changed reference passing for easier submodule usage

TRON-Bioinformatics · Feb 6, 2024 · 00ff6ab · 00ff6ab
1 parent 5d138c8
commit 00ff6ab
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Showing 5 changed files with 31 additions and 22 deletions.
diff --git a/main.nf b/main.nf
@@ -78,25 +78,25 @@ workflow {
 
         // alignment
         if (params.algorithm == "aln" && !params.inception) {
-            BWA_ALN(trimmed_fastqs.map {name, fq1, fq2 -> tuple(name, fq1)})
-            BWA_ALN_2(trimmed_fastqs.map {name, fq1, fq2 -> tuple(name, fq2)})
-            BWA_SAMPE(BWA_ALN.out.alignment_output.join(BWA_ALN_2.out.alignment_output))
+            BWA_ALN(trimmed_fastqs.map {name, fq1, fq2 -> tuple(name, fq1)},params.reference)
+            BWA_ALN_2(trimmed_fastqs.map {name, fq1, fq2 -> tuple(name, fq2)},params.reference)
+            BWA_SAMPE(BWA_ALN.out.alignment_output.join(BWA_ALN_2.out.alignment_output),params.reference)
             output_bams = BWA_SAMPE.out.bams
         }
         else if (params.algorithm == "aln" && params.inception) {
-            BWA_ALN_INCEPTION(trimmed_fastqs)
+            BWA_ALN_INCEPTION(trimmed_fastqs,params.reference)
             output_bams = BWA_ALN_INCEPTION.out.bams
         }
         else if (params.algorithm == "mem") {
-            BWA_MEM(trimmed_fastqs)
+            BWA_MEM(trimmed_fastqs,params.reference)
             output_bams = BWA_MEM.out.bams
         }
         else if (params.algorithm == "mem2") {
-            BWA_MEM_2(trimmed_fastqs)
+            BWA_MEM_2(trimmed_fastqs,params.reference)
             output_bams = BWA_MEM_2.out.bams
         }
         else if (params.algorithm == "star") {
-            STAR(trimmed_fastqs)
+            STAR(trimmed_fastqs,params.reference)
             output_bams = STAR.out.bams
         }
         else {
@@ -112,20 +112,20 @@ workflow {
             trimmed_fastqs = FASTP_SINGLE.out.trimmed_fastqs
         }
         if (params.algorithm == "aln"  && !params.inception) {
-            BWA_ALN(trimmed_fastqs)
+            BWA_ALN(trimmed_fastqs,params.reference)
             BWA_SAMSE(BWA_ALN.out.alignment_output)
             output_bams = BWA_SAMSE.out.bams
         }
         else if (params.algorithm == "mem") {
-            BWA_MEM_SE(trimmed_fastqs)
+            BWA_MEM_SE(trimmed_fastqs,params.reference)
             output_bams = BWA_MEM_SE.out.bams
         }
         else if (params.algorithm == "mem2") {
-            BWA_MEM_2_SE(trimmed_fastqs)
+            BWA_MEM_2_SE(trimmed_fastqs,params.reference)
             output_bams = BWA_MEM_2_SE.out.bams
         }
         else if (params.algorithm == "star") {
-            STAR_SE(trimmed_fastqs)
+            STAR_SE(trimmed_fastqs,params.reference)
             output_bams = STAR_SE.out.bams
         }
         else {

diff --git a/modules/02_bwa_aln.nf b/modules/02_bwa_aln.nf
@@ -9,13 +9,14 @@ process BWA_ALN {
 
     input:
         tuple val(name), file(fastq)
+        val(reference)
 
     output:
         tuple val("${name}"), file("${fastq}"), file("${fastq.baseName}.sai"), emit: alignment_output
         file("software_versions.BWA_ALN.txt")
 
     """
-    bwa aln -t ${task.cpus} ${params.reference} ${fastq} > ${fastq.baseName}.sai
+    bwa aln -t ${task.cpus} ${reference} ${fastq} > ${fastq.baseName}.sai
 
     echo ${params.manifest} >> software_versions.BWA_ALN.txt
     echo "bwa=0.7.17"  >> software_versions.BWA_ALN.txt
@@ -34,13 +35,14 @@ process BWA_SAMPE {
     input:
       // joins both channels by key using the first element in the tuple, the name
       tuple val(name), file(fastq1), file(sai1), file(fastq2), file(sai2)
+      val(reference)
 
     output:
       tuple val("${name}"), file("${name}.bam"), emit: bams
       file("software_versions.BWA_SAMPE.txt")
 
     """
-    bwa sampe ${params.reference} ${sai1} ${sai2} ${fastq1} ${fastq2} | samtools view -uS - | samtools sort - > ${name}.bam
+    bwa sampe ${reference} ${sai1} ${sai2} ${fastq1} ${fastq2} | samtools view -uS - | samtools sort - > ${name}.bam
 
     echo ${params.manifest} >> software_versions.BWA_SAMPE.txt
     echo "bwa=0.7.17"  >> software_versions.BWA_SAMPE.txt
@@ -60,13 +62,14 @@ process BWA_SAMSE {
     input:
       // joins both channels by key using the first element in the tuple, the name
       tuple val(name), file(fastq), file(sai)
+      val(reference)
 
     output:
       tuple val("${name}"), file("${name}.bam"), emit: bams
       file("software_versions.BWA_SAMSE.txt")
 
     """
-    bwa samse ${params.reference} ${sai} ${fastq} | samtools view -uS - | samtools sort - > ${name}.bam
+    bwa samse ${reference} ${sai} ${fastq} | samtools view -uS - | samtools sort - > ${name}.bam
 
     echo ${params.manifest} >> software_versions.BWA_SAMSE.txt
     echo "bwa=0.7.17"  >> software_versions.BWA_SAMSE.txt
@@ -86,14 +89,15 @@ process BWA_ALN_INCEPTION {
     input:
       // joins both channels by key using the first element in the tuple, the name
       tuple val(name), file(fastq1), file(fastq2)
+      val(reference)
 
     output:
       tuple val("${name}"), file("${name}.bam"), emit: bams
       file("software_versions.BWA_ALN_INCEPTION.txt")
 
     """
-    bwa sampe ${params.reference} <( bwa aln -t ${params.cpus} ${params.reference} ${fastq1} ) \
-    <( bwa aln -t ${params.cpus} ${params.reference} ${fastq2} ) ${fastq1} ${fastq2} \
+    bwa sampe ${reference} <( bwa aln -t ${params.cpus} ${reference} ${fastq1} ) \
+    <( bwa aln -t ${params.cpus} ${reference} ${fastq2} ) ${fastq1} ${fastq2} \
     | samtools view -uS - | samtools sort - > ${name}.bam
 
     echo ${params.manifest} >> software_versions.BWA_ALN_INCEPTION.txt

diff --git a/modules/02_bwa_mem.nf b/modules/02_bwa_mem.nf
@@ -10,13 +10,14 @@ process BWA_MEM {
 
     input:
       tuple val(name), file(fastq1), file(fastq2)
+      val(reference)
 
     output:
       tuple val("${name}"), file("${name}.bam"), emit: bams
       file("software_versions.BWA_MEM.txt")
 
     """
-    bwa mem ${params.additional_args} -t ${task.cpus} ${params.reference} ${fastq1} ${fastq2} | samtools view -uS - | samtools sort - > ${name}.bam
+    bwa mem ${params.additional_args} -t ${task.cpus} ${reference} ${fastq1} ${fastq2} | samtools view -uS - | samtools sort - > ${name}.bam
 
     echo ${params.manifest} >> software_versions.BWA_MEM.txt
     echo "bwa=0.7.17"  >> software_versions.BWA_MEM.txt
@@ -36,13 +37,14 @@ process BWA_MEM_SE {
     input:
       // joins both channels by key using the first element in the tuple, the name
       tuple val(name), file(fastq)
+      val(reference)
 
     output:
       tuple val("${name}"), file("${name}.bam"), emit: bams
       file("software_versions.BWA_MEM_SE.txt")
 
     """
-    bwa mem ${params.additional_args} -t ${task.cpus} ${params.reference} ${fastq} | samtools view -uS - | samtools sort - > ${name}.bam
+    bwa mem ${params.additional_args} -t ${task.cpus} ${reference} ${fastq} | samtools view -uS - | samtools sort - > ${name}.bam
 
     echo ${params.manifest} >> software_versions.BWA_MEM_SE.txt
     echo "bwa=0.7.17"  >> software_versions.BWA_MEM_SE.txt

diff --git a/modules/02_bwa_mem_2.nf b/modules/02_bwa_mem_2.nf
@@ -10,13 +10,14 @@ process BWA_MEM_2 {
 
     input:
       tuple val(name), file(fastq1), file(fastq2)
+      val(reference)
 
     output:
       tuple val("${name}"), file("${name}.bam"), emit: bams
       file("software_versions.BWA_MEM_2.txt")
 
     """
-    bwa-mem2 mem ${params.additional_args} -t ${task.cpus} ${params.reference} ${fastq1} ${fastq2} | samtools view -uS - | samtools sort - > ${name}.bam
+    bwa-mem2 mem ${params.additional_args} -t ${task.cpus} ${reference} ${fastq1} ${fastq2} | samtools view -uS - | samtools sort - > ${name}.bam
 
     echo ${params.manifest} >> software_versions.BWA_MEM_2.txt
     bwa-mem2 version  >> software_versions.BWA_MEM_2.txt
@@ -36,13 +37,14 @@ process BWA_MEM_2_SE {
     input:
       // joins both channels by key using the first element in the tuple, the name
       tuple val(name), file(fastq)
+      val(reference)
 
     output:
       tuple val("${name}"), file("${name}.bam"), emit: bams
       file("software_versions.BWA_MEM_2_SE.txt")
 
     """
-    bwa-mem2 mem ${params.additional_args} -t ${task.cpus} ${params.reference} ${fastq} | samtools view -uS - | samtools sort - > ${name}.bam
+    bwa-mem2 mem ${params.additional_args} -t ${task.cpus} ${reference} ${fastq} | samtools view -uS - | samtools sort - > ${name}.bam
 
     echo ${params.manifest} >> software_versions.BWA_MEM_2_SE.txt
     bwa-mem2 version  >> software_versions.BWA_MEM_2_SE.txt

diff --git a/modules/02_star.nf b/modules/02_star.nf
@@ -18,7 +18,7 @@ process STAR {
     script:
     two_pass_mode_param = params.star_two_pass_mode ? "--twopassMode Basic" : ""
     """
-    STAR --genomeDir ${params.reference} ${two_pass_mode_param} ${params.additional_args} \
+    STAR --genomeDir ${reference} ${two_pass_mode_param} ${params.additional_args} \
     --readFilesCommand "gzip -d -c -f" \
     --readFilesIn ${fastq1} ${fastq2} \
     --outSAMmode Full \
@@ -48,6 +48,7 @@ process STAR_SE {
 
     input:
       tuple val(name), file(fastq)
+      val(reference)
 
     output:
       tuple val("${name}"), file("${name}.bam"), emit: bams
@@ -56,7 +57,7 @@ process STAR_SE {
     script:
     two_pass_mode_param = params.star_two_pass_mode ? "--twopassMode Basic" : ""
     """
-    STAR --genomeDir ${params.reference} ${two_pass_mode_param} ${params.additional_args} \
+    STAR --genomeDir ${reference} ${two_pass_mode_param} ${params.additional_args} \
     --readFilesCommand "gzip -d -c -f" \
     --readFilesIn ${fastq} \
     --outSAMmode Full \