From a7e5e000431c65eba8ecc938a3798631e2857782 Mon Sep 17 00:00:00 2001
From: Silas Kieser <silas.kieser@gmail.com>
Date: Wed, 26 Jul 2023 17:13:50 +0200
Subject: [PATCH] added comparison based on screens

---
 workflow/Snakefile        |  1 +
 workflow/rules/screen.smk | 40 ++++++++++++++++++++++++++++++---------
 2 files changed, 32 insertions(+), 9 deletions(-)

diff --git a/workflow/Snakefile b/workflow/Snakefile
index e626da30..c1149ab4 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -41,6 +41,7 @@ wildcard_constraints:
 
 include: "rules/sample_table.smk"
 include: "rules/download.smk"  # contains hard coded variables
+include: "rules/screen.smk"
 include: "rules/qc.smk"
 include: "rules/assemble.smk"
 include: "rules/binning.smk"
diff --git a/workflow/rules/screen.smk b/workflow/rules/screen.smk
index 1d747227..8fd19527 100644
--- a/workflow/rules/screen.smk
+++ b/workflow/rules/screen.smk
@@ -3,13 +3,12 @@ rule generate_sketch:
     input:
         unpack(get_input_fastq),
     output:
-        "{sample}/.sketch.gz"
-    priority: 100
+        "Intermediate/screen/sketches/{sample}.sketch.gz"
     log:
-        "{sample}/logs/QC/make_sketch.log",
+        "logs/screen/make_sketch/{sample}.log",
     conda:
-        "../enva/required_packages.yaml"
-    threads: config["simplejob_threads"]
+        "../envs/required_packages.yaml"
+    threads: 1
     resources:
         mem=config["simplejob_mem"],
         java_mem=int(config["simplejob_mem"] * JAVA_MEM_FRACTION),
@@ -18,10 +17,33 @@ rule generate_sketch:
         "in={input[0]}" # take only one read
         " samplerate=0.5"
         " minkeycount=2 "
-        " out= blacklist=nt ssu=f name0=sample1 depth=t overwrite=t"
-        "bbsketch.sh in=test_reads/sample2_R1.fastq.gz reads=10M samplerate=0.5 minkeycount=2 out=sample2.sketch blacklist=nt ssu=f name0=sample2 depth=t overwrite=t"
+        " out={output} "
+        " blacklist=nt ssu=f name0={sample} depth=t overwrite=t "
+        " -Xmx{resources.java_mem}g "
+        " &> {log}"
+
+
+rule compare_sketch:
+    input:
+        expand( rules.generate_sketch.output, sample =SAMPLES ),
+    output:
+        "QC/screen/sketch_comparison.tsv.gz"
+    priority: 100
+    log:
+        "logs/screen/compare_sketch.log",
+    conda:
+        "../envs/required_packages.yaml"
+    threads: 1
+    resources:
+        mem=config["mem"],
+        java_mem=int(config["mem"] * JAVA_MEM_FRACTION),
+    shell:
+        "comparesketch.sh alltoall "
+        " format=3 out={output} "
+        " {input} "
+        " -Xmx{resources.java_mem}g "
+        " &> {log}"
 
 
-        comparesketch.sh alltoall format=3 out=sketch_comparison.tsv sample?.sketch 
 
-        sendsketch.sh sample2.sketch printdepth2=t level=2 printqfname=f printvolume=t color=f out
\ No newline at end of file
+#        sendsketch.sh sample2.sketch printdepth2=t level=2 printqfname=f printvolume=t color=f out
\ No newline at end of file