Merge pull request #553 from metagenome-atlas/screen

screen

test/test_ci.sh

@@ -22,6 +22,10 @@ rm -f $WD/samples.tsv
 #
 atlas init --db-dir --interleaved-fastq $databaseDir  -w $WD $reads_dir
 
+atlas run None screen -w $WD qc  $@
+
+echo "\n\nFinished screen\n\n"
+
 atlas run -w $WD qc  $@
 
 echo "\n\nFinished qc\n\n"

workflow/Snakefile

@@ -42,6 +42,7 @@ wildcard_constraints:
 include: "rules/sample_table.smk"
 include: "rules/download.smk"  # contains hard coded variables
 include: "rules/qc.smk"
+include: "rules/screen.smk" # expects function get_input_fastq defined in qc
 include: "rules/assemble.smk"
 include: "rules/binning.smk"
 include: "rules/derep.smk"
@@ -202,6 +203,10 @@ rule qc:
     output:
         touch("finished_QC"),
 
+rule screen:
+    input:
+        "QC/screen/sketch_comparison.tsv.gz"
+
 
 # overwrite commands in rules/download.snakefile
 onsuccess:

workflow/rules/screen.smk

@@ -0,0 +1,50 @@
+
+rule generate_sketch:
+    input:
+        unpack(get_input_fastq),
+    output:
+        "Intermediate/screen/sketches/{sample}.sketch.gz"
+    log:
+        "logs/screen/make_sketch/{sample}.log",
+    conda:
+        "../envs/required_packages.yaml"
+    threads: 1
+    resources:
+        mem=config["simplejob_mem"],
+        java_mem=int(config["simplejob_mem"] * JAVA_MEM_FRACTION),
+    shell:
+        "bbsketch.sh "
+        "in={input[0]}" # take only one read
+        " samplerate=0.5"
+        " minkeycount=2 "
+        " out={output} "
+        " blacklist=nt ssu=f name0={wildcards.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} "
+        " records=5000 "
+        " {input} "
+        " -Xmx{resources.java_mem}g "
+        " &> {log}"
+
+
+
+#        sendsketch.sh sample2.sketch printdepth2=t level=2 printqfname=f printvolume=t color=f out