfile_genome_boundaries.py b/pipelines/tools/fix_bedfile_genome_boundaries.py index 08613db..0254e00 100755 --- a/pipelines/tools/fix_bedfile_genome_boundaries.py +++ b/pipelines/tools/fix_bedfile_genome_boundaries.py @@ -19,7 +19,8 @@ def getChrSizes(chrmFile): "hg38": "/data/groups/lab_bock/shared/resources/genomes/hg38/hg38.chromSizes", "hg19": "/data/groups/lab_bock/shared/resources/genomes/hg19/hg19.chromSizes", "mm10": "/data/groups/lab_bock/shared/resources/genomes/mm10/mm10.chromSizes", - "dr7": "/data/groups/lab_bock/shared/resources/genomes/dr7/dr7.chromSizes" + "dr7": "/data/groups/lab_bock/shared/resources/genomes/dr7/dr7.chromSizes", + "Calbicans_SC5314_A22": "/data/groups/lab_bock/shared/resources/genomes/Calbicans_SC5314_A22/Calbicans_SC5314_A22.chromSizes" } genome = sys.argv[1]