hotfix for host rm and host vs reference names

Microbial-Ecology-Group · Apr 11, 2023 · 39af493 · 39af493
1 parent ef9772d
commit 39af493
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Showing 3 changed files with 8 additions and 5 deletions.
diff --git a/main_AMR++.nf b/main_AMR++.nf
@@ -59,15 +59,15 @@ 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") {
 
         FAST_AMRplusplus(fastq_files, params.amr, params.annotation)
     } 
     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
@@ -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
@@ -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