From b158ad1bfbcfda2116ec9b3bcc04dc0623748848 Mon Sep 17 00:00:00 2001
From: alsmith <asmith151@outlook.com>
Date: Mon, 5 Feb 2024 11:25:45 +0000
Subject: [PATCH] fix: multiple errors with get_control_X files

---
 seqnado/workflow/rules/peak_call_chip.smk | 24 +++++++++++++++++------
 1 file changed, 18 insertions(+), 6 deletions(-)

diff --git a/seqnado/workflow/rules/peak_call_chip.smk b/seqnado/workflow/rules/peak_call_chip.smk
index 43f360b4..785bd25f 100644
--- a/seqnado/workflow/rules/peak_call_chip.smk
+++ b/seqnado/workflow/rules/peak_call_chip.smk
@@ -12,17 +12,26 @@ def get_lanceotron_threshold(wildcards):
 
 def get_control_bam(wildcards):
     exp = DESIGN.query(sample_name=wildcards.sample, ip=wildcards.treatment)
-    return f"seqnado_output/aligned/{sample}_{exp.control}.bam"
+    control = f"seqnado_output/aligned/{wildcards.sample}_{exp.control}.bam".replace(
+        " ", ""
+    )
+    return control
 
 
 def get_control_tag(wildcards):
     exp = DESIGN.query(sample_name=wildcards.sample, ip=wildcards.treatment)
-    return f"seqnado_output/tag_dirs/{sample}_{exp.control}"
+    control = f"seqnado_output/tag_dirs/{wildcards.sample}_{exp.control}".replace(
+        " ", ""
+    )
+    return control
 
 
 def get_control_bigwig(wildcards):
     exp = DESIGN.query(sample_name=wildcards.sample, ip=wildcards.treatment)
-    return f"seqnado_output/bigwigs/deeptools/{sample}_{exp.control}.bigWig"
+    control = f"seqnado_output/bigwigs/deeptools/{wildcards.sample}_{exp.control}.bigWig".replace(
+        " ", ""
+    )
+    return control
 
 
 rule macs2_with_input:
@@ -43,7 +52,8 @@ rule macs2_with_input:
     shell:
         """
         macs2 callpeak -t {input.treatment} -c {input.control} -n seqnado_output/peaks/macs/{wildcards.treatment} -f BAMPE {params.options} > {log} 2>&1 &&
-        cat {params.narrow} | cut -f 1-3 > {output.peaks}
+        cat {params.narrow} | cut -f 1-3 > {output.peaks} &&
+        touch {output.sentinel}
         """
 
 
@@ -87,7 +97,8 @@ rule homer_with_input:
         """
         findPeaks {input.treatment} {params.options} -o {output.peaks}.tmp  -i {input.control} > {log} 2>&1 &&
         pos2bed.pl {output.peaks}.tmp -o {output.peaks} >> {log} 2>&1 &&
-        rm {output.peaks}.tmp
+        rm {output.peaks}.tmp &&
+        touch {output.sentinel}
         """
 
 
@@ -132,7 +143,8 @@ rule lanceotron_with_input:
     shell:
         """
         lanceotron callPeaksInput {input.treatment} -i {input.control} -f {params.outdir} --skipheader > {log} 2>&1 &&
-        cat {params.outdir}/{wildcards.treatment}_L-tron.bed | awk 'BEGIN{{OFS="\\t"}} $4 >= {params.threshold} {{print $1, $2, $3}}' > {output.peaks}
+        cat {params.outdir}/{wildcards.treatment}_L-tron.bed | awk 'BEGIN{{OFS="\\t"}} $4 >= {params.threshold} {{print $1, $2, $3}}' > {output.peaks} &&
+        touch {output.sentinel}
         """