From a2ec8359e798ecc9713dfd1bb3f836168dd6fb09 Mon Sep 17 00:00:00 2001
From: Austin Gillen <4809242+agillen@users.noreply.github.com>
Date: Sun, 13 Oct 2024 15:38:41 -0600
Subject: [PATCH 1/2] Update cutadapt_star.snake

correct interpretation of basename in _get_fq_paths
---
 rules/cutadapt_star.snake | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/rules/cutadapt_star.snake b/rules/cutadapt_star.snake
index 44956f8..6cc1e56 100644
--- a/rules/cutadapt_star.snake
+++ b/rules/cutadapt_star.snake
@@ -7,7 +7,7 @@ import pandas as pd
 
 """ Extract per-sample fastq paths """
 def _get_fq_paths(wildcards):
-    fqs = map(lambda x: os.path.join(DATA, x + "*R1*"), SAMPLES[wildcards.sample]["basename"])
+    fqs = map(lambda x: os.path.join(DATA, x + "*R1*"), [SAMPLES[wildcards.sample]["basename"]])
     fqs = map(lambda x: glob.glob(x), fqs)
     fqs = list(chain.from_iterable(fqs))
     

From 8a4c01d62b3e65731f11773bbefab89adf7c3a24 Mon Sep 17 00:00:00 2001
From: Austin Gillen <4809242+agillen@users.noreply.github.com>
Date: Sun, 13 Oct 2024 21:31:58 -0600
Subject: [PATCH 2/2] Update count.snake

add bam indexing to filter rules
---
 rules/count.snake | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/rules/count.snake b/rules/count.snake
index 12156b2..8f24f0a 100644
--- a/rules/count.snake
+++ b/rules/count.snake
@@ -150,6 +150,7 @@ rule filter_R1:
     if [[ {params.length} == 'False') ]]; then
       ln -s {input} {output}
     else
+      samtools index {input}
       samtools view -h {input} | grep -v 'CB:Z:-\|UB:Z:-' | samtools view -b - > {params.temp}
       set +e
       python3 inst/scripts/filter_bam_correct.py -i {params.temp} -o {params.temp2} -l {params.length} -s -c 20
@@ -183,6 +184,7 @@ rule filter_R2:
     mem_mb = 8000
   shell:
     """
+    samtools index {input}
     samtools view -h {input} | grep -v 'CB:Z:-\|UB:Z:-' | samtools view -b - > {params.temp}
     samtools index {params.temp}
     python3 inst/scripts/filter_bam.py -i {params.temp} -o {output}
@@ -213,6 +215,7 @@ rule filter_paired:
     if [[ {params.length} == 'False') ]]; then
       ln -s {input} {output}
     else
+      samtools index {input}
       samtools view -h {input} | grep -v 'CB:Z:-\|UB:Z:-' | samtools view -b - > {params.temp}
       set +e
       python3 inst/scripts/filter_bam_correct.py -i {params.temp} -o {params.temp2} -l {params.length}