Create index option and tests

main.nf

@@ -26,10 +26,10 @@ workflow {
     fastp_done = fastp(seqtk_done)
 
     // Alignment
-    bowtie2_index_done = params.bowtie2_index == null ? bowtie2_create_index() : channel.fromPath(params.bowtie2_index)
+    genome_channel = channel.fromPath(params.genome_fasta)
+    bowtie2_index_done = params.bowtie2_index == null ? bowtie2_create_index(genome_channel) : channel.fromPath(params.bowtie2_index)
 
-    bowtie2_input_channel                   = fastp_done.combine(bowtie2_index_done)
-    bowtie2_done                            = bowtie2_align(bowtie2_input_channel)
+    bowtie2_done                            = bowtie2_align(fastp_done, bowtie2_index_done)
     markduplicates_done                     = picard_MarkDuplicates(bowtie2_done)
 
     // bedfile

modules/aligners.nf

@@ -1,40 +1,44 @@
 process bowtie2_create_index {
     tag {"creating index"}
     conda "bioconda:bowtie2=2.5.3"
-    publishDir "${bt2_index}/"
+    publishDir "reference_bowtie2_index/"
+    cpus 4
 
     input:
-    path(genome_fasta)
+        path(genome_fasta)
 
     output:
     // nf-core use the name of the path as index though...
     path("*.bt2")
 
     shell:
     '''
-    index_name=$(basename !{params.genome_fasta} | cut -f 1 -d '.')
-    bowtie2-build !{params.genome_fasta} ${index_name}
+    index_name=$(basename !{genome_fasta} | awk -F"/" '{print $NF}'| cut -f 1 -d '.')
+    bowtie2-build --threads !{task.cpus} !{genome_fasta} ${index_name}
+    # touch testing.1.bt2 testing.2.bt2 testing.3.bt2
     '''
 }
 
 process bowtie2_align {
-    cpus 8
+    cpus 4
     tag {library}
     conda "bioconda:bowtie2=2.5.3 bioconda:samtools=1.19.2"
     publishDir "${library}/"
 
     input:
     tuple val(library),
           path(read1),
-          path(read2),
-          path(index)
+          path(read2)
+    path(index)
 
     output:
     tuple val(library), 
           path("*bam")
 
     shell:
     '''
+    echo !{index}    
+
     INDEX=$(find -L !{index} -name "*.1.bt2" | sed 's/\\.1.bt2\$//' | grep -v "rev")
 
     bowtie2  -p !{task.cpus} -x $INDEX -1 !{read1} -2 !{read2} \
@@ -44,7 +48,7 @@ process bowtie2_align {
 }
 
 process picard_MarkDuplicates{
-    cpus 8
+    cpus 4
     tag {library}
     conda "bioconda::picard=3.1.1"
     publishDir "${library}/"

modules/preprocessing.nf

@@ -1,5 +1,5 @@
 process seqtk_sample {
-    cpus 8
+    cpus 4
     tag {library}
     conda "bioconda::seqtk=1.4"
     publishDir "${library}/"
@@ -23,7 +23,7 @@ process seqtk_sample {
 }
 
 process fastp {
-    cpus 8
+    cpus 4
     tag {library}
     conda "bioconda::fastp=0.23.2"
     publishDir "${library}/"

modules/qc.nf

@@ -1,5 +1,5 @@
 process samtools_flagstat{
-    cpus 8
+    cpus 4
     tag {library}
     conda "bioconda::samtools=1.15.1"
     publishDir "${library}/"
@@ -20,7 +20,7 @@ process samtools_flagstat{
 
 
 process picard_CollectGcBiasMetrics{
-    cpus 8
+    cpus 4
     tag {library}
     conda "bioconda::picard=3.1.1"
     publishDir "${library}/"
@@ -46,7 +46,7 @@ process picard_CollectGcBiasMetrics{
 }
 
 process picard_CollectAlignmentSummaryMetrics{
-    cpus 8
+    cpus 4
     tag {library}
     conda "bioconda::picard=3.1.1"
     publishDir "${library}/"
@@ -71,7 +71,7 @@ process picard_CollectAlignmentSummaryMetrics{
 }
 
 process picard_EstimateLibraryComplexity {
-    cpus 8
+    cpus 4
     tag {library}
     conda "bioconda::picard=3.1.1"
     publishDir "${library}/"
@@ -96,7 +96,7 @@ process picard_EstimateLibraryComplexity {
 }
 
 process picard_CollectInsertSizeMetrics {
-    cpus 8
+    cpus 4
     tag {library}
     conda "bioconda::picard=3.1.1"
     publishDir "${library}/"
@@ -125,7 +125,7 @@ process picard_CollectInsertSizeMetrics {
 }
 
 process fastqc { 
-    cpus 8
+    cpus 4
     tag {library}
     conda "bioconda::fastqc=0.12.1"
     publishDir "${library}/"
@@ -150,7 +150,7 @@ process fastqc {
 }
 
 process bedtools_genome_coverage { 
-    cpus 8
+    cpus 4
     tag {library}
     conda "bioconda::bedtools=2.30"
     publishDir "${library}/"
@@ -172,7 +172,7 @@ process bedtools_genome_coverage {
 }
 
 process multiqc { 
-    cpus 8
+    cpus 4
     tag {library}
     conda "bioconda::multiqc=1.11"
     publishDir "${library}/"
@@ -197,7 +197,7 @@ process multiqc {
 }
 
 process tasmanian {
-    cpus 8
+    cpus 1
     tag {library}
     conda "bioconda::tasmanian-mismatch=1.0.7 bioconda::samtools=1.13"
     publishDir "${library}/"

test/run_tests.sh

@@ -0,0 +1,11 @@
+gunzip small_ref.fa
+
+# run tests and report
+echo " test WITHOUT alignmnet index" > test_out.log
+nextflow run ../main.nf --genome_fasta /mnt/home/aerijman/seqhimem02/FFPE_nextflow_workflow/test/small_ref.fa -with-conda -resume >> test_out.log 2>> test_out.log
+
+echo "test WITH alignment index" >> test_out.log
+nextflow run ../main.nf --genome_fasta /mnt/home/aerijman/seqhimem02/FFPE_nextflow_workflow/test/small_ref.fa \
+                     --bowtie2_index /mnt/home/aerijman/seqhimem02/FFPE_nextflow_workflow/test/reference_bowtie2_index/ -with-conda -resume >> test_out.log 2>> test_out.log
+
+rm -r reference_bowtie2_index/ r/ test_read/ work/