From 4c41d5f68613fb851ed96851dbf40c82c0d9e7d5 Mon Sep 17 00:00:00 2001
From: Yossi Farjoun <farjoun@gmail.com>
Date: Fri, 3 Dec 2021 15:45:08 -0500
Subject: [PATCH 1/3] fixed config.yaml and uncorrupted bam files

---
 example/config.yaml                           |   2 ++
 .../data/TDP43_knockdown_1_unique_kcnq2.bam   | Bin 861671 -> 861828 bytes
 .../data/TDP43_knockdown_2_unique_kcnq2.bam   | Bin 584423 -> 584580 bytes
 .../data/TDP43_knockdown_3_unique_kcnq2.bam   | Bin 159511 -> 159668 bytes
 .../data/control_scramble_1_unique_kcnq2.bam  | Bin 492566 -> 492723 bytes
 .../data/control_scramble_2_unique_kcnq2.bam  | Bin 518177 -> 518334 bytes
 .../data/control_scramble_3_unique_kcnq2.bam  | Bin 181665 -> 181822 bytes
 7 files changed, 2 insertions(+)

diff --git a/example/config.yaml b/example/config.yaml
index 2e7c90c..c261fd3 100644
--- a/example/config.yaml
+++ b/example/config.yaml
@@ -35,6 +35,8 @@ stranded: 0
 ## Leafcutter settings ---------------------------------
 
 # cluster using regtools junctions or STAR-like junctions
+junctionQC: False
+
 # regtools or rapid
 clusterRegtools: True
 
diff --git a/example/data/TDP43_knockdown_1_unique_kcnq2.bam b/example/data/TDP43_knockdown_1_unique_kcnq2.bam
index b0872178382a1e78f2e6fbe1c294c9b98c74c04b..4df0a3f0f6a0d2d7adff65bb01a0d349110d6eae 100644
GIT binary patch
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diff --git a/example/data/TDP43_knockdown_2_unique_kcnq2.bam b/example/data/TDP43_knockdown_2_unique_kcnq2.bam
index f3187823a494d62478c37c48aa7afd7f96b1b41a..03e9cc1f7710c7ee685e726c1c9e64e9999c21f7 100644
GIT binary patch
delta 3556
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diff --git a/example/data/TDP43_knockdown_3_unique_kcnq2.bam b/example/data/TDP43_knockdown_3_unique_kcnq2.bam
index 75282745dad45c606f4884cf06a783ae640e4ebe..f5c4f02be02592774cc8bcc2e8b4a009504cd390 100644
GIT binary patch
delta 3531
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F0vrX^rAGh&

delta 3396
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diff --git a/example/data/control_scramble_1_unique_kcnq2.bam b/example/data/control_scramble_1_unique_kcnq2.bam
index 6f90c444b5fd005fb61af235051af941da1c5d3b..444c231da393821f255c0f9ed6ba210837a6cf12 100644
GIT binary patch
delta 3552
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zKr<>7=Ohcb0O*J*vwBX$1wd#?lqA`}Q0Kqo=075{fq$XSeJ)iL$2uEh>by5mA)3pq
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z(TGt@Oy|u}B{eD+=j5c+GD5^iloR8Ti7O^X@?w+{)EX`LYGTMRIaXLzaV#W+=fy~#
z^3;oo{C}#Fn6rV&6*3{rS;?LF%7)1(ii~dsIl<!Wy1XwJnN-k>9F1a?J47O}S4de*
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delta 3417
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diff --git a/example/data/control_scramble_2_unique_kcnq2.bam b/example/data/control_scramble_2_unique_kcnq2.bam
index 33601e77994ce7e4846129fa9e31f2e06ec6ce92..ff6bfa6e55cf9354fdd33bb0f21d28e3c2a056d2 100644
GIT binary patch
delta 3576
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delta 3417
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diff --git a/example/data/control_scramble_3_unique_kcnq2.bam b/example/data/control_scramble_3_unique_kcnq2.bam
index 9e778d4c787d6a5f76e6dc9a5e4c8b2232e7f094..27a97d6feccbfe3140fc0745b68c518c0ba7a9f1 100644
GIT binary patch
delta 3556
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From b8c9ca0341648f5aa362597ff0e1f3080b83e87a Mon Sep 17 00:00:00 2001
From: Yossi Farjoun <farjoun@gmail.com>
Date: Wed, 8 Dec 2021 15:44:20 -0500
Subject: [PATCH 2/3] fixing example script

---
 Snakefile                | 10 +++++-----
 example/config.yaml      | 12 ++++++------
 example/run_snakemake.sh |  2 +-
 3 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/Snakefile b/Snakefile
index e45437c..f5afcbd 100644
--- a/Snakefile
+++ b/Snakefile
@@ -156,11 +156,11 @@ rule extractJunctions:
     output:
         'junctions/{samples}' + juncSuffix
     shell:
-        #"samtools index {input};"  redundant if indexes are present
-        #"regtools junctions extract -a 8 -m 50 -M 500000 -s {stranded} -o {output} {input}"
+        "samtools index {input};" # redundant if indexes are present
+        "regtools junctions extract -a 8 -i 50 -I 500000 -s {stranded} -o {output} {input.bam}"
         # conda version of regtools uses i and I instead of m and M 
-        "ml regtools/0.5.1; "
-        "regtools junctions extract -a 8 -m 50 -M 500000 -s {stranded} -o {output} {input.bam}"
+        # "ml regtools/0.5.1; "
+        # "regtools junctions extract -a 8 -m 50 -M 500000 -s {stranded} -o {output} {input.bam}"
 
 
 # remove weird contigs that cause add_chr() to break by adding "chr" to normal chr names
@@ -313,7 +313,7 @@ rule getTerminalExons:
     input:
         refFolder + refFile
     params:
-        gtftogenepred= "/sc/arion/projects/ad-omics/data/software/UCSC/gtfToGenePred",
+        gtftogenepred= "gtfToGenePred",
         genepredtobed = "scripts/genepred_to_bed.py",
         get_regions = "scripts/create_regions_from_gencode.R",
         outFolder = refFolder + refCode + "/"
diff --git a/example/config.yaml b/example/config.yaml
index c261fd3..6fc0077 100644
--- a/example/config.yaml
+++ b/example/config.yaml
@@ -35,12 +35,12 @@ stranded: 0
 ## Leafcutter settings ---------------------------------
 
 # cluster using regtools junctions or STAR-like junctions
-junctionQC: False
-
 # regtools or rapid
+
 clusterRegtools: True
+junctionQC: False 
 
-leafcutterPath: '/hpc/users/humphj04/software/leafcutter'
+leafcutterPath: '/app/leafcutter'
 
 leafcutter:
         # clustering options
@@ -60,7 +60,7 @@ leafcutter:
 python3Path: 'python3'
 python2Path: 'python2'
 
-refFolder: "/sc/arion/projects/ad-omics/data/references/hg38_reference/GENCODE/"
-refFile: "gencode.v30.annotation.gtf.gz"
-refCode: "gencode_hg38_v30"
+refFolder: "/app/reference/"
+refFile: "gencode.v38.annotation.gtf.gz"
+refCode: "gencode_hg38_v38"
 
diff --git a/example/run_snakemake.sh b/example/run_snakemake.sh
index 3ac94db..b978b86 100644
--- a/example/run_snakemake.sh
+++ b/example/run_snakemake.sh
@@ -3,4 +3,4 @@
 #ml R
 # this version of R has the current version of leafcutter
 
-snakemake  -s ../Snakefile --configfile config.yaml
+snakemake -c1 -s ../Snakefile --configfile config.yaml

From 6c6046b0bd2865d1d9d5bd527a09e2fcf02be4ab Mon Sep 17 00:00:00 2001
From: Yossi Farjoun <farjoun@gmail.com>
Date: Thu, 9 Dec 2021 10:25:31 -0500
Subject: [PATCH 3/3] - make mkdir not fail on existing dir - remove references
 to `ml` from makefile

---
 Snakefile | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/Snakefile b/Snakefile
index f5afcbd..8353dbc 100644
--- a/Snakefile
+++ b/Snakefile
@@ -107,8 +107,8 @@ minCoverage = leafcutterOpt["minCoverage"]
 isChimera = "hpc.mssm.edu" in socket.getfqdn()
 
 # not sure if this works when running in serial on interactive node
-if isChimera:
-    shell.prefix('export PS1="";source activate snakemake;ml R/3.6.0;')
+#if isChimera:
+#    shell.prefix('export PS1="";source activate snakemake;ml R/3.6.0;')
 #else:
 #shell.prefix('conda activate leafcutterpipeline;')
 
@@ -246,7 +246,7 @@ rule junctionQC:
     params:
         script = "scripts/cluster_QC.R"
     shell:
-        "ml R/3.6.0; "
+        #"ml R/3.6.0; "
         "Rscript {params.script} "
         "--outFolder {outFolder} "
         "--dataCode {dataCode} "
@@ -284,7 +284,7 @@ rule leafcutterDS:
     params:
         n_threads = leafcutterOpt['n_threads']
     shell:  
-        'ml R/3.6.0; ' 
+        #'ml R/3.6.0; ' 
         'Rscript {leafcutterPath}/scripts/leafcutter_ds.R '
         '   --output_prefix {outFolder}{wildcards.contrast}/{dataCode}_{wildcards.contrast} '
         '   --num_threads {params.n_threads} '
@@ -326,7 +326,7 @@ rule getTerminalExons:
         "{params.gtftogenepred} {input} {output.genepred};"
         "python {params.genepredtobed} --first_exon {output.genepred} > {output.starts} ; "
         "python {params.genepredtobed} --last_exon {output.genepred} > {output.ends}; "
-        "mkdir {params.outFolder}; "
+        "mkdir -p {params.outFolder}; "
         "Rscript {params.get_regions} {input} {params.outFolder}"
 
 # prepare results for shiny visualisation