From 39af493ff6cb9c03d1be1ce455558ac78d614b2e Mon Sep 17 00:00:00 2001
From: EnriqueDoster <enriquedoster@gmail.com>
Date: Tue, 11 Apr 2023 00:25:35 -0600
Subject: [PATCH] hotfix for host rm and host vs reference names

---
 main_AMR++.nf                  | 4 ++--
 modules/Alignment/bwa.nf       | 4 ++--
 modules/Resistome/resistome.nf | 5 ++++-
 3 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/main_AMR++.nf b/main_AMR++.nf
index 13daa09..b2a1eca 100755
--- a/main_AMR++.nf
+++ b/main_AMR++.nf
@@ -59,7 +59,7 @@ workflow {
         
     } else if(params.pipeline == "standard_AMR") {
 
-        STANDARD_AMRplusplus(fastq_files,params.reference, params.amr, params.annotation)
+        STANDARD_AMRplusplus(fastq_files,params.host, params.amr, params.annotation)
         
     } else if(params.pipeline == "fast_AMR") {
 
@@ -67,7 +67,7 @@ workflow {
     } 
     else if(params.pipeline == "standard_AMR_wKraken") {
 
-        STANDARD_AMRplusplus_wKraken(fastq_files,params.reference, params.amr, params.annotation, params.kraken_db)
+        STANDARD_AMRplusplus_wKraken(fastq_files,params.host, params.amr, params.annotation, params.kraken_db)
     } 
     else if(params.pipeline == "eval_qc") {
 
diff --git a/modules/Alignment/bwa.nf b/modules/Alignment/bwa.nf
index 6c9a9da..4637b45 100755
--- a/modules/Alignment/bwa.nf
+++ b/modules/Alignment/bwa.nf
@@ -118,8 +118,8 @@ process bwa_rm_contaminant_fq {
        bamtofastq \
       -i ${pair_id}.host.sorted.removed.bam \
       -fq ${pair_id}.non.host.R1.fastq.gz \
-      -fq2 ${pair_id}.non.host.R2.fastq.gz \
-      -paired
+      -fq2 ${pair_id}.non.host.R2.fastq.gz 
+      
     rm *.bam
     """
 
diff --git a/modules/Resistome/resistome.nf b/modules/Resistome/resistome.nf
index 12947d7..48f0fcb 100755
--- a/modules/Resistome/resistome.nf
+++ b/modules/Resistome/resistome.nf
@@ -219,7 +219,10 @@ process runsnp {
     """
     ln -s $baseDir/bin/AmrPlusPlus_SNP/* .
 
-    python3 SNP_Verification.py -c config.ini -a true -i ${bam} -o ${sample_id}.${prefix}_SNPs --count_matrix ${snp_count_matrix}
+    # change name to stay consistent with count matrix name
+    mv ${bam} ${sample_id}.bam
+
+    python3 SNP_Verification.py -c config.ini -a true -i ${sample_id}.bam -o ${sample_id}.${prefix}_SNPs --count_matrix ${snp_count_matrix}
 
     cut -d ',' -f `awk -v RS=',' "/${sample_id}/{print NR; exit}" ${sample_id}.${prefix}_SNPs${snp_count_matrix}` ${sample_id}.${prefix}_SNPs${snp_count_matrix} > ${sample_id}.${prefix}_SNP_count_col