From 95935cfe69956ca50307a9c6a774c4b96dff860f Mon Sep 17 00:00:00 2001
From: Max Schubach <max.schubach@bih-charite.de>
Date: Wed, 2 Nov 2022 14:50:18 +0100
Subject: [PATCH] fix: using multiple fastq inputs in counts

---
 workflow/rules/common.smk | 26 +++++++++++++-------------
 workflow/rules/counts.smk |  7 ++-----
 2 files changed, 15 insertions(+), 18 deletions(-)

diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
index 7ca7661..6543ec5 100644
--- a/workflow/rules/common.smk
+++ b/workflow/rules/common.smk
@@ -127,15 +127,15 @@ def getFW(project, condition, replicate, rnaDna_type):
     exp = getExperiments(project)
     exp = exp[exp.Condition == condition]
     exp = exp[exp.Replicate.astype(str) == replicate]
-    return "%s/%s" % (
-        config["experiments"][project]["data_folder"],
-        exp["%s_BC_F" % rnaDna_type].iloc[0],
-    )
+    return [
+        "%s/%s" % (config["experiments"][project]["data_folder"], f)
+        for f in exp["%s_BC_F" % rnaDna_type].iloc[0].split(";")
+    ]
 
 
 def getFWWithIndex(project):
     return [
-        "%s%s" % (config["experiments"][project]["data_folder"], f)
+        "%s/%s" % (config["experiments"][project]["data_folder"], f)
         for f in getExperiments(project).BC_F.iloc[0].split(";")
     ]
 
@@ -144,10 +144,10 @@ def getRev(project, condition, replicate, rnaDna_type):
     exp = getExperiments(project)
     exp = exp[exp.Condition == condition]
     exp = exp[exp.Replicate.astype(str) == replicate]
-    return "%s/%s" % (
-        config["experiments"][project]["data_folder"],
-        exp["%s_BC_R" % rnaDna_type].iloc[0],
-    )
+    return [
+        "%s/%s" % (config["experiments"][project]["data_folder"], f)
+        for f in exp["%s_BC_R" % rnaDna_type].iloc[0].split(";")
+    ]
 
 
 def getRevWithIndex(project):
@@ -161,10 +161,10 @@ def getUMI(project, condition, replicate, rnaDna_type):
     exp = getExperiments(project)
     exp = exp[exp.Condition == condition]
     exp = exp[exp.Replicate.astype(str) == replicate]
-    return "%s/%s" % (
-        config["experiments"][project]["data_folder"],
-        exp["%s_UMI" % rnaDna_type].iloc[0],
-    )
+    return [
+        "%s/%s" % (config["experiments"][project]["data_folder"], f)
+        for f in exp["%s_UMI" % rnaDna_type].iloc[0].split(";")
+    ]
 
 
 def getUMIWithIndex(project):
diff --git a/workflow/rules/counts.smk b/workflow/rules/counts.smk
index 6f55f51..07e3b79 100644
--- a/workflow/rules/counts.smk
+++ b/workflow/rules/counts.smk
@@ -112,6 +112,7 @@ rule counts_create_BAM_umi:
         "results/experiments/{project}/counts/{condition}_{replicate}_{type}.bam",
     params:
         bc_length=lambda wc: config["experiments"][wc.project]["bc_length"],
+        umi_length=lambda wc: config["experiments"][wc.project]["umi_length"],
         datasetID="{condition}_{replicate}_{type}",
     conda:
         "../envs/python27.yaml"
@@ -123,9 +124,6 @@ rule counts_create_BAM_umi:
         """
         set +o pipefail;
 
-        umi_length=`zcat {input.umi_fastq} | head -2 | tail -1 | wc -c`;
-        umi_length=$(expr $(($umi_length-1)));
-
         fwd_length=`zcat {input.fw_fastq} | head -2 | tail -1 | wc -c`;
         fwd_length=$(expr $(($fwd_length-1)));
 
@@ -134,12 +132,11 @@ rule counts_create_BAM_umi:
         minoverlap=`echo ${{fwd_length}} ${{fwd_length}} {params.bc_length} | awk '{{print ($1+$2-$3-1 < 11) ? $1+$2-$3-1 : 11}}'`;
 
         echo $rev_start
-        echo $umi_length
         echo $minoverlap
 
         paste <( zcat {input.fw_fastq} ) <( zcat {input.rev_fastq}  ) <( zcat {input.umi_fastq} ) | \
         awk '{{if (NR % 4 == 2 || NR % 4 == 0) {{print $1$2$3}} else {{print $1}}}}' | \
-        python {input.script_FastQ2doubleIndexBAM} -p -s $rev_start -l 0 -m $umi_length --RG {params.datasetID} | \
+        python {input.script_FastQ2doubleIndexBAM} -p -s $rev_start -l 0 -m {params.umi_length} --RG {params.datasetID} | \
         python {input.script_MergeTrimReadsBAM} --FirstReadChimeraFilter '' --adapterFirstRead '' --adapterSecondRead '' -p --mergeoverlap --minoverlap $minoverlap > {output} 2> {log}
         """